Starting phenix.real_space_refine
on Sun Aug 24 01:23:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u6z_41964/08_2025/8u6z_41964_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u6z_41964/08_2025/8u6z_41964.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u6z_41964/08_2025/8u6z_41964_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u6z_41964/08_2025/8u6z_41964_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u6z_41964/08_2025/8u6z_41964.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u6z_41964/08_2025/8u6z_41964.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.015 sd=   0.048
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
     P       3      5.49       5
     S      82      5.16       5
     C   10499      2.51       5
     N    2608      2.21       5
     O    2854      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16046
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 7842
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 999, 7842
          Classifications: {'peptide': 999}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 969}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 64
          Unresolved non-hydrogen dihedrals: 43
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 28
    Chain: "B"
      Number of atoms: 7842
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 999, 7842
          Classifications: {'peptide': 999}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 969}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 64
          Unresolved non-hydrogen dihedrals: 43
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 28
    Chain: "A"
      Number of atoms: 162
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 162
          Unusual residues: {'AJP': 2, 'POV': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 65
          Unresolved non-hydrogen angles: 96
          Unresolved non-hydrogen dihedrals: 127
          Unresolved non-hydrogen chiralities: 23
    Chain: "B"
      Number of atoms: 200
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 200
          Unusual residues: {'AJP': 2, 'POV': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 79
          Unresolved non-hydrogen angles: 113
          Unresolved non-hydrogen dihedrals: 139
          Unresolved non-hydrogen chiralities: 23
  Time building chain proxies: 3.24, per 1000 atoms: 0.20
  Number of scatterers: 16046
  At special positions: 0
  Unit cell: (109.02, 142.14, 126.96, 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      82     16.00
     P       3     15.00
     O    2854      8.00
     N    2608      7.00
     C   10499      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.20
  Conformation dependent library (CDL) restraints added in 711.9 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3764

