Starting phenix.real_space_refine
on Sun Aug 24 09:51:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8h1c_34427/08_2025/8h1c_34427.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8h1c_34427/08_2025/8h1c_34427.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8h1c_34427/08_2025/8h1c_34427.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8h1c_34427/08_2025/8h1c_34427.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8h1c_34427/08_2025/8h1c_34427.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8h1c_34427/08_2025/8h1c_34427.cif"
  }
  resolution = 4.5
  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=  -0.001 sd=   0.054
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     148      5.49       5
     S      62      5.16       5
     C   11199      2.51       5
     N    3182      2.21       5
     O    3892      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s

  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: 18483
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 7715
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 983, 7710
          Classifications: {'peptide': 983}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PCIS': 3, 'PTRANS': 43, 'TRANS': 936}
          Chain breaks: 1
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 77
          Unresolved non-hydrogen angles: 93
          Unresolved non-hydrogen dihedrals: 62
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 7, 'ASP:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 58
      Conformer: "B"
        Number of residues, atoms: 983, 7710
          Classifications: {'peptide': 983}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PCIS': 3, 'PTRANS': 43, 'TRANS': 936}
          Chain breaks: 1
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 77
          Unresolved non-hydrogen angles: 93
          Unresolved non-hydrogen dihedrals: 62
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 7, 'ASP:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 58
          bond proxies already assigned to first conformer: 7861
    Chain: "C"
      Number of atoms: 1560
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 1560
          Unusual residues: {'GTP': 1}
          Classifications: {'RNA': 72, 'undetermined': 1}
          Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 31, 'rna3p_pyr': 33}
          Link IDs: {'rna2p': 8, 'rna3p': 63, None: 1}
            Not linked:
              pdbres="GTP C   1 "
              pdbres="  C C   2 "
    Chain: "A"
      Number of atoms: 7688
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 983, 7683
          Classifications: {'peptide': 983}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PCIS': 3, 'PTRANS': 43, 'TRANS': 936}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 104
          Unresolved non-hydrogen angles: 126
          Unresolved non-hydrogen dihedrals: 82
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 71
      Conformer: "B"
        Number of residues, atoms: 983, 7683
          Classifications: {'peptide': 983}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PCIS': 3, 'PTRANS': 43, 'TRANS': 936}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 104
          Unresolved non-hydrogen angles: 126
          Unresolved non-hydrogen dihedrals: 82
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 4, 'GLN:plan1': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 71
          bond proxies already assigned to first conformer: 7834
    Chain: "D"
      Number of atoms: 1520
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 71, 1520
          Unusual residues: {'GTP': 1}
          Classifications: {'RNA': 70, 'undetermined': 1}
          Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 5, 'rna3p_pur': 31, 'rna3p_pyr': 30}
          Link IDs: {'rna2p': 9, 'rna3p': 60, None: 1}
            Not linked:
              pdbres="GTP D   1 "
              pdbres="  C D   2 "
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  AALA B 940 " occ=0.50
      ... (8 atoms not shown)
      pdb=" CB BALA B 940 " occ=0.50
    residue:
      pdb=" N  AALA A 940 " occ=0.50
      ... (8 atoms not shown)
      pdb=" CB BALA A 940 " occ=0.50
  Time building chain proxies: 7.43, per 1000 atoms: 0.40
  Number of scatterers: 18483
  At special positions: 0
  Unit cell: (202.4, 160.6, 112.2, 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      62     16.00
     P     148     15.00
     O    3892      8.00
     N    3182      7.00
     C   11199      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.60
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  3928 Ramachandran restraints generated.
    1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3694

