Starting phenix.real_space_refine
on Mon May 19 19:33:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8h1c_34427/05_2025/8h1c_34427.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8h1c_34427/05_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_34427/05_2025/8h1c_34427.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8h1c_34427/05_2025/8h1c_34427.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8h1c_34427/05_2025/8h1c_34427.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8h1c_34427/05_2025/8h1c_34427.cif"
  }
  resolution = 4.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 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): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 4, 'ASP:plan': 2}
          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: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 4, 'ASP:plan': 2}
          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: {'GLN:plan1': 1, 'GLU:plan': 10, 'ARG:plan': 3, 'ASP:plan': 4}
          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: {'GLN:plan1': 1, 'GLU:plan': 10, 'ARG:plan': 3, 'ASP:plan': 4}
          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: 19.18, per 1000 atoms: 1.04
  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: 4.81
  Conformation dependent library (CDL) restraints added in 3.8 seconds
  

  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: 6.85
  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: 7.53

  Time building geometry restraints manager: 5.58 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:             4.600
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.810
  Check model and map are aligned:         0.140
  Set scattering table:                    0.190
  Process input model:                     58.650
  Find NCS groups from input model:        0.670
  Set up NCS constraints:                  0.110
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   67.760
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.24 (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
 TRP   0.012   0.002   TRP A 298 
 HIS   0.005   0.001   HIS A 586 
 PHE   0.024   0.002   PHE A1014 
 TYR   0.019   0.002   TYR A 584 
 ARG   0.006   0.001   ARG A 432 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16677 (  619)
  hydrogen bonds       : angle       6.65477 ( 1660)
  covalent geometry    : bond        0.00833 (19155)
  covalent geometry    : angle       0.80712 (26677)
  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  : 1.753 
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: 0.8845 (mmp)
REVERT: B  420 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7741 (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: 0.8212 (ttm)
REVERT: B  743 MET cc_start: 0.9420 (mmt) cc_final: 0.8361 (mmp)
REVERT: B  768 LYS cc_start: 0.9560 (mtpp) cc_final: 0.9312 (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: 0.8204 (m)
REVERT: A   81 LEU cc_start: 0.9517 (mt) cc_final: 0.9192 (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: 0.8864 (mm)
REVERT: A  441 LEU cc_start: 0.9649 (tp) cc_final: 0.9360 (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: 0.8396 (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: 0.8825 (tp)
REVERT: A  714 MET cc_start: 0.9614 (ttp) cc_final: 0.9314 (ttp)
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: 0.8831 (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: 0.7905 (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: 0.2870
  time to fit residues: 101.8880
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  : 1.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 177 optimal weight:    2.9990
   chunk 159 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 54 optimal weight:    8.9990
   chunk 107 optimal weight:    4.9990
   chunk 85 optimal weight:    0.8980
   chunk 164 optimal weight:    5.9990
   chunk 63 optimal weight:    2.9990
   chunk 100 optimal weight:   10.0000
   chunk 122 optimal weight:    0.7980
   chunk 190 optimal weight:    0.4980
   overall best weight:    1.6384

-------------------------------------------------------------------------------
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 214 GLN
A 442 ASN
A 547 HIS
A 631 ASN
** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 781 ASN
A 856 ASN
A1031 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.041815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.031760 restraints weight = 226183.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.032605 restraints weight = 143791.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.033196 restraints weight = 102194.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2988
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2988 r_free = 0.2988    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2988 r_free = 0.2988    target_work(ls_wunit_k1) = 0.032         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2988
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.2570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  19157  Z= 0.147
  Angle     :  0.638   8.196  26677  Z= 0.326
  Chirality :  0.042   0.204   3140
  Planarity :  0.005   0.056   2916
  Dihedral  : 18.422 179.830   4365
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.06 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  2.12 %
    Favored  : 97.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.47 (0.18), residues: 1964
  helix: -1.26 (0.17), residues: 874
  sheet: -1.19 (0.36), residues: 217
  loop : -2.07 (0.19), residues: 873