  Finding SS restraints...
    Secondary structure from input PDB file:
      79 helices and 9 sheets defined
      75.3% alpha, 4.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.55
  Creating SS restraints...
    Processing helix  chain 'A' and resid 77 through 95
    Processing helix  chain 'A' and resid 102 through 120
      removed outlier: 3.539A  pdb=" N   LEU A 106 " --> pdb=" O   TYR A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.623A  pdb=" N   GLU A 124 " --> pdb=" O   VAL A 120 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   ASP A 129 " --> pdb=" O   GLU A 125 " (cutoff:3.500A)
      removed outlier: 5.474A  pdb=" N   VAL A 130 " --> pdb=" O   HIS A 126 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   HIS A 132 " --> pdb=" O   ARG A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 154
      removed outlier: 3.734A  pdb=" N   LEU A 138 " --> pdb=" O   ASP A 134 " (cutoff:3.500A)
      removed outlier: 5.038A  pdb=" N   LEU A 143 " --> pdb=" O   LEU A 139 " (cutoff:3.500A)
      Proline residue:  A 144  - end of helix
      removed outlier: 3.675A  pdb=" N   MET A 154 " --> pdb=" O   SER A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 161
    Processing helix  chain 'A' and resid 162 through 189
    Processing helix  chain 'A' and resid 194 through 205
    Processing helix  chain 'A' and resid 210 through 221
    Processing helix  chain 'A' and resid 223 through 254
      removed outlier: 3.908A  pdb=" N   SER A 234 " --> pdb=" O   ILE A 230 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   LEU A 235 " --> pdb=" O   GLU A 231 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   LEU A 236 " --> pdb=" O   GLY A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 291
      removed outlier: 4.101A  pdb=" N   GLY A 275 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      Proline residue:  A 276  - end of helix
    Processing helix  chain 'A' and resid 297 through 319
    Processing helix  chain 'A' and resid 321 through 337
      removed outlier: 4.204A  pdb=" N   LEU A 325 " --> pdb=" O   VAL A 321 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   VAL A 329 " --> pdb=" O   LEU A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 377
      removed outlier: 3.955A  pdb=" N   THR A 373 " --> pdb=" O   GLY A 369 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   GLN A 374 " --> pdb=" O   VAL A 370 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LYS A 375 " --> pdb=" O   VAL A 371 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   LEU A 377 " --> pdb=" O   THR A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 413
      removed outlier: 3.882A  pdb=" N   LEU A 388 " --> pdb=" O   ASP A 384 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   ILE A 389 " --> pdb=" O   TRP A 385 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ILE A 390 " --> pdb=" O   PHE A 386 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ILE A 403 " --> pdb=" O   ARG A 399 " (cutoff:3.500A)
      Proline residue:  A 408  - end of helix
    Processing helix  chain 'A' and resid 418 through 428
    Processing helix  chain 'A' and resid 432 through 447
      removed outlier: 3.792A  pdb=" N   LEU A 436 " --> pdb=" O   GLY A 432 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   GLY A 447 " --> pdb=" O   GLU A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 481
      removed outlier: 4.443A  pdb=" N   SER A 453 " --> pdb=" O   ASP A 449 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   VAL A 468 " --> pdb=" O   VAL A 464 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   ALA A 471 " --> pdb=" O   LEU A 467 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   GLN A 475 " --> pdb=" O   ALA A 471 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   THR A 476 " --> pdb=" O   THR A 472 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   LEU A 481 " --> pdb=" O   LEU A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 513
    Processing helix  chain 'A' and resid 522 through 530
      removed outlier: 3.567A  pdb=" N   CYS A 530 " --> pdb=" O   ALA A 526 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 601
    Processing helix  chain 'A' and resid 604 through 621
    Processing helix  chain 'A' and resid 627 through 636
      removed outlier: 4.274A  pdb=" N   LEU A 631 " --> pdb=" O   LEU A 627 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 637 through 639
      No H-bonds generated for 'chain 'A' and resid 637 through 639'
    Processing helix  chain 'A' and resid 640 through 653
      removed outlier: 3.606A  pdb=" N   LEU A 644 " --> pdb=" O   ILE A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 677 through 699
      removed outlier: 4.072A  pdb=" N   GLU A 681 " --> pdb=" O   HIS A 677 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   VAL A 693 " --> pdb=" O   VAL A 689 " (cutoff:3.500A)
      Proline residue:  A 694  - end of helix
      removed outlier: 3.578A  pdb=" N   PHE A 699 " --> pdb=" O   ILE A 695 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 731 through 756
      removed outlier: 4.007A  pdb=" N   SER A 735 " --> pdb=" O   ALA A 731 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 761 through 777
      removed outlier: 3.676A  pdb=" N   LYS A 765 " --> pdb=" O   SER A 761 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ASP A 777 " --> pdb=" O   VAL A 773 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 798 through 806
    Processing helix  chain 'A' and resid 807 through 816
      removed outlier: 4.219A  pdb=" N   MET A 810 " --> pdb=" O   GLY A 807 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   LYS A 815 " --> pdb=" O   ARG A 812 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 817 through 854
      removed outlier: 3.906A  pdb=" N   LEU A 835 " --> pdb=" O   ASN A 831 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   GLY A 840 " --> pdb=" O   GLY A 836 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 860 through 889
      removed outlier: 4.112A  pdb=" N   HIS A 889 " --> pdb=" O   LEU A 885 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 889 through 919
      removed outlier: 4.162A  pdb=" N   ALA A 893 " --> pdb=" O   HIS A 889 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   SER A 895 " --> pdb=" O   GLY A 891 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 923 through 943
    Processing helix  chain 'A' and resid 952 through 959
      removed outlier: 3.689A  pdb=" N   LEU A 956 " --> pdb=" O   PRO A 952 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 966 through 977
    Processing helix  chain 'A' and resid 1044 through 1049
    Processing helix  chain 'A' and resid 1070 through 1080
    Processing helix  chain 'A' and resid 1085 through 1107
      Proline residue:  A1101  - end of helix
      removed outlier: 3.715A  pdb=" N   MET A1107 " --> pdb=" O   ILE A1103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1113 through 1123
      removed outlier: 3.577A  pdb=" N   ARG A1123 " --> pdb=" O   LEU A1119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 95
    Processing helix  chain 'B' and resid 101 through 120
      removed outlier: 4.398A  pdb=" N   VAL B 105 " --> pdb=" O   PRO B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 132
      removed outlier: 3.624A  pdb=" N   GLU B 124 " --> pdb=" O   VAL B 120 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   ASP B 129 " --> pdb=" O   GLU B 125 " (cutoff:3.500A)
      removed outlier: 5.411A  pdb=" N   VAL B 130 " --> pdb=" O   HIS B 126 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   HIS B 132 " --> pdb=" O   ARG B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 154
      removed outlier: 3.620A  pdb=" N   LEU B 138 " --> pdb=" O   ASP B 134 " (cutoff:3.500A)
      removed outlier: 5.000A  pdb=" N   LEU B 143 " --> pdb=" O   LEU B 139 " (cutoff:3.500A)
      Proline residue:  B 144  - end of helix
      removed outlier: 3.654A  pdb=" N   MET B 154 " --> pdb=" O   SER B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 161
    Processing helix  chain 'B' and resid 162 through 189
    Processing helix  chain 'B' and resid 194 through 205
    Processing helix  chain 'B' and resid 210 through 221
    Processing helix  chain 'B' and resid 223 through 254
      removed outlier: 3.882A  pdb=" N   SER B 234 " --> pdb=" O   ILE B 230 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   LEU B 235 " --> pdb=" O   GLU B 231 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   LEU B 236 " --> pdb=" O   GLY B 232 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   PHE B 254 " --> pdb=" O   LYS B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 291
      removed outlier: 4.145A  pdb=" N   GLY B 275 " --> pdb=" O   VAL B 271 " (cutoff:3.500A)
      Proline residue:  B 276  - end of helix
    Processing helix  chain 'B' and resid 297 through 319
      removed outlier: 3.504A  pdb=" N   LEU B 319 " --> pdb=" O   GLY B 315 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 321 through 337
      removed outlier: 4.155A  pdb=" N   LEU B 325 " --> pdb=" O   VAL B 321 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   VAL B 329 " --> pdb=" O   LEU B 325 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 342 through 375
    Processing helix  chain 'B' and resid 376 through 380
      removed outlier: 4.233A  pdb=" N   VAL B 380 " --> pdb=" O   LEU B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 413
      removed outlier: 3.886A  pdb=" N   LEU B 388 " --> pdb=" O   ASP B 384 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   ILE B 389 " --> pdb=" O   TRP B 385 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ILE B 390 " --> pdb=" O   PHE B 386 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ILE B 403 " --> pdb=" O   ARG B 399 " (cutoff:3.500A)
      Proline residue:  B 408  - end of helix
    Processing helix  chain 'B' and resid 418 through 428
    Processing helix  chain 'B' and resid 432 through 447
      removed outlier: 3.836A  pdb=" N   LEU B 436 " --> pdb=" O   GLY B 432 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   GLY B 447 " --> pdb=" O   GLU B 443 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 450 through 481
      removed outlier: 3.528A  pdb=" N   VAL B 468 " --> pdb=" O   VAL B 464 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   ALA B 471 " --> pdb=" O   LEU B 467 " (cutoff:3.500A)
      removed outlier: 4.834A  pdb=" N   GLN B 475 " --> pdb=" O   ALA B 471 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   THR B 476 " --> pdb=" O   THR B 472 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   LEU B 481 " --> pdb=" O   LEU B 477 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 487 through 513
    Processing helix  chain 'B' and resid 522 through 530
      removed outlier: 3.588A  pdb=" N   CYS B 530 " --> pdb=" O   ALA B 526 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 571 through 601
    Processing helix  chain 'B' and resid 604 through 621
    Processing helix  chain 'B' and resid 627 through 636
      removed outlier: 4.266A  pdb=" N   LEU B 631 " --> pdb=" O   LEU B 627 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 637 through 639
      No H-bonds generated for 'chain 'B' and resid 637 through 639'
    Processing helix  chain 'B' and resid 640 through 653
      removed outlier: 3.610A  pdb=" N   LEU B 644 " --> pdb=" O   ILE B 640 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 677 through 699
      removed outlier: 4.085A  pdb=" N   GLU B 681 " --> pdb=" O   HIS B 677 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   VAL B 693 " --> pdb=" O   VAL B 689 " (cutoff:3.500A)
      Proline residue:  B 694  - end of helix
    Processing helix  chain 'B' and resid 731 through 756
      removed outlier: 4.027A  pdb=" N   SER B 735 " --> pdb=" O   ALA B 731 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 761 through 777
      removed outlier: 3.700A  pdb=" N   LYS B 765 " --> pdb=" O   SER B 761 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ASP B 777 " --> pdb=" O   VAL B 773 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 798 through 806
    Processing helix  chain 'B' and resid 807 through 816
      removed outlier: 4.223A  pdb=" N   MET B 810 " --> pdb=" O   GLY B 807 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   LYS B 815 " --> pdb=" O   ARG B 812 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 817 through 854
      removed outlier: 3.943A  pdb=" N   LEU B 835 " --> pdb=" O   ASN B 831 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   GLY B 840 " --> pdb=" O   GLY B 836 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 860 through 889
      removed outlier: 4.077A  pdb=" N   HIS B 889 " --> pdb=" O   LEU B 885 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 889 through 919
      removed outlier: 4.179A  pdb=" N   ALA B 893 " --> pdb=" O   HIS B 889 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   SER B 895 " --> pdb=" O   GLY B 891 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 923 through 943
    Processing helix  chain 'B' and resid 952 through 959
      removed outlier: 3.579A  pdb=" N   LEU B 956 " --> pdb=" O   PRO B 952 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 966 through 977
    Processing helix  chain 'B' and resid 1044 through 1049
    Processing helix  chain 'B' and resid 1070 through 1080
    Processing helix  chain 'B' and resid 1085 through 1107
      Proline residue:  B1101  - end of helix
      removed outlier: 3.597A  pdb=" N   MET B1107 " --> pdb=" O   ILE B1103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1113 through 1123
      removed outlier: 3.578A  pdb=" N   ARG B1123 " --> pdb=" O   LEU B1119 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 978 through 982
      removed outlier: 6.216A  pdb=" N   GLN A1064 " --> pdb=" O   VAL A1002 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1033 through 1037
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1126
      removed outlier: 3.721A  pdb=" N   VAL A1188 " --> pdb=" O   TYR A1125 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ASN A1149 " --> pdb=" O   ARG A1185 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   PHE A1187 " --> pdb=" O   LEU A1147 " (cutoff:3.500A)
      removed outlier: 5.151A  pdb=" N   LEU A1147 " --> pdb=" O   PHE A1187 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   VAL A1189 " --> pdb=" O   VAL A1145 " (cutoff:3.500A)
      removed outlier: 5.846A  pdb=" N   VAL A1145 " --> pdb=" O   VAL A1189 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1135 through 1137
      removed outlier: 3.631A  pdb=" N   TYR A1153 " --> pdb=" O   THR A1175 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 978 through 982
      removed outlier: 6.229A  pdb=" N   GLN B1064 " --> pdb=" O   VAL B1002 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 1033 through 1036
    Processing sheet with id=AA7, first strand: chain 'B' and resid 1135 through 1137
    Processing sheet with id=AA8, first strand: chain 'B' and resid 1144 through 1149
      removed outlier: 5.836A  pdb=" N   VAL B1145 " --> pdb=" O   VAL B1189 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   VAL B1189 " --> pdb=" O   VAL B1145 " (cutoff:3.500A)
      removed outlier: 5.156A  pdb=" N   LEU B1147 " --> pdb=" O   PHE B1187 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   PHE B1187 " --> pdb=" O   LEU B1147 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ASN B1149 " --> pdb=" O   ARG B1185 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 1151 through 1153