  Finding SS restraints...
    Secondary structure from input PDB file:
      82 helices and 15 sheets defined
      48.0% alpha, 9.8% beta
      33 base pairs and 70 stacking pairs defined.
    Time for finding SS restraints: 2.37
  Creating SS restraints...
    Processing helix  chain 'B' and resid 73 through 89
      removed outlier: 3.814A  pdb=" N   ILE B  78 " --> pdb=" O   PHE B  74 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   GLN B  79 " --> pdb=" O   GLN B  75 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ASP B  83 " --> pdb=" O   GLN B  79 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   TYR B  84 " --> pdb=" O   ARG B  80 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   TRP B  85 " --> pdb=" O   LEU B  81 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   SER B  87 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   GLY B  89 " --> pdb=" O   TRP B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 133
    Processing helix  chain 'B' and resid 158 through 171
      removed outlier: 3.996A  pdb=" N   PHE B 163 " --> pdb=" O   SER B 159 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   LEU B 164 " --> pdb=" O   GLN B 160 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   GLY B 171 " --> pdb=" O   LEU B 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 232 through 240
      removed outlier: 4.121A  pdb=" N   LEU B 236 " --> pdb=" O   LEU B 232 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   MET B 237 " --> pdb=" O   GLU B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 261 through 274
      removed outlier: 3.985A  pdb=" N   GLU B 266 " --> pdb=" O   GLU B 262 " (cutoff:3.500A)
      removed outlier: 4.752A  pdb=" N   MET B 267 " --> pdb=" O   ASN B 263 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   HIS B 274 " --> pdb=" O   TYR B 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 296
      removed outlier: 4.112A  pdb=" N   ILE B 280 " --> pdb=" O   ASN B 276 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   GLN B 281 " --> pdb=" O   VAL B 277 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   LYS B 282 " --> pdb=" O   ASP B 278 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   ASP B 285 " --> pdb=" O   GLN B 281 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ASP B 286 " --> pdb=" O   LYS B 282 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 321
      removed outlier: 3.501A  pdb=" N   ALA B 303 " --> pdb=" O   LEU B 299 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   VAL B 307 " --> pdb=" O   ALA B 303 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU B 308 " --> pdb=" O   TYR B 304 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   LYS B 309 " --> pdb=" O   ASP B 305 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ALA B 313 " --> pdb=" O   LYS B 309 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   PHE B 314 " --> pdb=" O   ALA B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 326 through 352
      removed outlier: 4.153A  pdb=" N   ARG B 330 " --> pdb=" O   THR B 326 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   LEU B 345 " --> pdb=" O   GLN B 341 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   TRP B 346 " --> pdb=" O   CYS B 342 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   VAL B 347 " --> pdb=" O   ALA B 343 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   LYS B 348 " --> pdb=" O   GLN B 344 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   ASN B 352 " --> pdb=" O   LYS B 348 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 399 through 418
      removed outlier: 3.537A  pdb=" N   LYS B 405 " --> pdb=" O   ILE B 401 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   GLU B 408 " --> pdb=" O   THR B 404 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   SER B 410 " --> pdb=" O   GLN B 406 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   GLN B 413 " --> pdb=" O   LYS B 409 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ILE B 414 " --> pdb=" O   SER B 410 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   LEU B 415 " --> pdb=" O   LEU B 411 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   GLU B 416 " --> pdb=" O   ILE B 412 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 456 through 461
    Processing helix  chain 'B' and resid 468 through 479
      removed outlier: 3.636A  pdb=" N   GLU B 472 " --> pdb=" O   THR B 468 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 481 through 485
    Processing helix  chain 'B' and resid 508 through 521
      Proline residue:  B 516  - end of helix
      removed outlier: 3.642A  pdb=" N   SER B 520 " --> pdb=" O   PRO B 516 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 584 through 591
      removed outlier: 3.572A  pdb=" N   GLU B 589 " --> pdb=" O   LEU B 585 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 600 through 613
      removed outlier: 3.875A  pdb=" N   HIS B 606 " --> pdb=" O   GLN B 602 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ASP B 607 " --> pdb=" O   ARG B 603 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   SER B 609 " --> pdb=" O   LEU B 605 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ILE B 610 " --> pdb=" O   HIS B 606 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLU B 613 " --> pdb=" O   SER B 609 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 622 through 631
      removed outlier: 4.118A  pdb=" N   GLU B 628 " --> pdb=" O   SER B 624 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   ASN B 631 " --> pdb=" O   GLN B 627 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 644 through 650
      removed outlier: 3.835A  pdb=" N   PHE B 647 " --> pdb=" O   ASP B 644 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   ALA B 649 " --> pdb=" O   SER B 646 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   LEU B 650 " --> pdb=" O   PHE B 647 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 651 through 662
      removed outlier: 3.684A  pdb=" N   LEU B 655 " --> pdb=" O   PRO B 651 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ILE B 656 " --> pdb=" O   LYS B 652 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   THR B 657 " --> pdb=" O   ASP B 653 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   HIS B 662 " --> pdb=" O   VAL B 658 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 689 through 716
      removed outlier: 3.764A  pdb=" N   VAL B 693 " --> pdb=" O   LYS B 689 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ARG B 694 " --> pdb=" O   GLU B 690 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   ALA B 699 " --> pdb=" O   LYS B 695 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   VAL B 700 " --> pdb=" O   GLY B 696 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ALA B 703 " --> pdb=" O   ALA B 699 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   TYR B 705 " --> pdb=" O   LEU B 701 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   GLU B 706 " --> pdb=" O   ARG B 702 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ASP B 707 " --> pdb=" O   ALA B 703 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 719 through 729
      removed outlier: 4.402A  pdb=" N   LEU B 727 " --> pdb=" O   ARG B 724 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   SER B 728 " --> pdb=" O   ASP B 725 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   SER B 729 " --> pdb=" O   GLN B 726 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 739 through 757
      removed outlier: 5.064A  pdb=" N   ALA B 751 " --> pdb=" O   GLU B 747 " (cutoff:3.500A)
      removed outlier: 5.435A  pdb=" N   GLU B 752 " --> pdb=" O   ASN B 748 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   VAL B 753 " --> pdb=" O   THR B 749 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 760 through 762
      No H-bonds generated for 'chain 'B' and resid 760 through 762'
    Processing helix  chain 'B' and resid 763 through 771
      removed outlier: 3.664A  pdb=" N   ILE B 767 " --> pdb=" O   MET B 763 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 776 through 780
      removed outlier: 3.710A  pdb=" N   ALA B 779 " --> pdb=" O   SER B 776 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 781 through 786
      removed outlier: 4.254A  pdb=" N   GLU B 785 " --> pdb=" O   ASN B 781 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   PHE B 786 " --> pdb=" O   ILE B 782 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 781 through 786'
    Processing helix  chain 'B' and resid 787 through 790
    Processing helix  chain 'B' and resid 792 through 802
      removed outlier: 3.517A  pdb=" N   GLY B 802 " --> pdb=" O   ALA B 798 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 804 through 813
      removed outlier: 3.734A  pdb=" N   ALA B 808 " --> pdb=" O   SER B 804 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   GLU B 809 " --> pdb=" O   GLU B 805 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   ALA B 810 " --> pdb=" O   GLN B 806 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 827 through 848
      removed outlier: 3.621A  pdb=" N   VAL B 832 " --> pdb=" O   ASP B 828 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LEU B 833 " --> pdb=" O   PRO B 829 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ALA B 848 " --> pdb=" O   GLY B 844 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 860 through 874
    Processing helix  chain 'B' and resid 880 through 891
      removed outlier: 4.096A  pdb=" N   THR B 886 " --> pdb=" O   THR B 882 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   LEU B 887 " --> pdb=" O   LYS B 883 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   GLU B 891 " --> pdb=" O   LEU B 887 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 897 through 917
      removed outlier: 4.424A  pdb=" N   ILE B 901 " --> pdb=" O   ASP B 897 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ASP B 902 " --> pdb=" O   SER B 898 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 922 through 930
      removed outlier: 3.581A  pdb=" N   SER B 928 " --> pdb=" O   GLU B 924 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 936 through 951
      removed outlier: 4.005A  pdb=" N   GLU B 946 " --> pdb=" O   GLN B 942 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   GLU B 948 " --> pdb=" O   ALA B 944 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   ALA B 949 " --> pdb=" O   ILE B 945 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 955 through 964
      removed outlier: 3.755A  pdb=" N   SER B 964 " --> pdb=" O   VAL B 960 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 966 through 971
      removed outlier: 3.544A  pdb=" N   ILE B 970 " --> pdb=" O   PRO B 966 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ARG B 971 " --> pdb=" O   THR B 967 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 966 through 971'
    Processing helix  chain 'B' and resid 974 through 978
    Processing helix  chain 'B' and resid 988 through 1003
      removed outlier: 3.907A  pdb=" N   ARG B 992 " --> pdb=" O   LYS B 988 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   ASP B1003 " --> pdb=" O   LEU B 999 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1013 through 1019
    Processing helix  chain 'B' and resid 1021 through 1032
      removed outlier: 3.804A  pdb=" N   LEU B1025 " --> pdb=" O   LEU B1021 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   GLU B1026 " --> pdb=" O   LEU B1022 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   ASP B1027 " --> pdb=" O   GLN B1023 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1038 through 1054
    Processing helix  chain 'A' and resid 73 through 89
      removed outlier: 3.900A  pdb=" N   ILE A  78 " --> pdb=" O   PHE A  74 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   ASP A  83 " --> pdb=" O   GLN A  79 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ALA A  86 " --> pdb=" O   GLN A  82 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   GLY A  89 " --> pdb=" O   TRP A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 111
      removed outlier: 3.608A  pdb=" N   LEU A 111 " --> pdb=" O   PRO A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 133
    Processing helix  chain 'A' and resid 162 through 170
      removed outlier: 3.629A  pdb=" N   SER A 168 " --> pdb=" O   LEU A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 247
    Processing helix  chain 'A' and resid 256 through 273
      removed outlier: 7.199A  pdb=" N   GLU A 262 " --> pdb=" O   GLU A 258 " (cutoff:3.500A)
      removed outlier: 5.268A  pdb=" N   ASN A 263 " --> pdb=" O   LEU A 259 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   SER A 268 " --> pdb=" O   GLU A 264 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ALA A 269 " --> pdb=" O   LYS A 265 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   TYR A 270 " --> pdb=" O   GLU A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 294
      removed outlier: 3.869A  pdb=" N   ASP A 285 " --> pdb=" O   GLN A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 319
      removed outlier: 4.217A  pdb=" N   VAL A 307 " --> pdb=" O   ALA A 303 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ALA A 313 " --> pdb=" O   LYS A 309 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ASN A 315 " --> pdb=" O   SER A 311 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ILE A 316 " --> pdb=" O   HIS A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 352
      removed outlier: 3.656A  pdb=" N   GLY A 333 " --> pdb=" O   ALA A 329 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   SER A 337 " --> pdb=" O   GLY A 333 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   LEU A 338 " --> pdb=" O   ARG A 334 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ALA A 339 " --> pdb=" O   MET A 335 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   GLN A 341 " --> pdb=" O   SER A 337 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ALA A 343 " --> pdb=" O   ALA A 339 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   GLN A 344 " --> pdb=" O   ARG A 340 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   LEU A 345 " --> pdb=" O   GLN A 341 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   LYS A 348 " --> pdb=" O   GLN A 344 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLU A 351 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 418
      removed outlier: 3.949A  pdb=" N   ILE A 414 " --> pdb=" O   SER A 410 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   GLU A 416 " --> pdb=" O   ILE A 412 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ARG A 418 " --> pdb=" O   ILE A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 477
      removed outlier: 3.719A  pdb=" N   GLY A 473 " --> pdb=" O   LYS A 469 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   LYS A 477 " --> pdb=" O   GLY A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 520
      removed outlier: 3.538A  pdb=" N   ASP A 514 " --> pdb=" O   VAL A 510 " (cutoff:3.500A)
      Proline residue:  A 516  - end of helix
    Processing helix  chain 'A' and resid 584 through 589
    Processing helix  chain 'A' and resid 597 through 605
      removed outlier: 3.650A  pdb=" N   LYS A 601 " --> pdb=" O   MET A 597 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   GLN A 602 " --> pdb=" O   GLN A 598 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   ARG A 603 " --> pdb=" O   GLU A 599 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 616
      removed outlier: 3.955A  pdb=" N   LEU A 611 " --> pdb=" O   ASP A 607 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   VAL A 615 " --> pdb=" O   LEU A 611 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 625 through 630
    Processing helix  chain 'A' and resid 631 through 633
      No H-bonds generated for 'chain 'A' and resid 631 through 633'
    Processing helix  chain 'A' and resid 644 through 648
      removed outlier: 3.795A  pdb=" N   PHE A 647 " --> pdb=" O   ASP A 644 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 651 through 662
      removed outlier: 4.193A  pdb=" N   THR A 657 " --> pdb=" O   ASP A 653 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   HIS A 662 " --> pdb=" O   VAL A 658 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 692 through 698
    Processing helix  chain 'A' and resid 703 through 716
      removed outlier: 3.726A  pdb=" N   PHE A 710 " --> pdb=" O   GLU A 706 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 719 through 729
      removed outlier: 4.064A  pdb=" N   ARG A 724 " --> pdb=" O   SER A 721 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ASP A 725 " --> pdb=" O   GLU A 722 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   GLN A 726 " --> pdb=" O   PHE A 723 " (cutoff:3.500A)
      removed outlier: 4.699A  pdb=" N   SER A 728 " --> pdb=" O   ASP A 725 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 739 through 748
      removed outlier: 3.790A  pdb=" N   GLU A 747 " --> pdb=" O   MET A 743 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   ASN A 748 " --> pdb=" O   LYS A 744 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 752 through 757
    Processing helix  chain 'A' and resid 760 through 763
      removed outlier: 3.567A  pdb=" N   MET A 763 " --> pdb=" O   ASN A 760 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 760 through 763'
    Processing helix  chain 'A' and resid 764 through 773
      removed outlier: 3.793A  pdb=" N   LYS A 768 " --> pdb=" O   ILE A 764 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ASP A 769 " --> pdb=" O   PRO A 765 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   ALA A 770 " --> pdb=" O   ALA A 766 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   LEU A 773 " --> pdb=" O   ASP A 769 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 776 through 779
    Processing helix  chain 'A' and resid 780 through 786
      removed outlier: 3.589A  pdb=" N   THR A 784 " --> pdb=" O   THR A 780 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   GLU A 785 " --> pdb=" O   ASN A 781 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 791 through 802
      removed outlier: 3.592A  pdb=" N   ARG A 795 " --> pdb=" O   GLY A 791 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   TYR A 797 " --> pdb=" O   MET A 793 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 804 through 811
      removed outlier: 3.594A  pdb=" N   ALA A 808 " --> pdb=" O   SER A 804 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 827 through 847
      removed outlier: 3.760A  pdb=" N   ILE A 831 " --> pdb=" O   THR A 827 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   VAL A 832 " --> pdb=" O   ASP A 828 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   LEU A 833 " --> pdb=" O   PRO A 829 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ALA A 834 " --> pdb=" O   GLY A 830 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   ARG A 838 " --> pdb=" O   ALA A 834 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   LEU A 845 " --> pdb=" O   SER A 841 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 862 through 874
      removed outlier: 3.808A  pdb=" N   LEU A 868 " --> pdb=" O   ILE A 864 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   VAL A 869 " --> pdb=" O   SER A 865 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   GLN A 870 " --> pdb=" O   TYR A 866 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   LEU A 872 " --> pdb=" O   LEU A 868 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 880 through 885
      removed outlier: 3.695A  pdb=" N   LEU A 885 " --> pdb=" O   LEU A 881 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 900 through 918
      removed outlier: 3.810A  pdb=" N   VAL A 904 " --> pdb=" O   VAL A 900 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   VAL A 905 " --> pdb=" O   ILE A 901 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   GLN A 906 " --> pdb=" O   ASP A 902 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   ARG A 911 " --> pdb=" O   PHE A 907 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ASP A 918 " --> pdb=" O   GLN A 914 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 936 through 952
      removed outlier: 3.665A  pdb=" N   SER A 941 " --> pdb=" O   PRO A 937 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   ILE A 945 " --> pdb=" O   SER A 941 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   MET A 947 " --> pdb=" O   THR A 943 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   GLU A 948 " --> pdb=" O   ALA A 944 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ALA A 949 " --> pdb=" O   ILE A 945 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   PHE A 950 " --> pdb=" O   GLU A 946 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 955 through 963
      removed outlier: 3.681A  pdb=" N   GLU A 961 " --> pdb=" O   PRO A 957 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 964 through 969
      removed outlier: 3.568A  pdb=" N   ARG A 968 " --> pdb=" O   SER A 964 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   ILE A 969 " --> pdb=" O   ARG A 965 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 964 through 969'
    Processing helix  chain 'A' and resid 990 through 1003
      removed outlier: 4.417A  pdb=" N   SER A 996 " --> pdb=" O   ARG A 992 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ALA A 997 " --> pdb=" O   ALA A 993 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1010 through 1018
      removed outlier: 3.622A  pdb=" N   PHE A1014 " --> pdb=" O   ASP A1010 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1021 through 1029
      removed outlier: 3.595A  pdb=" N   LEU A1025 " --> pdb=" O   LEU A1021 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   GLU A1026 " --> pdb=" O   LEU A1022 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1043 through 1055
      removed outlier: 4.189A  pdb=" N   LEU A1049 " --> pdb=" O   ARG A1045 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   VAL A1052 " --> pdb=" O   LEU A1048 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 91 through 92
      removed outlier: 3.803A  pdb=" N   ALA B 122 " --> pdb=" O   ALA B  91 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 144 through 153
    current: chain 'B' and resid 193 through 202
      removed outlier: 6.582A  pdb=" N   TRP B 194 " --> pdb=" O   GLN B 214 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   THR B 208 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   MET B 202 " --> pdb=" O   GLU B 206 " (cutoff:3.500A)
      removed outlier: 5.731A  pdb=" N   GLU B 206 " --> pdb=" O   MET B 202 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 425 through 430
      removed outlier: 3.774A  pdb=" N   LEU B 434 " --> pdb=" O   ILE B 390 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   ILE B 390 " --> pdb=" O   LEU B 434 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   ASN B 440 " --> pdb=" O   ARG B 384 " (cutoff:3.500A)
      removed outlier: 5.836A  pdb=" N   ARG B 384 " --> pdb=" O   ASN B 440 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 450 through 451
    Processing sheet with id=AA4, first strand: chain 'B' and resid 555 through 556
    Processing sheet with id=AA5, first strand: chain 'B' and resid 564 through 565
    Processing sheet with id=AA6, first strand: chain 'B' and resid 617 through 619
      removed outlier: 7.056A  pdb=" N   PHE B 666 " --> pdb=" O   CYS B 679 " (cutoff:3.500A)
      removed outlier: 7.191A  pdb=" N   CYS B 679 " --> pdb=" O   PHE B 666 " (cutoff:3.500A)
      removed outlier: 5.171A  pdb=" N   VAL B 668 " --> pdb=" O   LEU B 677 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   MET B 637 " --> pdb=" O   ALA B 684 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 731 through 733
      removed outlier: 6.322A  pdb=" N   GLY B 737 " --> pdb=" O   PHE B 732 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 91 through 92
      removed outlier: 5.899A  pdb=" N   ALA A  91 " --> pdb=" O   ALA A 122 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 121 through 123
    current: chain 'A' and resid 144 through 152
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 144 through 152
    current: chain 'A' and resid 193 through 202
      removed outlier: 6.427A  pdb=" N   TRP A 194 " --> pdb=" O   GLN A 214 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   THR A 208 " --> pdb=" O   VAL A 200 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   MET A 202 " --> pdb=" O   GLU A 206 " (cutoff:3.500A)
      removed outlier: 5.595A  pdb=" N   GLU A 206 " --> pdb=" O   MET A 202 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   SER A 216 " --> pdb=" O   LEU A 219 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 249 through 251
      removed outlier: 6.906A  pdb=" N   ILE A 254 " --> pdb=" O   TYR A 250 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 425 through 427
      removed outlier: 4.045A  pdb=" N   ASN A 440 " --> pdb=" O   ARG A 384 " (cutoff:3.500A)
      removed outlier: 5.141A  pdb=" N   ARG A 384 " --> pdb=" O   ASN A 440 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   TRP A 542 " --> pdb=" O   GLY A 391 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 451 through 453
      removed outlier: 3.574A  pdb=" N   LEU A 452 " --> pdb=" O   ALA A 498 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ALA A 498 " --> pdb=" O   LEU A 452 " (cutoff:3.500A)
      removed outlier: 5.435A  pdb=" N   TYR A 495 " --> pdb=" O   ARG A 488 " (cutoff:3.500A)
      removed outlier: 5.174A  pdb=" N   ARG A 488 " --> pdb=" O   TYR A 495 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   TYR A 497 " --> pdb=" O   TYR A 486 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 555 through 556
    Processing sheet with id=AB4, first strand: chain 'A' and resid 564 through 565
    Processing sheet with id=AB5, first strand: chain 'A' and resid 617 through 619
      removed outlier: 7.198A  pdb=" N   PHE A 666 " --> pdb=" O   CYS A 679 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   CYS A 679 " --> pdb=" O   PHE A 666 " (cutoff:3.500A)
      removed outlier: 5.282A  pdb=" N   VAL A 668 " --> pdb=" O   LEU A 677 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   MET A 637 " --> pdb=" O   ALA A 684 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 731 through 733