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 530 
 HIS   0.004   0.001   HIS B 398 
 PHE   0.019   0.001   PHE A 986 
 TYR   0.028   0.002   TYR A 123 
 ARG   0.020   0.001   ARG B 292 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04041 (  619)
  hydrogen bonds       : angle       4.42894 ( 1660)
  covalent geometry    : bond        0.00303 (19155)
  covalent geometry    : angle       0.63809 (26677)
  Misc. bond           : bond        0.00042 (    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
  106 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 104
  time to evaluate  : 1.878 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 MET cc_start: 0.8947 (ptp) cc_final: 0.8700 (pmm)
REVERT: B  202 MET cc_start: 0.9158 (ppp) cc_final: 0.8811 (ppp)
REVERT: B  205 MET cc_start: 0.9121 (tpp) cc_final: 0.8338 (tpp)
REVERT: B  237 MET cc_start: 0.9329 (ptp) cc_final: 0.8845 (ptp)
REVERT: B  267 MET cc_start: 0.9192 (mmm) cc_final: 0.8909 (mmm)
REVERT: B  549 ASP cc_start: 0.9094 (t0) cc_final: 0.8775 (m-30)
REVERT: B  563 ASN cc_start: 0.8435 (p0) cc_final: 0.7801 (p0)
REVERT: B  659 MET cc_start: 0.8881 (mtt) cc_final: 0.8424 (ttm)
REVERT: B  743 MET cc_start: 0.9562 (mmp) cc_final: 0.8928 (mmp)
REVERT: B  775 MET cc_start: 0.8831 (tmm) cc_final: 0.7920 (ptm)
REVERT: A  202 MET cc_start: 0.9418 (ttp) cc_final: 0.9015 (tmm)
REVERT: A  205 MET cc_start: 0.8974 (tpp) cc_final: 0.8743 (tpt)
REVERT: A  441 LEU cc_start: 0.9404 (tp) cc_final: 0.9151 (tp)
REVERT: A  659 MET cc_start: 0.9013 (mtm) cc_final: 0.8577 (ttm)
REVERT: A  701 LEU cc_start: 0.9367 (pp) cc_final: 0.9012 (tp)
REVERT: A  739 MET cc_start: 0.8572 (mmm) cc_final: 0.8270 (tpp)
REVERT: A  759 ILE cc_start: 0.8198 (mp) cc_final: 0.7907 (tp)
REVERT: A  775 MET cc_start: 0.9129 (tpp) cc_final: 0.8655 (tpp)
REVERT: A 1035 MET cc_start: 0.9410 (mmp) cc_final: 0.9200 (mmt)
  outliers start: 2
  outliers final: 0
  residues processed: 106
  average time/residue: 0.3020
  time to fit residues: 51.0262
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  : 1.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 172 optimal weight:    0.9980
   chunk 139 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 179 optimal weight:    8.9990
   chunk 114 optimal weight:    0.9980
   chunk 164 optimal weight:    5.9990
   chunk 122 optimal weight:    0.8980
   chunk 203 optimal weight:    9.9990
   chunk 40 optimal weight:    8.9990
   chunk 197 optimal weight:    0.5980
   chunk 168 optimal weight:    0.5980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 875 ASN
A 138 ASN
A 185 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.041256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.031219 restraints weight = 225215.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.032057 restraints weight = 142442.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.032647 restraints weight = 100811.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2967
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2967 r_free = 0.2967    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 = 0.2967 r_free = 0.2967    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2967
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.3250

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= 0.107
  Angle     :  0.573   7.266  26677  Z= 0.285
  Chirality :  0.040   0.146   3140
  Planarity :  0.004   0.053   2916
  Dihedral  : 18.075 177.083   4365
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  1.70 %
    Favored  : 98.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.97 (0.19), residues: 1964
  helix: -0.84 (0.18), residues: 883
  sheet: -1.02 (0.34), residues: 231
  loop : -1.80 (0.20), residues: 850