    1123 hydrogen bonds defined for protein.
    3306 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.88

  Time building geometry restraints manager: 1.60 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 2710
        1.32 -     1.45: 4007
        1.45 -     1.57: 9504
        1.57 -     1.69: 6
        1.69 -     1.82: 150
  Bond restraints: 16377
  Sorted by residual:
  bond pdb=" C26 AJP A1402 "
       pdb=" O25 AJP A1402 "
    ideal  model  delta    sigma   weight residual
    1.375  1.406 -0.031 2.00e-02 2.50e+03 2.48e+00
  bond pdb=" C26 AJP B1404 "
       pdb=" O25 AJP B1404 "
    ideal  model  delta    sigma   weight residual
    1.375  1.406 -0.031 2.00e-02 2.50e+03 2.36e+00
  bond pdb=" C26 AJP B1403 "
       pdb=" O25 AJP B1403 "
    ideal  model  delta    sigma   weight residual
    1.375  1.405 -0.030 2.00e-02 2.50e+03 2.20e+00
  bond pdb=" C35 AJP A1403 "
       pdb=" O34 AJP A1403 "
    ideal  model  delta    sigma   weight residual
    1.380  1.409 -0.029 2.00e-02 2.50e+03 2.11e+00
  bond pdb=" C26 AJP A1403 "
       pdb=" O25 AJP A1403 "
    ideal  model  delta    sigma   weight residual
    1.375  1.404 -0.029 2.00e-02 2.50e+03 2.11e+00
  ... (remaining 16372 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 21503
        1.69 -     3.38: 580
        3.38 -     5.08: 109
        5.08 -     6.77: 48
        6.77 -     8.46: 18
  Bond angle restraints: 22258
  Sorted by residual:
  angle pdb=" C   PHE A 365 "
        pdb=" N   MET A 366 "
        pdb=" CA  MET A 366 "
      ideal   model   delta    sigma   weight residual
     120.31  115.25    5.06 1.52e+00 4.33e-01 1.11e+01
  angle pdb=" C   PHE B 294 "
        pdb=" N   ASN B 295 "
        pdb=" CA  ASN B 295 "
      ideal   model   delta    sigma   weight residual
     121.54  127.80   -6.26 1.91e+00 2.74e-01 1.07e+01
  angle pdb=" C   ALA B 272 "
        pdb=" N   VAL B 273 "
        pdb=" CA  VAL B 273 "
      ideal   model   delta    sigma   weight residual
     122.97  119.86    3.11 9.80e-01 1.04e+00 1.01e+01
  angle pdb=" C   PHE B 365 "
        pdb=" N   MET B 366 "
        pdb=" CA  MET B 366 "
      ideal   model   delta    sigma   weight residual
     120.31  115.69    4.62 1.52e+00 4.33e-01 9.23e+00
  angle pdb=" CA  MET B1107 "
        pdb=" CB  MET B1107 "
        pdb=" CG  MET B1107 "
      ideal   model   delta    sigma   weight residual
     114.10  119.83   -5.73 2.00e+00 2.50e-01 8.21e+00
  ... (remaining 22253 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.30: 9460
       23.30 -    46.59: 699
       46.59 -    69.89: 79
       69.89 -    93.19: 15
       93.19 -   116.49: 18
  Dihedral angle restraints: 10271
    sinusoidal: 4467
      harmonic: 5804
  Sorted by residual:
  dihedral pdb=" C02 AJP A1403 "
           pdb=" C85 AJP A1403 "
           pdb=" O84 AJP A1403 "
           pdb=" C05 AJP A1403 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -57.60   58.89 -116.49     1      3.00e+01 1.11e-03 1.54e+01
  dihedral pdb=" C02 AJP B1403 "
           pdb=" C85 AJP B1403 "
           pdb=" O84 AJP B1403 "
           pdb=" C05 AJP B1403 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -57.60   58.05 -115.65     1      3.00e+01 1.11e-03 1.53e+01
  dihedral pdb=" C02 AJP A1402 "
           pdb=" C85 AJP A1402 "
           pdb=" O84 AJP A1402 "
           pdb=" C05 AJP A1402 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -57.60   56.46 -114.06     1      3.00e+01 1.11e-03 1.50e+01
  ... (remaining 10268 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 1958
       0.043 -    0.086: 593
       0.086 -    0.129: 142
       0.129 -    0.172: 19
       0.172 -    0.215: 9
  Chirality restraints: 2721
  Sorted by residual:
  chirality pdb=" C10 AJP B1404 "
            pdb=" C08 AJP B1404 "
            pdb=" C11 AJP B1404 "
            pdb=" O82 AJP B1404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.61    2.39    0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" C10 AJP A1402 "
            pdb=" C08 AJP A1402 "
            pdb=" C11 AJP A1402 "
            pdb=" O82 AJP A1402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.61    2.40    0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" C10 AJP B1403 "
            pdb=" C08 AJP B1403 "
            pdb=" C11 AJP B1403 "
            pdb=" O82 AJP B1403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.61    2.41    0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 2718 not shown)