    529 hydrogen bonds defined for protein.
    1480 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      90 hydrogen bonds
      180 hydrogen bond angles
      0 basepair planarities
      33 basepair parallelities
      70 stacking parallelities
  Total time for adding SS restraints: 4.05

  Time building geometry restraints manager: 2.14 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 2788
        1.30 -     1.43: 5741
        1.43 -     1.56: 10228
        1.56 -     1.68: 294
        1.68 -     1.81: 104
  Bond restraints: 19155
  Sorted by residual:
  bond pdb=" C8  GTP D   1 "
       pdb=" N9  GTP D   1 "
    ideal  model  delta    sigma   weight residual
    1.370  1.197  0.173 2.00e-02 2.50e+03 7.47e+01
  bond pdb=" C8  GTP C   1 "
       pdb=" N9  GTP C   1 "
    ideal  model  delta    sigma   weight residual
    1.370  1.198  0.172 2.00e-02 2.50e+03 7.40e+01
  bond pdb=" C4  GTP D   1 "
       pdb=" N9  GTP D   1 "
    ideal  model  delta    sigma   weight residual
    1.375  1.214  0.161 2.00e-02 2.50e+03 6.51e+01
  bond pdb=" O2G GTP C   1 "
       pdb=" PG  GTP C   1 "
    ideal  model  delta    sigma   weight residual
    1.510  1.650 -0.140 2.00e-02 2.50e+03 4.92e+01
  bond pdb=" O2G GTP D   1 "
       pdb=" PG  GTP D   1 "
    ideal  model  delta    sigma   weight residual
    1.510  1.648 -0.138 2.00e-02 2.50e+03 4.75e+01
  ... (remaining 19150 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.87: 26324
        2.87 -     5.74: 305
        5.74 -     8.61: 41
        8.61 -    11.48: 4
       11.48 -    14.36: 3
  Bond angle restraints: 26677
  Sorted by residual:
  angle pdb=" N   GLY A 737 "
        pdb=" CA  GLY A 737 "
        pdb=" C   GLY A 737 "
      ideal   model   delta    sigma   weight residual
     111.56  119.88   -8.32 1.01e+00 9.80e-01 6.79e+01
  angle pdb=" N   ARG B 965 "
        pdb=" CA  ARG B 965 "
        pdb=" C   ARG B 965 "
      ideal   model   delta    sigma   weight residual
     112.75  104.00    8.75 1.36e+00 5.41e-01 4.14e+01
  angle pdb=" C   VAL B1034 "
        pdb=" N   MET B1035 "
        pdb=" CA  MET B1035 "
      ideal   model   delta    sigma   weight residual
     120.95  113.33    7.62 1.40e+00 5.10e-01 2.96e+01
  angle pdb=" C4  GTP D   1 "
        pdb=" N9  GTP D   1 "
        pdb=" C8  GTP D   1 "
      ideal   model   delta    sigma   weight residual
     108.00  122.36  -14.36 3.00e+00 1.11e-01 2.29e+01
  angle pdb=" CA  ARG A 965 "
        pdb=" C   ARG A 965 "
        pdb=" N   PRO A 966 "
      ideal   model   delta    sigma   weight residual
     118.44  125.95   -7.51 1.59e+00 3.96e-01 2.23e+01
  ... (remaining 26672 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.69: 11199
       35.69 -    71.38: 468
       71.38 -   107.06: 59
      107.06 -   142.75: 4
      142.75 -   178.44: 4
  Dihedral angle restraints: 11734
    sinusoidal: 6020
      harmonic: 5714
  Sorted by residual:
  dihedral pdb=" O4'   U C  19 "
           pdb=" C1'   U C  19 "
           pdb=" N1    U C  19 "
           pdb=" C2    U C  19 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   49.89  150.11     1      1.50e+01 4.44e-03 7.97e+01
  dihedral pdb=" O4'   U D  19 "
           pdb=" C1'   U D  19 "
           pdb=" N1    U D  19 "
           pdb=" C2    U D  19 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   60.14  171.86     1      1.70e+01 3.46e-03 6.61e+01
  dihedral pdb=" O5' GTP D   1 "
           pdb=" O3A GTP D   1 "
           pdb=" PA  GTP D   1 "
           pdb=" PB  GTP D   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     274.12   95.68  178.44     1      2.00e+01 2.50e-03 4.80e+01
  ... (remaining 11731 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 2527
       0.060 -    0.119: 535
       0.119 -    0.179: 68
       0.179 -    0.239: 8
       0.239 -    0.298: 2
  Chirality restraints: 3140
  Sorted by residual:
  chirality pdb=" CB  ILE A 970 "
            pdb=" CA  ILE A 970 "
            pdb=" CG1 ILE A 970 "
            pdb=" CG2 ILE A 970 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.30 2.00e-01 2.50e+01 2.22e+00
  chirality pdb=" CB  VAL B1034 "
            pdb=" CA  VAL B1034 "
            pdb=" CG1 VAL B1034 "
            pdb=" CG2 VAL B1034 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.52e+00
  chirality pdb=" C1'   U D  57 "
            pdb=" O4'   U D  57 "
            pdb=" C2'   U D  57 "
            pdb=" N1    U D  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.24    0.22 2.00e-01 2.50e+01 1.26e+00
  ... (remaining 3137 not shown)