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 119 
 HIS   0.005   0.001   HIS B 274 
 PHE   0.038   0.001   PHE A 710 
 TYR   0.016   0.001   TYR A  84 
 ARG   0.007   0.000   ARG B 426 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03265 (  619)
  hydrogen bonds       : angle       4.15026 ( 1660)
  covalent geometry    : bond        0.00226 (19155)
  covalent geometry    : angle       0.57256 (26677)
  Misc. bond           : bond        0.00021 (    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
  81 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 80
  time to evaluate  : 1.753 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 MET cc_start: 0.8982 (ptp) cc_final: 0.8666 (pmm)
REVERT: B  237 MET cc_start: 0.9336 (ptp) cc_final: 0.8809 (ptp)
REVERT: B  267 MET cc_start: 0.9271 (mmm) cc_final: 0.9041 (mmm)
REVERT: B  549 ASP cc_start: 0.9154 (t0) cc_final: 0.8845 (m-30)
REVERT: B  659 MET cc_start: 0.8872 (mtt) cc_final: 0.8356 (ttm)
REVERT: B  763 MET cc_start: 0.9105 (tpp) cc_final: 0.8728 (mtm)
REVERT: B  775 MET cc_start: 0.8663 (tmm) cc_final: 0.8296 (ppp)
REVERT: B  842 LEU cc_start: 0.9577 (mt) cc_final: 0.9139 (pp)
REVERT: B  947 MET cc_start: 0.8919 (tmm) cc_final: 0.8690 (tmm)
REVERT: A  202 MET cc_start: 0.9406 (ttp) cc_final: 0.9110 (tmm)
REVERT: A  205 MET cc_start: 0.9068 (tpp) cc_final: 0.8720 (tpp)
REVERT: A  441 LEU cc_start: 0.9432 (tp) cc_final: 0.9207 (tp)
REVERT: A  637 MET cc_start: 0.8857 (mmp) cc_final: 0.8611 (mmm)
REVERT: A  759 ILE cc_start: 0.8141 (mp) cc_final: 0.7786 (tp)
REVERT: A  775 MET cc_start: 0.9285 (tpp) cc_final: 0.8909 (tpp)
REVERT: A  833 LEU cc_start: 0.8942 (mm) cc_final: 0.8578 (pt)
REVERT: A  947 MET cc_start: 0.8384 (ttm) cc_final: 0.7596 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 81
  average time/residue: 0.2655
  time to fit residues: 35.9972
Evaluate side-chains
  62 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 1.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 177 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9980
   chunk 149 optimal weight:    4.9990
   chunk 60 optimal weight:    3.9990
   chunk 205 optimal weight:   10.0000
   chunk 187 optimal weight:    0.8980
   chunk 141 optimal weight:    9.9990
   chunk 159 optimal weight:    5.9990
   chunk 115 optimal weight:    3.9990
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
B  76 GLN
B  79 GLN
** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 274 HIS
B 478 ASN
** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  82 GLN
A 138 ASN
** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 660 GLN
** A 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.040380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.030414 restraints weight = 225720.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.031231 restraints weight = 142262.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.031809 restraints weight = 100637.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2936
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2936 r_free = 0.2936    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 = 0.2936 r_free = 0.2936    target_work(ls_wunit_k1) = 0.031         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2936
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.3761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  19157  Z= 0.098
  Angle     :  0.541   8.398  26677  Z= 0.270
  Chirality :  0.039   0.163   3140
  Planarity :  0.004   0.053   2916
  Dihedral  : 17.923 176.974   4365
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  1.15 %
    Favored  : 98.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.50 (0.19), residues: 1964
  helix: -0.51 (0.18), residues: 877
  sheet: -0.87 (0.37), residues: 217
  loop : -1.44 (0.21), residues: 870

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 198 
 HIS   0.003   0.001   HIS A 422 
 PHE   0.016   0.001   PHE A 986 
 TYR   0.018   0.001   TYR A 705 
 ARG   0.005   0.000   ARG B 426 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02858 (  619)
  hydrogen bonds       : angle       3.91776 ( 1660)
  covalent geometry    : bond        0.00210 (19155)
  covalent geometry    : angle       0.54133 (26677)
  Misc. bond           : bond        0.00027 (    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
  76 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 75
  time to evaluate  : 1.932 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  267 MET cc_start: 0.9273 (mmm) cc_final: 0.8999 (mmm)
REVERT: B  488 ARG cc_start: 0.9132 (ttt180) cc_final: 0.8894 (tmm-80)
REVERT: B  549 ASP cc_start: 0.9174 (t0) cc_final: 0.8841 (m-30)
REVERT: B  659 MET cc_start: 0.8918 (mtt) cc_final: 0.8367 (ttm)
REVERT: B  763 MET cc_start: 0.9096 (tpp) cc_final: 0.8813 (mtm)
REVERT: B  842 LEU cc_start: 0.9547 (mt) cc_final: 0.9127 (pp)
REVERT: B  947 MET cc_start: 0.8999 (tmm) cc_final: 0.8745 (tmm)
REVERT: A  202 MET cc_start: 0.9445 (ttp) cc_final: 0.8858 (tmm)
REVERT: A  205 MET cc_start: 0.9120 (tpp) cc_final: 0.8644 (tpp)
REVERT: A  267 MET cc_start: 0.9020 (mmp) cc_final: 0.8588 (mmp)
REVERT: A  441 LEU cc_start: 0.9453 (tp) cc_final: 0.9174 (tp)
REVERT: A  659 MET cc_start: 0.8921 (ttm) cc_final: 0.8386 (ttp)
REVERT: A  759 ILE cc_start: 0.8183 (mp) cc_final: 0.7962 (tp)
REVERT: A  763 MET cc_start: 0.7472 (ttt) cc_final: 0.6658 (tpp)
REVERT: A  833 LEU cc_start: 0.8896 (mm) cc_final: 0.8504 (pt)
REVERT: A  947 MET cc_start: 0.8484 (ttm) cc_final: 0.7823 (tpp)
REVERT: A 1035 MET cc_start: 0.8817 (mpp) cc_final: 0.8276 (mpp)
  outliers start: 1
  outliers final: 0
  residues processed: 76
  average time/residue: 0.2829
  time to fit residues: 35.9364
Evaluate side-chains
  63 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 1.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 41 optimal weight:   10.0000
   chunk 56 optimal weight:    5.9990
   chunk 10 optimal weight:   10.0000
   chunk 180 optimal weight:    0.9990
   chunk 64 optimal weight:    4.9990
   chunk 185 optimal weight:   20.0000
   chunk 199 optimal weight:    0.0970
   chunk 159 optimal weight:    0.7980
   chunk 131 optimal weight:    8.9990
   chunk 194 optimal weight:   50.0000
   chunk 157 optimal weight:    0.0570
   overall best weight:    1.3900