  Planarity restraints: 2685
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 635 "    0.016 2.00e-02 2.50e+03   1.99e-02 9.87e+00
        pdb=" CG  TRP B 635 "   -0.053 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 635 "    0.028 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 635 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 635 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 635 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 635 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 635 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 635 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 635 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 635 "   -0.016 2.00e-02 2.50e+03   1.98e-02 9.75e+00
        pdb=" CG  TRP A 635 "    0.053 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 635 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 635 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 635 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 635 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 635 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 635 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 635 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 635 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 641 "    0.052 5.00e-02 4.00e+02   7.81e-02 9.75e+00
        pdb=" N   PRO B 642 "   -0.135 5.00e-02 4.00e+02
        pdb=" CA  PRO B 642 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO B 642 "    0.043 5.00e-02 4.00e+02
  ... (remaining 2682 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1309
        2.74 -     3.28: 16191
        3.28 -     3.82: 26232
        3.82 -     4.36: 26565
        4.36 -     4.90: 48569
  Nonbonded interactions: 118866
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 872 "
            pdb=" NH2 ARG A 875 "
     model   vdw
     2.200 3.120
  nonbonded pdb=" OE2 GLU B 872 "
            pdb=" NH2 ARG B 875 "
     model   vdw
     2.200 3.120
  nonbonded pdb=" OG  SER B1132 "
            pdb=" O   GLN B1135 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OG  SER A1132 "
            pdb=" O   GLN A1135 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" O   PHE A 288 "
            pdb=" OG  SER A 291 "
     model   vdw
     2.286 3.040
  ... (remaining 118861 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 76 through 1193 or (resid 1401 and (name C1 or name C2 or  \ 
name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 \ 
 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or name  \ 
C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name O11 or n \ 
ame O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32  \ 
or name P or name C210 or name C211 or name C212 or name C213 or name C214 or na \ 
me C215 or name C310 or name C311 or name C312)) or (resid 1403 and (name C01 or \ 
 name C02 or name C03 or name C04 or name C05 or name C06 or name C07 or name C0 \ 
8 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or nam \ 
e C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or \ 
 name C23 or name C24 or name C26 or name C27 or name C28 or name C29 or name C3 \ 
0 or name C32 or name C35 or name C36 or name C37 or name C38 or name C39 or nam \ 
e C41 or name C80 or name C81 or name C83 or name C85 or name O09 or name O25 or \ 
 name O31 or name O33 or name O34 or name O40 or name O42 or name O43 or name O4 \ 
4 or name O54 or name O77 or name O78 or name O79 or name O82 or name O84))))
  selection = (chain 'B' and (resid 76 through 1401 or resid 1403))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.050
  Set scattering table:                    0.030
  Process input model:                     14.380
  Find NCS groups from input model:        0.330
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
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      :  0.004   0.051  16377  Z= 0.181
  Angle     :  0.719   8.462  22258  Z= 0.337
  Chirality :  0.044   0.215   2721
  Planarity :  0.005   0.078   2685
  Dihedral  : 15.933 116.486   6507
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.06 %
    Favored  : 99.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.55 (0.19), residues: 1974
  helix:  1.59 (0.14), residues: 1442
  sheet:  1.40 (0.57), residues: 98
  loop : -0.90 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 573 
 TYR   0.015   0.001   TYR B 309 
 PHE   0.044   0.002   PHE B 201 
 TRP   0.053   0.002   TRP B 635 
 HIS   0.003   0.001   HIS B 908 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 (16377)
  covalent geometry    : angle       0.71869 (22258)
  hydrogen bonds       : bond        0.10668 ( 1123)
  hydrogen bonds       : angle       4.24055 ( 3306)

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

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

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.639 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 MET cc_start: 0.8548 (ttp) cc_final: 0.8270 (ttm)
REVERT: A  318 TRP cc_start: 0.6267 (t60) cc_final: 0.5851 (m100)
REVERT: A  319 LEU cc_start: 0.6790 (mp) cc_final: 0.6452 (mp)
REVERT: A 1047 VAL cc_start: 0.9512 (m) cc_final: 0.9165 (t)
REVERT: B  154 MET cc_start: 0.8481 (ttp) cc_final: 0.8243 (ttm)
REVERT: B  186 MET cc_start: 0.8063 (ttm) cc_final: 0.7855 (mtt)
REVERT: B  318 TRP cc_start: 0.6446 (t60) cc_final: 0.5926 (m100)
REVERT: B  319 LEU cc_start: 0.6710 (mp) cc_final: 0.6370 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 158
  average time/residue: 0.1113
  time to fit residues: 28.3265
Evaluate side-chains
  120 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 194 optimal weight:   20.0000
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    7.9990
   chunk 77 optimal weight:    9.9990
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    3.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A 860 ASN
B 860 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.129989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.102169 restraints weight = 31657.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.104732 restraints weight = 53467.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.105569 restraints weight = 28771.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.106167 restraints weight = 21117.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.106723 restraints weight = 18702.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.0884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  16377  Z= 0.112
  Angle     :  0.547   8.139  22258  Z= 0.260
  Chirality :  0.037   0.170   2721
  Planarity :  0.004   0.076   2685
  Dihedral  :  8.125  84.147   2873
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  5.79 %
    Favored  : 93.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.21 (0.20), residues: 1974
  helix:  2.12 (0.14), residues: 1444
  sheet:  1.41 (0.57), residues: 98
  loop : -0.80 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 583 
 TYR   0.016   0.001   TYR B 312 
 PHE   0.018   0.001   PHE B 201 
 TRP   0.029   0.001   TRP A 635 
 HIS   0.003   0.000   HIS B 908 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 (16377)
  covalent geometry    : angle       0.54660 (22258)
  hydrogen bonds       : bond        0.04300 ( 1123)
  hydrogen bonds       : angle       3.56892 ( 3306)