  Planarity restraints: 2916
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 637 "   -0.047 5.00e-02 4.00e+02   7.06e-02 7.97e+00
        pdb=" N   PRO A 638 "    0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO A 638 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 638 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 962 "    0.012 2.00e-02 2.50e+03   2.35e-02 5.52e+00
        pdb=" C   ALA A 962 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   ALA A 962 "    0.015 2.00e-02 2.50e+03
        pdb=" N   TYR A 963 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U D  57 "    0.028 2.00e-02 2.50e+03   1.51e-02 5.13e+00
        pdb=" N1    U D  57 "   -0.034 2.00e-02 2.50e+03
        pdb=" C2    U D  57 "    0.000 2.00e-02 2.50e+03
        pdb=" O2    U D  57 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3    U D  57 "    0.002 2.00e-02 2.50e+03
        pdb=" C4    U D  57 "    0.005 2.00e-02 2.50e+03
        pdb=" O4    U D  57 "    0.006 2.00e-02 2.50e+03
        pdb=" C5    U D  57 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    U D  57 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 2913 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 2385
        2.74 -     3.28: 17750
        3.28 -     3.82: 30270
        3.82 -     4.36: 35111
        4.36 -     4.90: 57511
  Nonbonded interactions: 143027
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 855 "
            pdb=" OP1   G C  69 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" O   LYS A1040 "
            pdb=" ND2 ASN A1043 "
     model   vdw
     2.205 3.120
  nonbonded pdb=" NH1 ARG A 724 "
            pdb=" O   ALA A 772 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" O   PHE B 950 "
            pdb=" OG1 THR B 953 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" O   VAL A1041 "
            pdb=" NH1 ARG A1045 "
     model   vdw
     2.229 3.120
  ... (remaining 143022 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 70 and (name CA or name C or name O or name CB or name OG \ 
 )) or resid 71 through 174 or (resid 175 and (name N or name CA or name C or na \ 
me O or name CB )) or resid 176 through 446 or (resid 447 through 449 and (name  \ 
N or name CA or name C or name O or name CB )) or resid 450 or (resid 451 and (n \ 
ame N or name CA or name C or name O or name CB )) or resid 452 through 939 or r \ 
esid 941 through 944 or (resid 945 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 946 through 1068))
  selection = (chain 'B' and (resid 70 through 493 or (resid 494 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 495 through 939 or resid 941 through 972 or \ 
 (resid 973 through 975 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 976 through 978 or (resid 979 through 983 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 984 through 986 or (resid 987 through 990  \ 
and (name N or name CA or name C or name O or name CB )) or resid 991 through 10 \ 
36 or (resid 1037 through 1040 and (name N or name CA or name C or name O or nam \ 
e CB )) or resid 1041 through 1047 or (resid 1048 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 1049 through 1068))
}
ncs_group {
  reference = (chain 'C' and resid 1 through 71)
  selection = chain 'D'
}

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=0.50 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:             3.650
  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:             0.020
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.030
  Process input model:                     23.590
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
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      :  0.008   0.173  19157  Z= 0.391
  Angle     :  0.807  14.356  26677  Z= 0.447
  Chirality :  0.049   0.298   3140
  Planarity :  0.005   0.071   2916
  Dihedral  : 17.946 178.441   8040
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 14.06 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    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: -3.24 (0.18), residues: 1964
  helix: -1.92 (0.17), residues: 860
  sheet: -1.19 (0.37), residues: 217
  loop : -2.58 (0.18), residues: 887

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 432 
 TYR   0.019   0.002   TYR A 584 
 PHE   0.024   0.002   PHE A1014 
 TRP   0.012   0.002   TRP A 298 
 HIS   0.005   0.001   HIS A 586 

Details of bonding type rmsd
  covalent geometry    : bond        0.00833 (19155)
  covalent geometry    : angle       0.80712 (26677)
  hydrogen bonds       : bond        0.16677 (  619)
  hydrogen bonds       : angle       6.65477 ( 1660)
  Misc. bond           : bond        0.02940 (    2)

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

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

  3928 Ramachandran restraints generated.
    1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3928 Ramachandran restraints generated.
    1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 164
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   81 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8344 (tp)
REVERT: B  267 MET cc_start: 0.9143 (mmm) cc_final: 0.8846 (mmp)
REVERT: B  420 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7740 (tp)
REVERT: B  488 ARG cc_start: 0.9098 (ttt180) cc_final: 0.8852 (tmm-80)
REVERT: B  549 ASP cc_start: 0.9191 (t0) cc_final: 0.8939 (m-30)
REVERT: B  563 ASN cc_start: 0.8434 (p0) cc_final: 0.7835 (p0)
REVERT: B  659 MET cc_start: 0.8445 (mtt) cc_final: 0.8211 (ttm)
REVERT: B  743 MET cc_start: 0.9420 (mmt) cc_final: 0.8359 (mmp)
REVERT: B  768 LYS cc_start: 0.9560 (mtpp) cc_final: 0.9327 (mmtt)
REVERT: B  775 MET cc_start: 0.9049 (tmm) cc_final: 0.7940 (ttt)
REVERT: B  875 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8365 (t0)
REVERT: B  947 MET cc_start: 0.9160 (tmm) cc_final: 0.8932 (tpt)
REVERT: B 1034 VAL cc_start: 0.8758 (OUTLIER) cc_final: 0.8446 (m)
REVERT: A   81 LEU cc_start: 0.9517 (mt) cc_final: 0.9193 (tp)
REVERT: A  202 MET cc_start: 0.9393 (ttp) cc_final: 0.9019 (tmm)
REVERT: A  264 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8370 (tp30)
REVERT: A  420 LEU cc_start: 0.9162 (mt) cc_final: 0.8865 (mm)
REVERT: A  441 LEU cc_start: 0.9649 (tp) cc_final: 0.9351 (tp)
REVERT: A  528 MET cc_start: 0.9368 (mtp) cc_final: 0.8942 (mtp)
REVERT: A  659 MET cc_start: 0.8913 (mtm) cc_final: 0.8395 (ttm)
REVERT: A  677 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8712 (tt)
REVERT: A  701 LEU cc_start: 0.9132 (pp) cc_final: 0.8828 (tp)
REVERT: A  714 MET cc_start: 0.9614 (ttp) cc_final: 0.9231 (ptp)
REVERT: A  739 MET cc_start: 0.8753 (mmm) cc_final: 0.7985 (tpp)
REVERT: A  743 MET cc_start: 0.9499 (mmm) cc_final: 0.8830 (mmm)
REVERT: A  833 LEU cc_start: 0.9164 (mt) cc_final: 0.8630 (pt)
REVERT: A  846 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.7904 (m-80)
REVERT: A  947 MET cc_start: 0.8739 (ttt) cc_final: 0.8399 (ttp)
  outliers start: 73
  outliers final: 7
  residues processed: 229
  average time/residue: 0.1356
  time to fit residues: 48.0619
Evaluate side-chains
  103 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 98 optimal weight:   20.0000
   chunk 194 optimal weight:   50.0000
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    7.9990
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:   20.0000
   chunk 200 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    0.8980
   overall best weight:    2.9786