-------------------------------------------------------------------------------
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 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 341 GLN
** 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**
A 870 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.038659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.028610 restraints weight = 229438.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.029387 restraints weight = 143879.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.029946 restraints weight = 101724.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2864
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2864 r_free = 0.2864    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 = 0.2864 r_free = 0.2864    target_work(ls_wunit_k1) = 0.029         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2864
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.4452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.079  19157  Z= 0.119
  Angle     :  0.555   8.083  26677  Z= 0.276
  Chirality :  0.041   0.627   3140
  Planarity :  0.004   0.052   2916
  Dihedral  : 17.933 175.237   4365
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  1.33 %
    Favored  : 98.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.19), residues: 1964
  helix: -0.21 (0.18), residues: 891
  sheet: -0.93 (0.36), residues: 223
  loop : -1.32 (0.21), residues: 850

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 186 
 HIS   0.004   0.001   HIS A 244 
 PHE   0.020   0.001   PHE A 846 
 TYR   0.017   0.001   TYR A 705 
 ARG   0.005   0.000   ARG B 426 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03005 (  619)
  hydrogen bonds       : angle       3.87671 ( 1660)
  covalent geometry    : bond        0.00251 (19155)
  covalent geometry    : angle       0.55530 (26677)
  Misc. bond           : bond        0.00007 (    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
  73 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 72
  time to evaluate  : 1.782 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  267 MET cc_start: 0.9338 (mmm) cc_final: 0.8988 (mmm)
REVERT: B  549 ASP cc_start: 0.9241 (t0) cc_final: 0.8886 (m-30)
REVERT: B  659 MET cc_start: 0.9050 (mtt) cc_final: 0.8354 (ttm)
REVERT: B  775 MET cc_start: 0.8578 (tmm) cc_final: 0.8132 (ppp)
REVERT: B  842 LEU cc_start: 0.9585 (mt) cc_final: 0.9175 (pp)
REVERT: A   90 CYS cc_start: 0.8344 (m) cc_final: 0.8078 (p)
REVERT: A  202 MET cc_start: 0.9467 (ttp) cc_final: 0.8853 (tmm)
REVERT: A  205 MET cc_start: 0.9288 (tpp) cc_final: 0.8905 (tpp)
REVERT: A  267 MET cc_start: 0.9140 (mmp) cc_final: 0.8640 (mmp)
REVERT: A  441 LEU cc_start: 0.9441 (tp) cc_final: 0.9208 (tp)
REVERT: A  637 MET cc_start: 0.9029 (mmp) cc_final: 0.8748 (mmm)
REVERT: A  775 MET cc_start: 0.9444 (tpp) cc_final: 0.9101 (tpp)
REVERT: A  833 LEU cc_start: 0.9018 (mm) cc_final: 0.8565 (pt)
REVERT: A  947 MET cc_start: 0.8559 (ttm) cc_final: 0.7964 (tpp)
REVERT: A 1035 MET cc_start: 0.8912 (mpp) cc_final: 0.8341 (mpp)
  outliers start: 1
  outliers final: 0
  residues processed: 73
  average time/residue: 0.2788
  time to fit residues: 34.0921
Evaluate side-chains
  62 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 1.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 195 optimal weight:    9.9990
   chunk 117 optimal weight:    2.9990
   chunk 98 optimal weight:   20.0000
   chunk 134 optimal weight:    8.9990
   chunk 16 optimal weight:    7.9990
   chunk 88 optimal weight:    4.9990
   chunk 153 optimal weight:   10.0000
   chunk 103 optimal weight:   20.0000
   chunk 182 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0020
   overall best weight:    2.7996

-------------------------------------------------------------------------------
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 215 GLN
** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 942 GLN
A 138 ASN
A 149 GLN
A 263 ASN
A 631 ASN
A 660 GLN
A 717 GLN
A 760 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.035279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2725 r_free = 0.2725 target = 0.025429 restraints weight = 241786.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2758 r_free = 0.2758 target = 0.026145 restraints weight = 147397.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.026641 restraints weight = 103031.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2720
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2720 r_free = 0.2720    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 = 0.2720 r_free = 0.2720    target_work(ls_wunit_k1) = 0.026         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2720
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.6067