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

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

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 135
  time to evaluate  : 0.622 
Fit side-chains
REVERT: A  233 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7812 (tm-30)
REVERT: A  318 TRP cc_start: 0.5839 (t60) cc_final: 0.5576 (m100)
REVERT: A 1047 VAL cc_start: 0.9456 (m) cc_final: 0.9128 (t)
REVERT: B  233 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7912 (tm-30)
REVERT: B  318 TRP cc_start: 0.6344 (t60) cc_final: 0.5857 (m100)
REVERT: B  319 LEU cc_start: 0.6658 (mp) cc_final: 0.6391 (mp)
  outliers start: 10
  outliers final: 5
  residues processed: 137
  average time/residue: 0.1146
  time to fit residues: 25.4009
Evaluate side-chains
  129 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 124
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain B residue  129 ASP
Chi-restraints excluded: chain B residue  477 LEU
Chi-restraints excluded: chain B residue  811 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 150 optimal weight:    6.9990
   chunk 63 optimal weight:   20.0000
   chunk 40 optimal weight:    9.9990
   chunk 158 optimal weight:    3.9990
   chunk 60 optimal weight:    8.9990
   chunk 19 optimal weight:    0.0270
   chunk 16 optimal weight:    6.9990
   chunk 162 optimal weight:   40.0000
   chunk 114 optimal weight:    6.9990
   chunk 94 optimal weight:   20.0000
   chunk 11 optimal weight:    5.9990
   overall best weight:    4.8046

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.123667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.094479 restraints weight = 32850.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.096960 restraints weight = 59379.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.098164 restraints weight = 32829.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.098873 restraints weight = 22506.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.099866 restraints weight = 19510.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.1270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060  16377  Z= 0.251
  Angle     :  0.647   8.559  22258  Z= 0.320
  Chirality :  0.041   0.179   2721
  Planarity :  0.004   0.075   2685
  Dihedral  :  7.899  83.286   2873
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  9.81 %
    Favored  : 88.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.00 (0.19), residues: 1974
  helix:  1.95 (0.14), residues: 1452
  sheet:  0.94 (0.52), residues: 110
  loop : -0.80 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 583 
 TYR   0.019   0.001   TYR B 312 
 PHE   0.026   0.002   PHE B 201 
 TRP   0.016   0.002   TRP B 643 
 HIS   0.006   0.001   HIS B 889 

Details of bonding type rmsd
  covalent geometry    : bond        0.00595 (16377)
  covalent geometry    : angle       0.64674 (22258)
  hydrogen bonds       : bond        0.05580 ( 1123)
  hydrogen bonds       : angle       3.85859 ( 3306)

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

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

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 124
  time to evaluate  : 0.640 
Fit side-chains
REVERT: A  199 MET cc_start: 0.8544 (tpp) cc_final: 0.8323 (tpp)
REVERT: A  233 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8075 (tm-30)
REVERT: A  318 TRP cc_start: 0.6250 (t60) cc_final: 0.5626 (m100)
REVERT: B  233 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8101 (tm-30)
REVERT: B  318 TRP cc_start: 0.6386 (t60) cc_final: 0.5811 (m100)
REVERT: B  319 LEU cc_start: 0.6925 (mp) cc_final: 0.6462 (mp)
  outliers start: 23
  outliers final: 16
  residues processed: 133
  average time/residue: 0.1137
  time to fit residues: 24.7074
Evaluate side-chains
  134 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 CYS
Chi-restraints excluded: chain A residue  213 VAL
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  811 LEU
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain B residue  167 CYS
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  269 LEU
Chi-restraints excluded: chain B residue  321 VAL
Chi-restraints excluded: chain B residue  477 LEU
Chi-restraints excluded: chain B residue  811 LEU
Chi-restraints excluded: chain B residue  850 VAL
Chi-restraints excluded: chain B residue 1188 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 193 optimal weight:   20.0000
   chunk 150 optimal weight:    1.9990
   chunk 141 optimal weight:   10.0000
   chunk 159 optimal weight:   20.0000
   chunk 69 optimal weight:    6.9990
   chunk 158 optimal weight:    7.9990
   chunk 68 optimal weight:    9.9990
   chunk 24 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   chunk 138 optimal weight:    0.9980
   chunk 163 optimal weight:   10.0000
   overall best weight:    2.9786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.125059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.095554 restraints weight = 32215.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.098186 restraints weight = 60758.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.099656 restraints weight = 32364.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.100208 restraints weight = 22509.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.101138 restraints weight = 19347.572|
|-----------------------------------------------------------------------------|
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.1319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  16377  Z= 0.167
  Angle     :  0.565   9.795  22258  Z= 0.277
  Chirality :  0.038   0.190   2721
  Planarity :  0.004   0.077   2685
  Dihedral  :  7.601  83.103   2873
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 12.17 %
    Favored  : 86.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.18 (0.19), residues: 1974
  helix:  2.11 (0.14), residues: 1446
  sheet:  1.07 (0.52), residues: 114
  loop : -0.84 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 583 
 TYR   0.018   0.001   TYR B 309 
 PHE   0.020   0.001   PHE B 201 
 TRP   0.017   0.001   TRP A 643 
 HIS   0.004   0.001   HIS B 889 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 (16377)
  covalent geometry    : angle       0.56547 (22258)
  hydrogen bonds       : bond        0.05012 ( 1123)
  hydrogen bonds       : angle       3.69004 ( 3306)

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

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

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 127
  time to evaluate  : 0.548 
Fit side-chains
REVERT: A  199 MET cc_start: 0.8483 (tpp) cc_final: 0.8246 (tpp)
REVERT: A  233 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7840 (tm-30)
REVERT: A  318 TRP cc_start: 0.6206 (t60) cc_final: 0.5599 (m100)
REVERT: B  205 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7806 (mtt)
REVERT: B  233 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8040 (tm-30)
REVERT: B  318 TRP cc_start: 0.6315 (t60) cc_final: 0.5722 (m100)
REVERT: B  319 LEU cc_start: 0.6825 (mp) cc_final: 0.6257 (mp)
REVERT: B 1088 TYR cc_start: 0.7945 (t80) cc_final: 0.7630 (t80)
  outliers start: 25
  outliers final: 14
  residues processed: 140
  average time/residue: 0.1093
  time to fit residues: 24.7973
Evaluate side-chains
  136 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 121
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  167 CYS
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain B residue  167 CYS
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  269 LEU
Chi-restraints excluded: chain B residue  321 VAL
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain B residue  477 LEU
Chi-restraints excluded: chain B residue  811 LEU
Chi-restraints excluded: chain B residue  850 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 143 optimal weight:    8.9990
   chunk 13 optimal weight:    9.9990
   chunk 52 optimal weight:    1.9990
   chunk 165 optimal weight:    3.9990
   chunk 185 optimal weight:    0.8980
   chunk 43 optimal weight:    4.9990
   chunk 166 optimal weight:    6.9990
   chunk 163 optimal weight:    0.0170
   chunk 35 optimal weight:    2.9990
   chunk 3 optimal weight:    5.9990
   chunk 54 optimal weight:    3.9990
   overall best weight:    1.9824