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

Flipped N/Q/H residues before XYZ refinement:
** B  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 341 GLN
B 631 ASN
B 875 ASN
A 138 ASN
A 145 HIS
A 147 GLN
A 177 HIS
A 185 ASN
A 214 GLN
A 442 ASN
A 547 HIS
** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 781 ASN
A 856 ASN
A 870 GLN
A1031 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.039735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.029672 restraints weight = 229298.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.030447 restraints weight = 144843.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.031013 restraints weight = 103110.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.031405 restraints weight = 79236.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.031694 restraints weight = 64729.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2929
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2929 r_free = 0.2929    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2929 r_free = 0.2929    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2929
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.3155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  19157  Z= 0.215
  Angle     :  0.734   8.707  26677  Z= 0.375
  Chirality :  0.044   0.241   3140
  Planarity :  0.006   0.108   2916
  Dihedral  : 18.568 178.723   4365
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.57 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  2.30 %
    Favored  : 97.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    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 (0.18), residues: 1964
  helix: -1.34 (0.17), residues: 877
  sheet: -1.33 (0.36), residues: 211
  loop : -2.04 (0.20), residues: 876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 426 
 TYR   0.049   0.003   TYR A 123 
 PHE   0.019   0.002   PHE A 986 
 TRP   0.028   0.002   TRP A 530 
 HIS   0.006   0.002   HIS A 422 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 (19155)
  covalent geometry    : angle       0.73418 (26677)
  hydrogen bonds       : bond        0.04326 (  619)
  hydrogen bonds       : angle       4.63807 ( 1660)
  Misc. bond           : bond        0.00072 (    2)

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

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

  3928 Ramachandran restraints generated.
    1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3928 Ramachandran restraints generated.
    1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 95
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 MET cc_start: 0.9064 (ptp) cc_final: 0.8739 (pmm)
REVERT: B  202 MET cc_start: 0.9182 (ppp) cc_final: 0.8781 (ppp)
REVERT: B  267 MET cc_start: 0.9263 (mmm) cc_final: 0.8995 (mmm)
REVERT: B  549 ASP cc_start: 0.9224 (t0) cc_final: 0.8932 (m-30)
REVERT: B  659 MET cc_start: 0.9016 (mtt) cc_final: 0.8372 (ttm)
REVERT: B  743 MET cc_start: 0.9645 (mmp) cc_final: 0.9010 (mmm)
REVERT: B  775 MET cc_start: 0.8821 (tmm) cc_final: 0.7845 (ppp)
REVERT: B  947 MET cc_start: 0.9151 (tmm) cc_final: 0.8931 (tmm)
REVERT: A  202 MET cc_start: 0.9510 (ttp) cc_final: 0.9053 (tmm)
REVERT: A  441 LEU cc_start: 0.9457 (tp) cc_final: 0.9179 (tp)
REVERT: A  528 MET cc_start: 0.8928 (mtp) cc_final: 0.8146 (mtm)
REVERT: A  659 MET cc_start: 0.9186 (mtm) cc_final: 0.8631 (ttm)
REVERT: A  701 LEU cc_start: 0.9588 (pp) cc_final: 0.9197 (tp)
REVERT: A  714 MET cc_start: 0.9517 (ttp) cc_final: 0.9212 (ptp)
REVERT: A  739 MET cc_start: 0.8607 (mmm) cc_final: 0.8289 (tpp)
REVERT: A  759 ILE cc_start: 0.8297 (mp) cc_final: 0.8023 (tp)
REVERT: A  775 MET cc_start: 0.9274 (tpp) cc_final: 0.8922 (tpp)
REVERT: A  947 MET cc_start: 0.8636 (ttt) cc_final: 0.8374 (ttm)
REVERT: A 1035 MET cc_start: 0.9437 (mmp) cc_final: 0.9227 (mmt)
  outliers start: 2
  outliers final: 0
  residues processed: 97
  average time/residue: 0.1378
  time to fit residues: 21.4654
Evaluate side-chains
  66 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 84 optimal weight:    0.7980
   chunk 62 optimal weight:    3.9990
   chunk 173 optimal weight:    7.9990
   chunk 39 optimal weight:    4.9990
   chunk 119 optimal weight:    5.9990
   chunk 120 optimal weight:    1.9990
   chunk 190 optimal weight:    8.9990
   chunk 0 optimal weight:    7.9990
   chunk 197 optimal weight:    6.9990
   chunk 142 optimal weight:    0.8980
   chunk 207 optimal weight:   10.0000
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
** B  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  79 GLN
** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 341 GLN
B 875 ASN
A  82 GLN
A 138 ASN
A 214 GLN
A 263 ASN
A 760 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.037236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.027214 restraints weight = 234986.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.027959 restraints weight = 145695.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.028479 restraints weight = 102583.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.028841 restraints weight = 78585.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.029102 restraints weight = 64277.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2818
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2818 r_free = 0.2818    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2818 r_free = 0.2818    target_work(ls_wunit_k1) = 0.028         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2818
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.4665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  19157  Z= 0.173
  Angle     :  0.657   9.394  26677  Z= 0.331
  Chirality :  0.041   0.195   3140
  Planarity :  0.005   0.058   2916
  Dihedral  : 18.419 176.267   4365
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.03 %
    Favored  : 96.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    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: -1.98 (0.18), residues: 1964
  helix: -0.86 (0.17), residues: 894
  sheet: -1.33 (0.33), residues: 228
  loop : -1.68 (0.21), residues: 842

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B1045 
 TYR   0.015   0.002   TYR B 256 
 PHE   0.023   0.002   PHE B 824 
 TRP   0.018   0.002   TRP B 186 
 HIS   0.008   0.002   HIS B 274 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 (19155)
  covalent geometry    : angle       0.65691 (26677)
  hydrogen bonds       : bond        0.03992 (  619)
  hydrogen bonds       : angle       4.40770 ( 1660)
  Misc. bond           : bond        0.00036 (    2)

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

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

  3928 Ramachandran restraints generated.
    1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3928 Ramachandran restraints generated.
    1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 69
  time to evaluate  : 0.667 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  237 MET cc_start: 0.9521 (ptp) cc_final: 0.9186 (ptp)
REVERT: B  267 MET cc_start: 0.9333 (mmm) cc_final: 0.8943 (mmm)
REVERT: B  549 ASP cc_start: 0.9333 (t0) cc_final: 0.8963 (m-30)
REVERT: B  659 MET cc_start: 0.9142 (mtt) cc_final: 0.8322 (ttm)
REVERT: B  763 MET cc_start: 0.9011 (tpp) cc_final: 0.8704 (mtm)
REVERT: B  842 LEU cc_start: 0.9606 (mt) cc_final: 0.9175 (pp)
REVERT: B  947 MET cc_start: 0.9230 (tmm) cc_final: 0.8998 (tmm)
REVERT: A  202 MET cc_start: 0.9437 (ttp) cc_final: 0.8846 (tmm)
REVERT: A  214 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8236 (mm-40)
REVERT: A  441 LEU cc_start: 0.9442 (tp) cc_final: 0.9118 (tp)
REVERT: A  714 MET cc_start: 0.9576 (ttp) cc_final: 0.9265 (ptp)
REVERT: A  739 MET cc_start: 0.8651 (mmm) cc_final: 0.8413 (tpt)
REVERT: A  743 MET cc_start: 0.9595 (mmm) cc_final: 0.9367 (mmm)
REVERT: A  775 MET cc_start: 0.9221 (tpp) cc_final: 0.8851 (tpp)
REVERT: A  947 MET cc_start: 0.8808 (ttt) cc_final: 0.8054 (tpp)
  outliers start: 2
  outliers final: 0
  residues processed: 71
  average time/residue: 0.1375
  time to fit residues: 15.8287
Evaluate side-chains
  57 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 56
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 59 optimal weight:    6.9990
   chunk 153 optimal weight:    0.7980
   chunk 64 optimal weight:    7.9990
   chunk 201 optimal weight:    0.1980
   chunk 197 optimal weight:    0.0570
   chunk 7 optimal weight:    5.9990
   chunk 146 optimal weight:    7.9990
   chunk 79 optimal weight:    3.9990
   chunk 157 optimal weight:    0.9990
   chunk 168 optimal weight:    9.9990
   overall best weight:    0.6102

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

Flipped N/Q/H residues before XYZ refinement:
B  76 GLN
** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 274 HIS
B 478 ASN
B 631 ASN
** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 138 ASN
** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.037761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.027772 restraints weight = 232963.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.028532 restraints weight = 142827.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.029076 restraints weight = 99939.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.029458 restraints weight = 76283.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.029708 restraints weight = 61921.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2854
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2854 r_free = 0.2854    target_work(ls_wunit_k1) = 0.029         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2854 r_free = 0.2854    target_work(ls_wunit_k1) = 0.029         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2854
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.4822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  19157  Z= 0.096
  Angle     :  0.548   8.462  26677  Z= 0.272
  Chirality :  0.040   0.226   3140
  Planarity :  0.004   0.058   2916
  Dihedral  : 18.133 177.798   4365
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  0.85 %
    Favored  : 99.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    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: -1.50 (0.19), residues: 1964
  helix: -0.48 (0.17), residues: 904
  sheet: -0.91 (0.36), residues: 214
  loop : -1.48 (0.21), residues: 846