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= 0.189
  Angle     :  0.683  15.863  26677  Z= 0.344
  Chirality :  0.042   0.190   3140
  Planarity :  0.005   0.052   2916
  Dihedral  : 18.362 175.235   4365
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  1.27 %
    Favored  : 98.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.41 (0.18), residues: 1964
  helix: -0.35 (0.17), residues: 920
  sheet: -0.81 (0.36), residues: 211
  loop : -1.55 (0.21), residues: 833

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 186 
 HIS   0.009   0.002   HIS A 662 
 PHE   0.035   0.002   PHE B 260 
 TYR   0.032   0.003   TYR B 135 
 ARG   0.015   0.001   ARG A 933 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04255 (  619)
  hydrogen bonds       : angle       4.31673 ( 1660)
  covalent geometry    : bond        0.00393 (19155)
  covalent geometry    : angle       0.68308 (26677)
  Misc. bond           : bond        0.00069 (    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
  65 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 64
  time to evaluate  : 1.739 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  237 MET cc_start: 0.9377 (ptm) cc_final: 0.8350 (ttp)
REVERT: B  267 MET cc_start: 0.9406 (mmm) cc_final: 0.9046 (mmm)
REVERT: B  549 ASP cc_start: 0.9290 (t0) cc_final: 0.8960 (m-30)
REVERT: B  659 MET cc_start: 0.9268 (mtt) cc_final: 0.8498 (ttm)
REVERT: B  714 MET cc_start: 0.8316 (tmm) cc_final: 0.8047 (tmm)
REVERT: B  739 MET cc_start: 0.9179 (tpt) cc_final: 0.8677 (tpp)
REVERT: B  743 MET cc_start: 0.9516 (mmp) cc_final: 0.9311 (mmt)
REVERT: B  763 MET cc_start: 0.9074 (mpp) cc_final: 0.8605 (mpp)
REVERT: B  842 LEU cc_start: 0.9640 (mt) cc_final: 0.9243 (pp)
REVERT: A  176 GLU cc_start: 0.8741 (tt0) cc_final: 0.8331 (tm-30)
REVERT: A  202 MET cc_start: 0.9437 (ttp) cc_final: 0.9135 (ppp)
REVERT: A  441 LEU cc_start: 0.9454 (tp) cc_final: 0.9136 (tp)
REVERT: A  515 LEU cc_start: 0.9551 (mp) cc_final: 0.9332 (mp)
REVERT: A  637 MET cc_start: 0.9150 (mmp) cc_final: 0.8899 (mmm)
REVERT: A  659 MET cc_start: 0.9000 (ttt) cc_final: 0.8344 (ttp)
REVERT: A  759 ILE cc_start: 0.8634 (mp) cc_final: 0.8229 (tp)
REVERT: A  775 MET cc_start: 0.9393 (tpp) cc_final: 0.9176 (tpp)
REVERT: A  947 MET cc_start: 0.8727 (ttm) cc_final: 0.8258 (tpp)
REVERT: A 1035 MET cc_start: 0.8763 (mpp) cc_final: 0.8264 (mpp)
  outliers start: 1
  outliers final: 0
  residues processed: 65
  average time/residue: 0.2848
  time to fit residues: 30.7533
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  : 1.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 155 optimal weight:    0.0170
   chunk 193 optimal weight:    0.9980
   chunk 59 optimal weight:    0.0270
   chunk 49 optimal weight:    3.9990
   chunk 183 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   chunk 200 optimal weight:    2.9990
   chunk 173 optimal weight:    0.0060
   chunk 133 optimal weight:    3.9990
   chunk 77 optimal weight:    4.9990
   chunk 29 optimal weight:    8.9990
   overall best weight:    0.8094

-------------------------------------------------------------------------------
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 631 ASN
** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 138 ASN
** A 149 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 = 0.3184 r_free = 0.3184 target = 0.036068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.026201 restraints weight = 235598.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.026947 restraints weight = 143531.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.027459 restraints weight = 99892.575|
|-----------------------------------------------------------------------------|
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2755
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2755 r_free = 0.2755    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 = 0.2755 r_free = 0.2755    target_work(ls_wunit_k1) = 0.026         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2755
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.6082

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= 0.095
  Angle     :  0.539   8.666  26677  Z= 0.266
  Chirality :  0.039   0.156   3140
  Planarity :  0.004   0.050   2916
  Dihedral  : 18.124 175.419   4365
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  0.55 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.19), residues: 1964
  helix:  0.13 (0.18), residues: 905
  sheet: -0.76 (0.36), residues: 214
  loop : -1.29 (0.21), residues: 845