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.126214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.098631 restraints weight = 32356.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.101964 restraints weight = 59619.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.102442 restraints weight = 25896.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.103459 restraints weight = 20042.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.103642 restraints weight = 17089.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.1323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  16377  Z= 0.131
  Angle     :  0.524   7.267  22258  Z= 0.258
  Chirality :  0.037   0.202   2721
  Planarity :  0.004   0.077   2685
  Dihedral  :  7.290  82.922   2873
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 13.48 %
    Favored  : 84.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.33 (0.20), residues: 1974
  helix:  2.21 (0.14), residues: 1446
  sheet:  1.23 (0.51), residues: 114
  loop : -0.81 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 583 
 TYR   0.015   0.001   TYR B 309 
 PHE   0.018   0.001   PHE B 201 
 TRP   0.020   0.001   TRP A 643 
 HIS   0.003   0.001   HIS B 908 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (16377)
  covalent geometry    : angle       0.52389 (22258)
  hydrogen bonds       : bond        0.04533 ( 1123)
  hydrogen bonds       : angle       3.54526 ( 3306)

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

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

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 131
  time to evaluate  : 0.659 
Fit side-chains
REVERT: A  199 MET cc_start: 0.8395 (tpp) cc_final: 0.8163 (tpp)
REVERT: A  233 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7692 (tm-30)
REVERT: A  318 TRP cc_start: 0.6134 (t60) cc_final: 0.5579 (m100)
REVERT: A  438 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8862 (mt)
REVERT: A  578 MET cc_start: 0.8028 (mmt) cc_final: 0.7800 (mmm)
REVERT: A  733 ARG cc_start: 0.7347 (mmt180) cc_final: 0.5842 (ttt180)
REVERT: A 1088 TYR cc_start: 0.7765 (t80) cc_final: 0.7440 (t80)
REVERT: B  205 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.6969 (mtm)
REVERT: B  233 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7859 (tm-30)
REVERT: B  318 TRP cc_start: 0.6186 (t60) cc_final: 0.5693 (m100)
REVERT: B  319 LEU cc_start: 0.6678 (mp) cc_final: 0.6220 (mp)
REVERT: B  578 MET cc_start: 0.8027 (mmt) cc_final: 0.7777 (mmm)
REVERT: B 1088 TYR cc_start: 0.7892 (t80) cc_final: 0.7537 (t80)
  outliers start: 27
  outliers final: 15
  residues processed: 145
  average time/residue: 0.1041
  time to fit residues: 24.4357
Evaluate side-chains
  140 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 123
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  167 CYS
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  904 THR
Chi-restraints excluded: chain B residue  154 MET
Chi-restraints excluded: chain B residue  167 CYS
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  269 LEU
Chi-restraints excluded: chain B residue  321 VAL
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain B residue  384 ASP
Chi-restraints excluded: chain B residue  477 LEU
Chi-restraints excluded: chain B residue  998 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 190 optimal weight:    0.0010
   chunk 20 optimal weight:    6.9990
   chunk 150 optimal weight:    7.9990
   chunk 111 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 99 optimal weight:    2.9990
   chunk 80 optimal weight:   10.0000
   chunk 152 optimal weight:    6.9990
   chunk 142 optimal weight:    7.9990
   overall best weight:    1.7792

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

Flipped N/Q/H residues before XYZ refinement:
A 295 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.126924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.097807 restraints weight = 32187.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.100626 restraints weight = 54906.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.101523 restraints weight = 31133.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.102715 restraints weight = 21871.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.103276 restraints weight = 18656.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.1390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  16377  Z= 0.123
  Angle     :  0.526  10.596  22258  Z= 0.255
  Chirality :  0.037   0.212   2721
  Planarity :  0.004   0.077   2685
  Dihedral  :  7.104  82.318   2873
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 14.01 %
    Favored  : 84.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.39 (0.20), residues: 1974
  helix:  2.24 (0.14), residues: 1446
  sheet:  1.33 (0.52), residues: 114
  loop : -0.77 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 161 
 TYR   0.015   0.001   TYR B 309 
 PHE   0.017   0.001   PHE B 201 
 TRP   0.021   0.001   TRP B 643 
 HIS   0.003   0.001   HIS A 908 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (16377)
  covalent geometry    : angle       0.52558 (22258)
  hydrogen bonds       : bond        0.04348 ( 1123)
  hydrogen bonds       : angle       3.49117 ( 3306)

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

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

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 138
  time to evaluate  : 0.476 
Fit side-chains
REVERT: A  199 MET cc_start: 0.8331 (tpp) cc_final: 0.8113 (tpp)
REVERT: A  233 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7652 (tm-30)
REVERT: A  318 TRP cc_start: 0.6121 (t60) cc_final: 0.5589 (m100)
REVERT: A  578 MET cc_start: 0.8149 (mmt) cc_final: 0.7885 (mmm)
REVERT: A  733 ARG cc_start: 0.7468 (mmt180) cc_final: 0.5951 (ttt180)
REVERT: A 1088 TYR cc_start: 0.7811 (t80) cc_final: 0.7501 (t80)
REVERT: B  205 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.6759 (mtm)
REVERT: B  233 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7736 (tm-30)
REVERT: B  318 TRP cc_start: 0.6192 (t60) cc_final: 0.5724 (m100)
REVERT: B  319 LEU cc_start: 0.6666 (mp) cc_final: 0.6220 (mp)
REVERT: B  578 MET cc_start: 0.8135 (mmt) cc_final: 0.7842 (mmm)
REVERT: B 1088 TYR cc_start: 0.7932 (t80) cc_final: 0.7587 (t80)
  outliers start: 26
  outliers final: 15
  residues processed: 149
  average time/residue: 0.0962
  time to fit residues: 23.0004
Evaluate side-chains
  141 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 125
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  167 CYS
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  811 LEU
Chi-restraints excluded: chain A residue  904 THR
Chi-restraints excluded: chain B residue  154 MET
Chi-restraints excluded: chain B residue  167 CYS
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  269 LEU
Chi-restraints excluded: chain B residue  321 VAL
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain B residue  477 LEU
Chi-restraints excluded: chain B residue  811 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 142 optimal weight:    0.9990
   chunk 110 optimal weight:   10.0000
   chunk 28 optimal weight:    0.8980
   chunk 106 optimal weight:    1.9990
   chunk 174 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 131 optimal weight:    0.8980
   chunk 120 optimal weight:    0.6980
   overall best weight:    0.8582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.129207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.101293 restraints weight = 31952.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.104410 restraints weight = 55008.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.105093 restraints weight = 27698.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.105830 restraints weight = 20615.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.106462 restraints weight = 18003.847|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.1460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  16377  Z= 0.101
  Angle     :  0.510   7.357  22258  Z= 0.245
  Chirality :  0.037   0.226   2721
  Planarity :  0.004   0.078   2685
  Dihedral  :  6.785  80.195   2873
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 15.07 %
    Favored  : 83.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.53 (0.20), residues: 1974
  helix:  2.35 (0.14), residues: 1446
  sheet:  1.41 (0.52), residues: 114
  loop : -0.72 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 161 
 TYR   0.013   0.001   TYR B 312 
 PHE   0.015   0.001   PHE B 201 
 TRP   0.025   0.001   TRP A 643 
 HIS   0.004   0.000   HIS A 908 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 (16377)
  covalent geometry    : angle       0.50987 (22258)
  hydrogen bonds       : bond        0.03820 ( 1123)
  hydrogen bonds       : angle       3.36819 ( 3306)