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B1045 
 TYR   0.011   0.001   TYR A  84 
 PHE   0.016   0.001   PHE A 846 
 TRP   0.008   0.001   TRP A 186 
 HIS   0.003   0.001   HIS A 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00202 (19155)
  covalent geometry    : angle       0.54752 (26677)
  hydrogen bonds       : bond        0.02948 (  619)
  hydrogen bonds       : angle       3.99557 ( 1660)
  Misc. bond           : bond        0.00025 (    2)

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

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

  3928 Ramachandran restraints generated.
    1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3928 Ramachandran restraints generated.
    1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 68
  time to evaluate  : 0.678 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  237 MET cc_start: 0.9450 (ptp) cc_final: 0.8873 (ptp)
REVERT: B  267 MET cc_start: 0.9339 (mmm) cc_final: 0.8954 (mmm)
REVERT: B  549 ASP cc_start: 0.9268 (t0) cc_final: 0.8881 (m-30)
REVERT: B  659 MET cc_start: 0.8969 (mtt) cc_final: 0.8298 (ttm)
REVERT: B  842 LEU cc_start: 0.9608 (mt) cc_final: 0.9187 (pp)
REVERT: B  947 MET cc_start: 0.9208 (tmm) cc_final: 0.8975 (tmm)
REVERT: A  202 MET cc_start: 0.9400 (ttp) cc_final: 0.8845 (tmm)
REVERT: A  205 MET cc_start: 0.9303 (tpt) cc_final: 0.8892 (tpp)
REVERT: A  441 LEU cc_start: 0.9424 (tp) cc_final: 0.9155 (tp)
REVERT: A  446 MET cc_start: 0.8804 (mpp) cc_final: 0.8228 (tpp)
REVERT: A  714 MET cc_start: 0.9548 (ttp) cc_final: 0.9286 (ptp)
REVERT: A  743 MET cc_start: 0.9562 (mmm) cc_final: 0.9343 (mmm)
REVERT: A  775 MET cc_start: 0.9102 (tpp) cc_final: 0.8874 (tpp)
REVERT: A  947 MET cc_start: 0.8830 (ttt) cc_final: 0.8108 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 69
  average time/residue: 0.1322
  time to fit residues: 15.1674
Evaluate side-chains
  60 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 117 optimal weight:    0.0270
   chunk 98 optimal weight:   20.0000
   chunk 78 optimal weight:    8.9990
   chunk 41 optimal weight:    4.9990
   chunk 103 optimal weight:   20.0000
   chunk 64 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9980
   chunk 85 optimal weight:    2.9990
   chunk 161 optimal weight:    0.4980
   chunk 32 optimal weight:    7.9990
   chunk 91 optimal weight:    3.9990
   overall best weight:    1.7042

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

Flipped N/Q/H residues before XYZ refinement:
** B  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  97 ASN
** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 138 ASN
** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.036186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.026345 restraints weight = 237430.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.027067 restraints weight = 145442.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.027569 restraints weight = 102015.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.027914 restraints weight = 78187.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.028176 restraints weight = 64148.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2790
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2790 r_free = 0.2790    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2790 r_free = 0.2790    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2790
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
moved from start:          0.5525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  19157  Z= 0.126
  Angle     :  0.569   8.287  26677  Z= 0.284
  Chirality :  0.040   0.164   3140
  Planarity :  0.004   0.058   2916
  Dihedral  : 18.104 177.230   4365
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  1.03 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    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: -1.15 (0.19), residues: 1964
  helix: -0.12 (0.17), residues: 895
  sheet: -0.94 (0.36), residues: 208
  loop : -1.32 (0.21), residues: 861

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG A 538 
 TYR   0.021   0.002   TYR B 135 
 PHE   0.015   0.001   PHE A 846 
 TRP   0.015   0.002   TRP B 186 
 HIS   0.007   0.001   HIS A 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (19155)
  covalent geometry    : angle       0.56895 (26677)
  hydrogen bonds       : bond        0.03331 (  619)
  hydrogen bonds       : angle       3.97640 ( 1660)
  Misc. bond           : bond        0.00015 (    2)

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

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

  3928 Ramachandran restraints generated.
    1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3928 Ramachandran restraints generated.
    1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 62
  time to evaluate  : 0.562 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  267 MET cc_start: 0.9345 (mmm) cc_final: 0.8963 (mmm)
REVERT: B  549 ASP cc_start: 0.9225 (t0) cc_final: 0.8910 (m-30)
REVERT: B  659 MET cc_start: 0.9148 (mtt) cc_final: 0.8345 (ttm)
REVERT: B  739 MET cc_start: 0.9051 (tpt) cc_final: 0.8489 (tpp)
REVERT: B  743 MET cc_start: 0.9461 (mmt) cc_final: 0.9206 (mmt)
REVERT: B  763 MET cc_start: 0.8694 (mpp) cc_final: 0.8448 (mmm)
REVERT: B  842 LEU cc_start: 0.9630 (mt) cc_final: 0.9215 (pp)
REVERT: B  947 MET cc_start: 0.9305 (tmm) cc_final: 0.9090 (tmm)
REVERT: A  176 GLU cc_start: 0.8721 (tt0) cc_final: 0.8368 (tm-30)
REVERT: A  202 MET cc_start: 0.9389 (ttp) cc_final: 0.8884 (tmm)
REVERT: A  205 MET cc_start: 0.9308 (tpt) cc_final: 0.8882 (tpp)
REVERT: A  441 LEU cc_start: 0.9399 (tp) cc_final: 0.9074 (tp)
REVERT: A  446 MET cc_start: 0.8818 (mpp) cc_final: 0.8289 (tpp)
REVERT: A  714 MET cc_start: 0.9561 (ttp) cc_final: 0.9278 (ptp)
REVERT: A  739 MET cc_start: 0.8743 (tpt) cc_final: 0.7574 (tpt)
REVERT: A  743 MET cc_start: 0.9525 (mmm) cc_final: 0.8637 (mmm)
REVERT: A  947 MET cc_start: 0.8826 (ttt) cc_final: 0.8251 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 63
  average time/residue: 0.1385
  time to fit residues: 14.4143
Evaluate side-chains
  55 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 106 optimal weight:    0.9980
   chunk 137 optimal weight:    7.9990
   chunk 40 optimal weight:    6.9990
   chunk 191 optimal weight:    7.9990
   chunk 16 optimal weight:    1.9990
   chunk 134 optimal weight:    8.9990
   chunk 156 optimal weight:    0.8980
   chunk 73 optimal weight:    7.9990
   chunk 53 optimal weight:    0.2980
   chunk 92 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
** B  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  97 ASN
** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 138 ASN
A 160 GLN
** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.036068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2764 r_free = 0.2764 target = 0.026264 restraints weight = 235479.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.027005 restraints weight = 143450.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.027512 restraints weight = 99684.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.027850 restraints weight = 75944.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.028102 restraints weight = 62085.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2784
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2784 r_free = 0.2784    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2784 r_free = 0.2784    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2784
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.5873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  19157  Z= 0.104
  Angle     :  0.539   9.993  26677  Z= 0.267
  Chirality :  0.039   0.152   3140
  Planarity :  0.004   0.057   2916
  Dihedral  : 18.044 177.789   4365
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  0.97 %
    Favored  : 98.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    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: -0.94 (0.19), residues: 1964
  helix:  0.14 (0.18), residues: 905
  sheet: -0.87 (0.36), residues: 217
  loop : -1.33 (0.21), residues: 842

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B1045 
 TYR   0.014   0.001   TYR B 256 
 PHE   0.015   0.001   PHE B 260 
 TRP   0.009   0.001   TRP A  85 
 HIS   0.005   0.001   HIS A 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 (19155)
  covalent geometry    : angle       0.53934 (26677)
  hydrogen bonds       : bond        0.02859 (  619)
  hydrogen bonds       : angle       3.84227 ( 1660)
  Misc. bond           : bond        0.00023 (    2)

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

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

  3928 Ramachandran restraints generated.
    1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3928 Ramachandran restraints generated.
    1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 61
  time to evaluate  : 0.670 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  267 MET cc_start: 0.9391 (mmm) cc_final: 0.9125 (mmp)
REVERT: B  549 ASP cc_start: 0.9221 (t0) cc_final: 0.8891 (m-30)
REVERT: B  659 MET cc_start: 0.9065 (mtt) cc_final: 0.8399 (ttm)
REVERT: B  763 MET cc_start: 0.8480 (mpp) cc_final: 0.7986 (mpp)
REVERT: B  775 MET cc_start: 0.8808 (tmm) cc_final: 0.8285 (ppp)
REVERT: B  842 LEU cc_start: 0.9648 (mt) cc_final: 0.9241 (pp)
REVERT: B  947 MET cc_start: 0.9297 (tmm) cc_final: 0.8844 (tpt)
REVERT: A  202 MET cc_start: 0.9347 (ttp) cc_final: 0.8859 (tmm)
REVERT: A  205 MET cc_start: 0.9313 (tpt) cc_final: 0.9015 (tpp)
REVERT: A  441 LEU cc_start: 0.9416 (tp) cc_final: 0.9131 (tp)
REVERT: A  446 MET cc_start: 0.8879 (mpp) cc_final: 0.8433 (tpp)
REVERT: A  528 MET cc_start: 0.9510 (ptp) cc_final: 0.8672 (pmm)
REVERT: A  714 MET cc_start: 0.9531 (ttp) cc_final: 0.9264 (ptp)
REVERT: A  739 MET cc_start: 0.8674 (tpt) cc_final: 0.8330 (tpt)
REVERT: A  763 MET cc_start: 0.8529 (ttt) cc_final: 0.8106 (tpt)
REVERT: A  775 MET cc_start: 0.9052 (tpp) cc_final: 0.8558 (tpp)
REVERT: A  947 MET cc_start: 0.8939 (ttt) cc_final: 0.8374 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 62
  average time/residue: 0.1382
  time to fit residues: 14.2318
Evaluate side-chains
  54 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 89 optimal weight:    8.9990
   chunk 207 optimal weight:   10.0000
   chunk 44 optimal weight:    6.9990
   chunk 117 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 153 optimal weight:   10.0000
   chunk 187 optimal weight:    0.8980
   chunk 179 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   chunk 36 optimal weight:    8.9990
   chunk 137 optimal weight:    0.7980
   overall best weight:    1.5182