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 186 
 HIS   0.004   0.001   HIS A 244 
 PHE   0.010   0.001   PHE B 210 
 TYR   0.014   0.001   TYR A 705 
 ARG   0.004   0.000   ARG B 426 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02874 (  619)
  hydrogen bonds       : angle       3.91220 ( 1660)
  covalent geometry    : bond        0.00205 (19155)
  covalent geometry    : angle       0.53922 (26677)
  Misc. bond           : bond        0.00033 (    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
  61 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 1.743 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  237 MET cc_start: 0.9301 (ptm) cc_final: 0.8319 (ttp)
REVERT: B  267 MET cc_start: 0.9443 (mmm) cc_final: 0.9221 (mmp)
REVERT: B  549 ASP cc_start: 0.9247 (t0) cc_final: 0.8939 (m-30)
REVERT: B  659 MET cc_start: 0.9175 (mtt) cc_final: 0.8439 (ttm)
REVERT: B  714 MET cc_start: 0.8340 (tmm) cc_final: 0.8056 (tmm)
REVERT: B  739 MET cc_start: 0.9156 (tpt) cc_final: 0.8597 (tpp)
REVERT: B  743 MET cc_start: 0.9489 (mmp) cc_final: 0.9265 (mmt)
REVERT: B  763 MET cc_start: 0.8626 (mpp) cc_final: 0.8173 (mpp)
REVERT: B  842 LEU cc_start: 0.9655 (mt) cc_final: 0.9246 (pp)
REVERT: A  202 MET cc_start: 0.9356 (ttp) cc_final: 0.8933 (tmm)
REVERT: A  441 LEU cc_start: 0.9422 (tp) cc_final: 0.9133 (tp)
REVERT: A  446 MET cc_start: 0.8963 (mpp) cc_final: 0.8473 (tpp)
REVERT: A  637 MET cc_start: 0.9120 (mmp) cc_final: 0.8844 (mmm)
REVERT: A  659 MET cc_start: 0.9213 (ttt) cc_final: 0.8720 (ttp)
REVERT: A  763 MET cc_start: 0.8557 (ttt) cc_final: 0.8049 (tpp)
REVERT: A  947 MET cc_start: 0.8803 (ttm) cc_final: 0.8438 (tpp)
REVERT: A 1035 MET cc_start: 0.8768 (mpp) cc_final: 0.8253 (mpp)
  outliers start: 1
  outliers final: 0
  residues processed: 61
  average time/residue: 0.2838
  time to fit residues: 28.8976
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  : 1.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 178 optimal weight:    0.0030
   chunk 146 optimal weight:    8.9990
   chunk 92 optimal weight:    0.0470
   chunk 149 optimal weight:    5.9990
   chunk 96 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9990
   chunk 195 optimal weight:    8.9990
   chunk 190 optimal weight:    0.9980
   chunk 206 optimal weight:   20.0000
   chunk 144 optimal weight:    9.9990
   chunk 180 optimal weight:    3.9990
   overall best weight:    1.2092

-------------------------------------------------------------------------------
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 = 0.3171 r_free = 0.3171 target = 0.035689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2752 r_free = 0.2752 target = 0.025871 restraints weight = 237622.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.026614 restraints weight = 143964.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.027126 restraints weight = 99788.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.2744
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2744
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2744 r_free = 0.2744    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 = 0.2744 r_free = 0.2744    target_work(ls_wunit_k1) = 0.026         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2744
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.6395

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= 0.102
  Angle     :  0.548   9.874  26677  Z= 0.269
  Chirality :  0.039   0.153   3140
  Planarity :  0.004   0.048   2916
  Dihedral  : 18.026 174.831   4365
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.19), residues: 1964
  helix:  0.37 (0.18), residues: 901
  sheet: -0.57 (0.36), residues: 223
  loop : -1.19 (0.22), residues: 840