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

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

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 141
  time to evaluate  : 0.631 
Fit side-chains
REVERT: A  233 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7618 (tm-30)
REVERT: A  318 TRP cc_start: 0.5946 (t60) cc_final: 0.5558 (m100)
REVERT: A  733 ARG cc_start: 0.7271 (mmt180) cc_final: 0.5857 (ttt180)
REVERT: A 1088 TYR cc_start: 0.7660 (t80) cc_final: 0.7317 (t80)
REVERT: B  205 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.6654 (mtm)
REVERT: B  233 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7654 (tm-30)
REVERT: B  318 TRP cc_start: 0.6078 (t60) cc_final: 0.5653 (m100)
REVERT: B  319 LEU cc_start: 0.6592 (mp) cc_final: 0.6392 (mp)
REVERT: B  733 ARG cc_start: 0.7267 (mmt180) cc_final: 0.6093 (ttt180)
REVERT: B 1088 TYR cc_start: 0.7738 (t80) cc_final: 0.7391 (t80)
  outliers start: 18
  outliers final: 11
  residues processed: 150
  average time/residue: 0.1004
  time to fit residues: 24.3571
Evaluate side-chains
  143 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 131
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 CYS
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  858 VAL
Chi-restraints excluded: chain B residue  154 MET
Chi-restraints excluded: chain B residue  167 CYS
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  321 VAL
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain B residue  477 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 148 optimal weight:    8.9990
   chunk 29 optimal weight:    0.7980
   chunk 121 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 165 optimal weight:    0.0970
   chunk 71 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 141 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 154 optimal weight:    8.9990
   chunk 174 optimal weight:    0.9990
   overall best weight:    0.9782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.129527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.101000 restraints weight = 31870.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.103360 restraints weight = 54903.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.104601 restraints weight = 32492.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.105599 restraints weight = 22945.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.105930 restraints weight = 19840.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.1525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  16377  Z= 0.102
  Angle     :  0.516  11.953  22258  Z= 0.246
  Chirality :  0.036   0.233   2721
  Planarity :  0.004   0.077   2685
  Dihedral  :  6.645  78.184   2873
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 15.84 %
    Favored  : 82.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.60 (0.20), residues: 1974
  helix:  2.38 (0.14), residues: 1446
  sheet:  1.48 (0.53), residues: 114
  loop : -0.63 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A1092 
 TYR   0.013   0.001   TYR B 312 
 PHE   0.017   0.001   PHE B 201 
 TRP   0.023   0.001   TRP B 643 
 HIS   0.003   0.000   HIS A 908 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 (16377)
  covalent geometry    : angle       0.51589 (22258)
  hydrogen bonds       : bond        0.03753 ( 1123)
  hydrogen bonds       : angle       3.33524 ( 3306)

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

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

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 138
  time to evaluate  : 0.495 
Fit side-chains
REVERT: A  199 MET cc_start: 0.8465 (tpp) cc_final: 0.8196 (tpp)
REVERT: A  233 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7621 (tm-30)
REVERT: A  318 TRP cc_start: 0.5986 (t60) cc_final: 0.5580 (m100)
REVERT: A  733 ARG cc_start: 0.7266 (mmt180) cc_final: 0.5875 (ttt180)
REVERT: A 1088 TYR cc_start: 0.7733 (t80) cc_final: 0.7399 (t80)
REVERT: B  205 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.6639 (mtm)
REVERT: B  233 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7636 (tm-30)
REVERT: B  318 TRP cc_start: 0.6106 (t60) cc_final: 0.5698 (m100)
REVERT: B  319 LEU cc_start: 0.6672 (mp) cc_final: 0.6468 (mp)
REVERT: B  733 ARG cc_start: 0.7268 (mmt180) cc_final: 0.6123 (ttt180)
REVERT: B 1088 TYR cc_start: 0.7800 (t80) cc_final: 0.7461 (t80)
  outliers start: 20
  outliers final: 13
  residues processed: 148
  average time/residue: 0.0967
  time to fit residues: 23.1264
Evaluate side-chains
  146 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 132
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  167 CYS
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  858 VAL
Chi-restraints excluded: chain B residue   78 ILE
Chi-restraints excluded: chain B residue  154 MET
Chi-restraints excluded: chain B residue  167 CYS
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  321 VAL
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain B residue  477 LEU
Chi-restraints excluded: chain B residue  837 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 99 optimal weight:    0.8980
   chunk 95 optimal weight:    7.9990
   chunk 173 optimal weight:   10.0000
   chunk 118 optimal weight:    0.9980
   chunk 94 optimal weight:    4.9990
   chunk 89 optimal weight:    0.9990
   chunk 175 optimal weight:    5.9990
   chunk 188 optimal weight:    5.9990
   chunk 102 optimal weight:    4.9990
   chunk 148 optimal weight:    9.9990
   chunk 30 optimal weight:    5.9990
   overall best weight:    2.5786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.128084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.098579 restraints weight = 31957.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.101589 restraints weight = 59718.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.102643 restraints weight = 30178.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.103761 restraints weight = 21141.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.104428 restraints weight = 18402.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.1540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  16377  Z= 0.150
  Angle     :  0.564   7.990  22258  Z= 0.270
  Chirality :  0.038   0.229   2721
  Planarity :  0.004   0.075   2685
  Dihedral  :  6.863  78.081   2873
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 15.78 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.52 (0.20), residues: 1974
  helix:  2.31 (0.14), residues: 1446
  sheet:  1.48 (0.53), residues: 114
  loop : -0.64 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 161 
 TYR   0.018   0.001   TYR B 309 
 PHE   0.019   0.001   PHE B 201 
 TRP   0.029   0.001   TRP A 643 
 HIS   0.004   0.001   HIS B 889 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 (16377)
  covalent geometry    : angle       0.56406 (22258)
  hydrogen bonds       : bond        0.04366 ( 1123)
  hydrogen bonds       : angle       3.45409 ( 3306)