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

Flipped N/Q/H residues before XYZ refinement:
** B  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  97 ASN
B 478 ASN
** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 138 ASN
A 214 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.035547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2740 r_free = 0.2740 target = 0.025732 restraints weight = 242336.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.026450 restraints weight = 146318.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.026946 restraints weight = 101477.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.027291 restraints weight = 77324.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.027516 restraints weight = 63129.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.2761
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2761
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2761 r_free = 0.2761    target_work(ls_wunit_k1) = 0.026         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2761 r_free = 0.2761    target_work(ls_wunit_k1) = 0.026         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2761
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.6275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  19157  Z= 0.112
  Angle     :  0.542   8.825  26677  Z= 0.268
  Chirality :  0.039   0.159   3140
  Planarity :  0.004   0.055   2916
  Dihedral  : 18.028 177.300   4365
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  0.61 %
    Favored  : 99.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    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: -0.68 (0.19), residues: 1964
  helix:  0.36 (0.18), residues: 906
  sheet: -0.74 (0.36), residues: 212
  loop : -1.20 (0.22), residues: 846

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B1045 
 TYR   0.011   0.001   TYR B 212 
 PHE   0.010   0.001   PHE B 284 
 TRP   0.010   0.001   TRP B 119 
 HIS   0.005   0.001   HIS A 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 (19155)
  covalent geometry    : angle       0.54175 (26677)
  hydrogen bonds       : bond        0.03042 (  619)
  hydrogen bonds       : angle       3.83462 ( 1660)
  Misc. bond           : bond        0.00021 (    2)

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

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

  3928 Ramachandran restraints generated.
    1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3928 Ramachandran restraints generated.
    1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 62
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  237 MET cc_start: 0.9574 (ptp) cc_final: 0.8930 (ttp)
REVERT: B  267 MET cc_start: 0.9476 (mmm) cc_final: 0.9200 (mmp)
REVERT: B  549 ASP cc_start: 0.9210 (t0) cc_final: 0.8893 (m-30)
REVERT: B  659 MET cc_start: 0.9105 (mtt) cc_final: 0.8403 (ttm)
REVERT: B  763 MET cc_start: 0.8566 (mpp) cc_final: 0.8013 (mpp)
REVERT: B  775 MET cc_start: 0.8786 (tmm) cc_final: 0.8092 (ppp)
REVERT: B  842 LEU cc_start: 0.9710 (mt) cc_final: 0.9284 (pp)
REVERT: B  947 MET cc_start: 0.9335 (tmm) cc_final: 0.8878 (tpt)
REVERT: A  202 MET cc_start: 0.9321 (ttp) cc_final: 0.8907 (tmm)
REVERT: A  205 MET cc_start: 0.9358 (tpt) cc_final: 0.9101 (tpp)
REVERT: A  237 MET cc_start: 0.9367 (ptp) cc_final: 0.9023 (ptt)
REVERT: A  441 LEU cc_start: 0.9374 (tp) cc_final: 0.9057 (tp)
REVERT: A  446 MET cc_start: 0.8943 (mpp) cc_final: 0.8497 (tpp)
REVERT: A  528 MET cc_start: 0.9470 (ptp) cc_final: 0.8828 (ptp)
REVERT: A  659 MET cc_start: 0.8957 (ttt) cc_final: 0.8040 (ttt)
REVERT: A  714 MET cc_start: 0.9520 (ttp) cc_final: 0.9262 (ptp)
REVERT: A  739 MET cc_start: 0.8719 (tpt) cc_final: 0.7672 (tpt)
REVERT: A  743 MET cc_start: 0.9593 (mmm) cc_final: 0.8544 (mmm)
REVERT: A  763 MET cc_start: 0.8783 (ttt) cc_final: 0.8446 (tpp)
REVERT: A  947 MET cc_start: 0.8957 (ttt) cc_final: 0.8486 (tpp)
REVERT: A 1035 MET cc_start: 0.9360 (mmp) cc_final: 0.9140 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 63
  average time/residue: 0.1254
  time to fit residues: 13.2352
Evaluate side-chains
  54 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 36 optimal weight:   10.0000
   chunk 23 optimal weight:    0.8980
   chunk 156 optimal weight:    6.9990
   chunk 194 optimal weight:   50.0000
   chunk 9 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 177 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 78 optimal weight:    6.9990
   chunk 182 optimal weight:    4.9990
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
** B  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  97 ASN
** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 138 ASN
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.035143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.025417 restraints weight = 237215.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2761 r_free = 0.2761 target = 0.026130 restraints weight = 142719.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.026624 restraints weight = 98979.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.026962 restraints weight = 75255.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.027206 restraints weight = 61392.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.2748
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2748
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2748 r_free = 0.2748    target_work(ls_wunit_k1) = 0.026         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2748 r_free = 0.2748    target_work(ls_wunit_k1) = 0.026         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2748
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8485
moved from start:          0.6750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  19157  Z= 0.111
  Angle     :  0.543   9.102  26677  Z= 0.267
  Chirality :  0.039   0.157   3140
  Planarity :  0.004   0.055   2916
  Dihedral  : 18.031 177.602   4365
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  0.48 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    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: -0.57 (0.19), residues: 1964
  helix:  0.48 (0.18), residues: 904
  sheet: -0.63 (0.36), residues: 219
  loop : -1.20 (0.22), residues: 841

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B1045 
 TYR   0.012   0.001   TYR A  84 
 PHE   0.009   0.001   PHE A 245 
 TRP   0.011   0.001   TRP A 530 
 HIS   0.005   0.001   HIS A 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 (19155)
  covalent geometry    : angle       0.54254 (26677)
  hydrogen bonds       : bond        0.02924 (  619)
  hydrogen bonds       : angle       3.86841 ( 1660)
  Misc. bond           : bond        0.00029 (    2)

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

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

  3928 Ramachandran restraints generated.
    1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3928 Ramachandran restraints generated.
    1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  237 MET cc_start: 0.9610 (ptp) cc_final: 0.8784 (ttp)
REVERT: B  267 MET cc_start: 0.9548 (mmm) cc_final: 0.9320 (mmp)
REVERT: B  549 ASP cc_start: 0.9166 (t0) cc_final: 0.8832 (m-30)
REVERT: B  659 MET cc_start: 0.9134 (mtt) cc_final: 0.8448 (ttm)
REVERT: B  775 MET cc_start: 0.8867 (tmm) cc_final: 0.8356 (ppp)
REVERT: B  842 LEU cc_start: 0.9720 (mt) cc_final: 0.9299 (pp)
REVERT: A  202 MET cc_start: 0.9310 (ttp) cc_final: 0.8907 (tmm)
REVERT: A  205 MET cc_start: 0.9375 (tpt) cc_final: 0.9149 (tpp)
REVERT: A  441 LEU cc_start: 0.9369 (tp) cc_final: 0.9094 (tp)
REVERT: A  446 MET cc_start: 0.9021 (mpp) cc_final: 0.8551 (tpp)
REVERT: A  659 MET cc_start: 0.9008 (ttt) cc_final: 0.8059 (ttt)
REVERT: A  714 MET cc_start: 0.9541 (ttp) cc_final: 0.9253 (ptp)
REVERT: A  739 MET cc_start: 0.8701 (tpt) cc_final: 0.7639 (tpt)
REVERT: A  743 MET cc_start: 0.9509 (mmm) cc_final: 0.8451 (mmm)
REVERT: A  763 MET cc_start: 0.8869 (ttt) cc_final: 0.8452 (tpp)
REVERT: A  947 MET cc_start: 0.9070 (ttt) cc_final: 0.8604 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 61
  average time/residue: 0.1278
  time to fit residues: 13.0264
Evaluate side-chains
  55 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 40 optimal weight:   10.0000
   chunk 49 optimal weight:    0.4980
   chunk 43 optimal weight:    4.9990
   chunk 163 optimal weight:    8.9990
   chunk 20 optimal weight:   10.0000
   chunk 89 optimal weight:    9.9990
   chunk 27 optimal weight:    0.9980
   chunk 48 optimal weight:    6.9990
   chunk 180 optimal weight:    0.0870
   chunk 92 optimal weight:    0.9990
   chunk 73 optimal weight:    7.9990
   overall best weight:    1.5162