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 119 
 HIS   0.004   0.001   HIS A 244 
 PHE   0.010   0.001   PHE B 284 
 TYR   0.018   0.001   TYR A 705 
 ARG   0.004   0.000   ARG B 426 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02975 (  619)
  hydrogen bonds       : angle       3.84248 ( 1660)
  covalent geometry    : bond        0.00222 (19155)
  covalent geometry    : angle       0.54840 (26677)
  Misc. bond           : bond        0.00030 (    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
  60 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 59
  time to evaluate  : 1.805 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  237 MET cc_start: 0.9316 (ptm) cc_final: 0.8421 (ttp)
REVERT: B  267 MET cc_start: 0.9553 (mmm) cc_final: 0.9307 (mmp)
REVERT: B  549 ASP cc_start: 0.9234 (t0) cc_final: 0.8901 (m-30)
REVERT: B  659 MET cc_start: 0.9111 (mtt) cc_final: 0.8499 (ttm)
REVERT: B  714 MET cc_start: 0.8307 (tmm) cc_final: 0.8019 (tmm)
REVERT: B  739 MET cc_start: 0.9163 (tpt) cc_final: 0.8553 (tpp)
REVERT: B  743 MET cc_start: 0.9522 (mmp) cc_final: 0.9243 (mmt)
REVERT: B  763 MET cc_start: 0.8634 (mpp) cc_final: 0.8166 (mpp)
REVERT: B  842 LEU cc_start: 0.9656 (mt) cc_final: 0.9247 (pp)
REVERT: A  202 MET cc_start: 0.9347 (ttp) cc_final: 0.8925 (tmm)
REVERT: A  441 LEU cc_start: 0.9373 (tp) cc_final: 0.9053 (tp)
REVERT: A  446 MET cc_start: 0.8980 (mpp) cc_final: 0.8538 (tpp)
REVERT: A  637 MET cc_start: 0.9128 (mmp) cc_final: 0.8908 (mmm)
REVERT: A  659 MET cc_start: 0.9211 (ttt) cc_final: 0.8704 (ttp)
REVERT: A  743 MET cc_start: 0.9641 (mmm) cc_final: 0.9126 (mmm)
REVERT: A  763 MET cc_start: 0.8603 (ttt) cc_final: 0.8164 (tpt)
REVERT: A  947 MET cc_start: 0.8920 (ttm) cc_final: 0.8475 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 60
  average time/residue: 0.2886
  time to fit residues: 28.8734
Evaluate side-chains
  56 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 1.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 194 optimal weight:   50.0000
   chunk 101 optimal weight:   20.0000
   chunk 195 optimal weight:    9.9990
   chunk 154 optimal weight:    8.9990
   chunk 62 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0060
   chunk 61 optimal weight:    0.9990
   chunk 190 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 196 optimal weight:    0.0070
   chunk 193 optimal weight:    7.9990
   overall best weight:    0.7218

-------------------------------------------------------------------------------
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 160 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.035985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.026156 restraints weight = 238006.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.026906 restraints weight = 143002.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.027434 restraints weight = 98964.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.2760
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2759
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2759 r_free = 0.2759    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 = 0.2759 r_free = 0.2759    target_work(ls_wunit_k1) = 0.026         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2759
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.6509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  19157  Z= 0.088
  Angle     :  0.528   9.116  26677  Z= 0.257
  Chirality :  0.039   0.152   3140
  Planarity :  0.004   0.047   2916
  Dihedral  : 17.942 173.947   4365
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  0.36 %
    Favored  : 99.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.20), residues: 1964
  helix:  0.54 (0.18), residues: 899
  sheet: -0.33 (0.37), residues: 210
  loop : -1.10 (0.22), residues: 855

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 186 
 HIS   0.004   0.001   HIS A 244 
 PHE   0.009   0.001   PHE A 986 
 TYR   0.011   0.001   TYR A 705 
 ARG   0.004   0.000   ARG B 426 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02666 (  619)
  hydrogen bonds       : angle       3.74159 ( 1660)
  covalent geometry    : bond        0.00190 (19155)
  covalent geometry    : angle       0.52755 (26677)
  Misc. bond           : bond        0.00037 (    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
  63 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 62
  time to evaluate  : 2.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  237 MET cc_start: 0.9291 (ptm) cc_final: 0.8247 (ttp)
REVERT: B  267 MET cc_start: 0.9553 (mmm) cc_final: 0.9278 (mmp)
REVERT: B  549 ASP cc_start: 0.9214 (t0) cc_final: 0.8882 (m-30)
REVERT: B  659 MET cc_start: 0.9080 (mtt) cc_final: 0.8477 (ttm)
REVERT: B  714 MET cc_start: 0.8298 (tmm) cc_final: 0.8011 (tmm)
REVERT: B  739 MET cc_start: 0.9201 (tpt) cc_final: 0.8823 (tpp)
REVERT: B  775 MET cc_start: 0.8687 (tmm) cc_final: 0.8317 (ppp)
REVERT: B  842 LEU cc_start: 0.9673 (mt) cc_final: 0.9261 (pp)
REVERT: A  202 MET cc_start: 0.9308 (ttp) cc_final: 0.9071 (tmm)
REVERT: A  441 LEU cc_start: 0.9369 (tp) cc_final: 0.9095 (tp)
REVERT: A  446 MET cc_start: 0.8995 (mpp) cc_final: 0.8512 (tpp)
REVERT: A  659 MET cc_start: 0.9186 (ttt) cc_final: 0.8677 (ttp)
REVERT: A  743 MET cc_start: 0.9636 (mmm) cc_final: 0.9233 (tpt)
REVERT: A  763 MET cc_start: 0.8761 (ttt) cc_final: 0.8416 (tpp)
REVERT: A  833 LEU cc_start: 0.9089 (mm) cc_final: 0.8591 (pt)
REVERT: A  947 MET cc_start: 0.8949 (ttm) cc_final: 0.8449 (tpp)
REVERT: A 1035 MET cc_start: 0.8858 (mpp) cc_final: 0.8370 (mpp)
  outliers start: 1
  outliers final: 0
  residues processed: 63
  average time/residue: 0.2979
  time to fit residues: 31.5131
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  : 1.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 139 optimal weight:    0.0770
   chunk 59 optimal weight:    4.9990
   chunk 184 optimal weight:    2.9990
   chunk 116 optimal weight:    4.9990
   chunk 165 optimal weight:    5.9990
   chunk 197 optimal weight:    9.9990
   chunk 4 optimal weight:    2.9990
   chunk 75 optimal weight:   10.0000
   chunk 22 optimal weight:    4.9990
   chunk 129 optimal weight:    0.7980
   overall best weight:    2.3744