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

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

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 124
  time to evaluate  : 0.486 
Fit side-chains
REVERT: A  233 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7693 (tm-30)
REVERT: A  318 TRP cc_start: 0.6146 (t60) cc_final: 0.5712 (m100)
REVERT: A  733 ARG cc_start: 0.7338 (mmt180) cc_final: 0.5956 (ttt180)
REVERT: A 1088 TYR cc_start: 0.7908 (t80) cc_final: 0.7580 (t80)
REVERT: B  205 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.6760 (mtm)
REVERT: B  233 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7819 (tm-30)
REVERT: B  318 TRP cc_start: 0.6093 (t60) cc_final: 0.5806 (m100)
REVERT: B  319 LEU cc_start: 0.6761 (mp) cc_final: 0.6409 (mp)
REVERT: B  586 MET cc_start: 0.8592 (ttm) cc_final: 0.8381 (ttp)
REVERT: B  733 ARG cc_start: 0.7352 (mmt180) cc_final: 0.6173 (ttt180)
REVERT: B 1088 TYR cc_start: 0.7870 (t80) cc_final: 0.7523 (t80)
REVERT: B 1107 MET cc_start: 0.5606 (tpp) cc_final: 0.5348 (tpp)
  outliers start: 23
  outliers final: 17
  residues processed: 139
  average time/residue: 0.0897
  time to fit residues: 20.2501
Evaluate side-chains
  142 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 124
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  167 CYS
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  401 MET
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  858 VAL
Chi-restraints excluded: chain A residue  904 THR
Chi-restraints excluded: chain B residue   78 ILE
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  154 MET
Chi-restraints excluded: chain B residue  167 CYS
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  321 VAL
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain B residue  477 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 79 optimal weight:    6.9990
   chunk 76 optimal weight:    6.9990
   chunk 54 optimal weight:    0.9990
   chunk 98 optimal weight:   20.0000
   chunk 166 optimal weight:    6.9990
   chunk 77 optimal weight:    0.0770
   chunk 20 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9980
   chunk 192 optimal weight:    7.9990
   chunk 128 optimal weight:    1.9990
   overall best weight:    1.2144

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.129311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.101558 restraints weight = 31748.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.104927 restraints weight = 55149.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.105639 restraints weight = 25726.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.106795 restraints weight = 19397.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.107013 restraints weight = 16661.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.1588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  16377  Z= 0.107
  Angle     :  0.536   8.031  22258  Z= 0.254
  Chirality :  0.037   0.233   2721
  Planarity :  0.004   0.076   2685
  Dihedral  :  6.662  76.710   2873
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 15.90 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.62 (0.20), residues: 1974
  helix:  2.38 (0.14), residues: 1446
  sheet:  1.51 (0.53), residues: 114
  loop : -0.58 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B1092 
 TYR   0.013   0.001   TYR B 309 
 PHE   0.016   0.001   PHE B 201 
 TRP   0.030   0.001   TRP A 643 
 HIS   0.003   0.000   HIS A 908 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 (16377)
  covalent geometry    : angle       0.53560 (22258)
  hydrogen bonds       : bond        0.03915 ( 1123)
  hydrogen bonds       : angle       3.35840 ( 3306)

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

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

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3948 Ramachandran restraints generated.
    1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 135
  time to evaluate  : 0.407 
Fit side-chains
REVERT: A  199 MET cc_start: 0.8499 (tpp) cc_final: 0.8234 (tpp)
REVERT: A  233 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7738 (tm-30)
REVERT: A  318 TRP cc_start: 0.5989 (t60) cc_final: 0.5564 (m100)
REVERT: A  733 ARG cc_start: 0.7144 (mmt180) cc_final: 0.5889 (ttt180)
REVERT: A 1088 TYR cc_start: 0.7739 (t80) cc_final: 0.7415 (t80)
REVERT: B  205 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.6709 (mtm)
REVERT: B  233 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7666 (tm-30)
REVERT: B  318 TRP cc_start: 0.6041 (t60) cc_final: 0.5643 (m100)
REVERT: B  319 LEU cc_start: 0.6707 (mp) cc_final: 0.6456 (mp)
REVERT: B  733 ARG cc_start: 0.7198 (mmt180) cc_final: 0.6137 (ttt180)
REVERT: B 1088 TYR cc_start: 0.7821 (t80) cc_final: 0.7488 (t80)
  outliers start: 17
  outliers final: 15
  residues processed: 144
  average time/residue: 0.0872
  time to fit residues: 20.2070
Evaluate side-chains
  144 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  167 CYS
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  858 VAL
Chi-restraints excluded: chain B residue   78 ILE
Chi-restraints excluded: chain B residue  154 MET
Chi-restraints excluded: chain B residue  167 CYS
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  321 VAL
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain B residue  401 MET
Chi-restraints excluded: chain B residue  477 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 198
   random chunks:
   chunk 87 optimal weight:    6.9990
   chunk 195 optimal weight:    7.9990
   chunk 68 optimal weight:   20.0000
   chunk 113 optimal weight:    7.9990
   chunk 48 optimal weight:    6.9990
   chunk 92 optimal weight:    2.9990
   chunk 52 optimal weight:    4.9990
   chunk 50 optimal weight:    9.9990
   chunk 114 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 162 optimal weight:   10.0000
   overall best weight:    3.7788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.124916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.100787 restraints weight = 32056.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.101847 restraints weight = 61075.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.102029 restraints weight = 26853.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.102307 restraints weight = 22725.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.103064 restraints weight = 17501.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.1688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  16377  Z= 0.201
  Angle     :  0.614   7.953  22258  Z= 0.298
  Chirality :  0.039   0.229   2721
  Planarity :  0.004   0.074   2685
  Dihedral  :  7.157  78.810   2873
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 16.19 %
    Favored  : 82.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.38 (0.20), residues: 1974
  helix:  2.21 (0.14), residues: 1452
  sheet:  1.10 (0.49), residues: 126
  loop : -0.65 (0.33), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 605 
 TYR   0.017   0.001   TYR A 309 
 PHE   0.021   0.001   PHE B 201 
 TRP   0.032   0.001   TRP A 643 
 HIS   0.004   0.001   HIS B 889 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 (16377)
  covalent geometry    : angle       0.61413 (22258)
  hydrogen bonds       : bond        0.05013 ( 1123)
  hydrogen bonds       : angle       3.61123 ( 3306)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1823.87 seconds
wall clock time: 32 minutes 32.01 seconds (1952.01 seconds total)