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

Flipped N/Q/H residues before XYZ refinement:
B  76 GLN
B  97 ASN
** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 138 ASN
A 160 GLN
A 570 ASN
A 717 GLN
** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.035005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.025300 restraints weight = 240321.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2756 r_free = 0.2756 target = 0.026028 restraints weight = 143220.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.026524 restraints weight = 98463.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.026864 restraints weight = 74484.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.027106 restraints weight = 60524.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2740
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2740 r_free = 0.2740    target_work(ls_wunit_k1) = 0.026         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2740 r_free = 0.2740    target_work(ls_wunit_k1) = 0.026         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2740
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.6950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  19157  Z= 0.109
  Angle     :  0.541  10.135  26677  Z= 0.266
  Chirality :  0.039   0.152   3140
  Planarity :  0.004   0.055   2916
  Dihedral  : 18.029 177.343   4365
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.36 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    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: -0.46 (0.19), residues: 1964
  helix:  0.62 (0.18), residues: 895
  sheet: -0.65 (0.36), residues: 221
  loop : -1.16 (0.22), residues: 848

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B1045 
 TYR   0.012   0.001   TYR B 212 
 PHE   0.009   0.001   PHE B 824 
 TRP   0.009   0.001   TRP B 119 
 HIS   0.004   0.001   HIS A 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 (19155)
  covalent geometry    : angle       0.54132 (26677)
  hydrogen bonds       : bond        0.02984 (  619)
  hydrogen bonds       : angle       3.86582 ( 1660)
  Misc. bond           : bond        0.00030 (    2)

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

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

  3928 Ramachandran restraints generated.
    1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3928 Ramachandran restraints generated.
    1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 62
  time to evaluate  : 0.569 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  205 MET cc_start: 0.9028 (tpt) cc_final: 0.8729 (tpp)
REVERT: B  237 MET cc_start: 0.9606 (ptp) cc_final: 0.8788 (ttp)
REVERT: B  267 MET cc_start: 0.9553 (mmm) cc_final: 0.9264 (mmp)
REVERT: B  549 ASP cc_start: 0.9153 (t0) cc_final: 0.8807 (m-30)
REVERT: B  659 MET cc_start: 0.9128 (mtt) cc_final: 0.8438 (ttm)
REVERT: B  775 MET cc_start: 0.8809 (tmm) cc_final: 0.8146 (ppp)
REVERT: B  842 LEU cc_start: 0.9718 (mt) cc_final: 0.9320 (pp)
REVERT: A  202 MET cc_start: 0.9282 (ttp) cc_final: 0.8874 (tmm)
REVERT: A  441 LEU cc_start: 0.9374 (tp) cc_final: 0.9072 (tp)
REVERT: A  446 MET cc_start: 0.9023 (mpp) cc_final: 0.8532 (tpp)
REVERT: A  528 MET cc_start: 0.9278 (ptp) cc_final: 0.8315 (pmm)
REVERT: A  659 MET cc_start: 0.9003 (ttt) cc_final: 0.8090 (ttt)
REVERT: A  714 MET cc_start: 0.9538 (ttp) cc_final: 0.9239 (ptp)
REVERT: A  739 MET cc_start: 0.8715 (tpt) cc_final: 0.7852 (tpt)
REVERT: A  743 MET cc_start: 0.9545 (mmm) cc_final: 0.8593 (mmm)
REVERT: A  763 MET cc_start: 0.8862 (ttt) cc_final: 0.8551 (tpp)
REVERT: A  947 MET cc_start: 0.9093 (ttt) cc_final: 0.8637 (tpp)
  outliers start: 2
  outliers final: 0
  residues processed: 64
  average time/residue: 0.1342
  time to fit residues: 14.0402
Evaluate side-chains
  57 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 64 optimal weight:    7.9990
   chunk 35 optimal weight:    7.9990
   chunk 19 optimal weight:    0.0030
   chunk 144 optimal weight:    8.9990
   chunk 56 optimal weight:    0.5980
   chunk 71 optimal weight:    0.0070
   chunk 121 optimal weight:    0.9980
   chunk 146 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 132 optimal weight:    2.9990
   chunk 196 optimal weight:    0.0020
   overall best weight:    0.3216

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

Flipped N/Q/H residues before XYZ refinement:
B  76 GLN
B  97 ASN
** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 138 ASN
A 160 GLN
** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.035780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2763 r_free = 0.2763 target = 0.026051 restraints weight = 236628.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.026801 restraints weight = 140295.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.027318 restraints weight = 96194.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.027677 restraints weight = 72394.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.027927 restraints weight = 58517.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.2783
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2783
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2783 r_free = 0.2783    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2783 r_free = 0.2783    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2783
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.6978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  19157  Z= 0.090
  Angle     :  0.535  10.206  26677  Z= 0.260
  Chirality :  0.039   0.158   3140
  Planarity :  0.004   0.055   2916
  Dihedral  : 17.922 177.980   4365
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  0.18 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    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: -0.34 (0.20), residues: 1964
  helix:  0.66 (0.18), residues: 893
  sheet: -0.45 (0.37), residues: 218
  loop : -1.07 (0.22), residues: 853

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 795 
 TYR   0.015   0.001   TYR B 797 
 PHE   0.009   0.001   PHE B 474 
 TRP   0.011   0.001   TRP B 542 
 HIS   0.009   0.001   HIS B 796 

Details of bonding type rmsd
  covalent geometry    : bond        0.00190 (19155)
  covalent geometry    : angle       0.53523 (26677)
  hydrogen bonds       : bond        0.02677 (  619)
  hydrogen bonds       : angle       3.74594 ( 1660)
  Misc. bond           : bond        0.00047 (    2)

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

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

  3928 Ramachandran restraints generated.
    1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3928 Ramachandran restraints generated.
    1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 66
  time to evaluate  : 0.699 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  205 MET cc_start: 0.8953 (tpt) cc_final: 0.8658 (tpp)
REVERT: B  237 MET cc_start: 0.9555 (ptp) cc_final: 0.8692 (ttp)
REVERT: B  267 MET cc_start: 0.9529 (mmm) cc_final: 0.9262 (mmp)
REVERT: B  549 ASP cc_start: 0.9129 (t0) cc_final: 0.8782 (m-30)
REVERT: B  659 MET cc_start: 0.9048 (mtt) cc_final: 0.8385 (ttm)
REVERT: B  775 MET cc_start: 0.8758 (tmm) cc_final: 0.8214 (ppp)
REVERT: B  842 LEU cc_start: 0.9722 (mt) cc_final: 0.9307 (pp)
REVERT: A  202 MET cc_start: 0.9237 (ttp) cc_final: 0.8991 (tmm)
REVERT: A  237 MET cc_start: 0.9401 (ptp) cc_final: 0.8911 (ptt)
REVERT: A  441 LEU cc_start: 0.9346 (tp) cc_final: 0.9089 (tp)
REVERT: A  446 MET cc_start: 0.8952 (mpp) cc_final: 0.8460 (tpp)
REVERT: A  528 MET cc_start: 0.9232 (ptp) cc_final: 0.8513 (pmm)
REVERT: A  659 MET cc_start: 0.8953 (ttt) cc_final: 0.8054 (ttt)
REVERT: A  714 MET cc_start: 0.9526 (ttp) cc_final: 0.9253 (ptp)
REVERT: A  739 MET cc_start: 0.8657 (tpt) cc_final: 0.7755 (tpt)
REVERT: A  743 MET cc_start: 0.9518 (mmm) cc_final: 0.8559 (mmm)
REVERT: A  763 MET cc_start: 0.8846 (ttt) cc_final: 0.8542 (tpp)
REVERT: A  947 MET cc_start: 0.9111 (ttt) cc_final: 0.8628 (tpp)
REVERT: A 1035 MET cc_start: 0.9322 (mmp) cc_final: 0.9121 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 67
  average time/residue: 0.1343
  time to fit residues: 15.0237
Evaluate side-chains
  57 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 183 optimal weight:    0.8980
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    8.9990
   chunk 71 optimal weight:    0.9990
   chunk 133 optimal weight:    0.7980
   chunk 138 optimal weight:    9.9990
   chunk 178 optimal weight:   10.0000
   chunk 7 optimal weight:    0.0040
   chunk 40 optimal weight:    8.9990
   chunk 154 optimal weight:    6.9990
   chunk 75 optimal weight:    9.9990
   overall best weight:    0.9396

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

Flipped N/Q/H residues before XYZ refinement:
B  76 GLN
B  97 ASN
** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 138 ASN
A 160 GLN
** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.035388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.025669 restraints weight = 239456.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.026399 restraints weight = 141990.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.026916 restraints weight = 97719.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.027270 restraints weight = 73584.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.027512 restraints weight = 59540.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2763
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2763 r_free = 0.2763    target_work(ls_wunit_k1) = 0.026         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2763 r_free = 0.2763    target_work(ls_wunit_k1) = 0.026         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2763
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
moved from start:          0.7152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  19157  Z= 0.091
  Angle     :  0.525   9.774  26677  Z= 0.255
  Chirality :  0.039   0.152   3140
  Planarity :  0.004   0.056   2916
  Dihedral  : 17.891 177.450   4365
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  0.30 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    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: -0.24 (0.20), residues: 1964
  helix:  0.79 (0.18), residues: 888
  sheet: -0.44 (0.37), residues: 219
  loop : -1.06 (0.22), residues: 857

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 426 
 TYR   0.011   0.001   TYR B 212 
 PHE   0.009   0.001   PHE B 474 
 TRP   0.009   0.001   TRP B 119 
 HIS   0.003   0.001   HIS A 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00198 (19155)
  covalent geometry    : angle       0.52537 (26677)
  hydrogen bonds       : bond        0.02780 (  619)
  hydrogen bonds       : angle       3.70953 ( 1660)
  Misc. bond           : bond        0.00042 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3154.89 seconds
wall clock time: 55 minutes 13.91 seconds (3313.91 seconds total)