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A 149 GLN
A 663 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.034592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2701 r_free = 0.2701 target = 0.024867 restraints weight = 243867.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2735 r_free = 0.2735 target = 0.025584 restraints weight = 146313.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2757 r_free = 0.2757 target = 0.026074 restraints weight = 101055.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.2693
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2694
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2694 r_free = 0.2694    target_work(ls_wunit_k1) = 0.025         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2694 r_free = 0.2694    target_work(ls_wunit_k1) = 0.025         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2694
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
moved from start:          0.7090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  19157  Z= 0.152
  Angle     :  0.608   9.554  26677  Z= 0.302
  Chirality :  0.040   0.154   3140
  Planarity :  0.004   0.045   2916
  Dihedral  : 18.126 174.089   4365
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.19), residues: 1964
  helix:  0.51 (0.18), residues: 885
  sheet: -0.72 (0.35), residues: 232
  loop : -1.13 (0.22), residues: 847

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 186 
 HIS   0.004   0.001   HIS B 145 
 PHE   0.014   0.002   PHE B 284 
 TYR   0.023   0.002   TYR A 705 
 ARG   0.005   0.001   ARG A 694 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03586 (  619)
  hydrogen bonds       : angle       4.02466 ( 1660)
  covalent geometry    : bond        0.00322 (19155)
  covalent geometry    : angle       0.60780 (26677)
  Misc. bond           : bond        0.00039 (    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
  60 residues out of total 1696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 1.872 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  237 MET cc_start: 0.9392 (ptm) cc_final: 0.8373 (ttp)
REVERT: B  267 MET cc_start: 0.9586 (mmm) cc_final: 0.9240 (mmp)
REVERT: B  549 ASP cc_start: 0.9226 (t0) cc_final: 0.8842 (m-30)
REVERT: B  637 MET cc_start: 0.9402 (mmp) cc_final: 0.9188 (mmm)
REVERT: B  659 MET cc_start: 0.9259 (mtt) cc_final: 0.8508 (ttm)
REVERT: B  714 MET cc_start: 0.8344 (tmm) cc_final: 0.8080 (tmm)
REVERT: B  739 MET cc_start: 0.9269 (tpt) cc_final: 0.8809 (tpp)
REVERT: B  743 MET cc_start: 0.9756 (mmp) cc_final: 0.9191 (mmm)
REVERT: B  775 MET cc_start: 0.8881 (tmm) cc_final: 0.8393 (ppp)
REVERT: B  842 LEU cc_start: 0.9739 (mt) cc_final: 0.9346 (pp)
REVERT: A  202 MET cc_start: 0.9365 (ttp) cc_final: 0.9114 (ppp)
REVERT: A  441 LEU cc_start: 0.9396 (tp) cc_final: 0.9074 (tp)
REVERT: A  446 MET cc_start: 0.9090 (mpp) cc_final: 0.8627 (tpp)
REVERT: A  637 MET cc_start: 0.9193 (mmp) cc_final: 0.8901 (mmm)
REVERT: A  659 MET cc_start: 0.9249 (ttt) cc_final: 0.8431 (ttt)
REVERT: A  763 MET cc_start: 0.8816 (ttt) cc_final: 0.8427 (tpp)
REVERT: A  947 MET cc_start: 0.8987 (ttm) cc_final: 0.8573 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.2903
  time to fit residues: 29.1646
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  : 1.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 37 optimal weight:    9.9990
   chunk 197 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 150 optimal weight:    0.9980
   chunk 184 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 188 optimal weight:    0.0170
   chunk 195 optimal weight:    8.9990
   chunk 202 optimal weight:    7.9990
   chunk 81 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.9422

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.035197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2736 r_free = 0.2736 target = 0.025449 restraints weight = 239017.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.026177 restraints weight = 143027.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2792 r_free = 0.2792 target = 0.026686 restraints weight = 98823.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2725
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2725 r_free = 0.2725    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 = 0.2725 r_free = 0.2725    target_work(ls_wunit_k1) = 0.026         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2725
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.7155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  19157  Z= 0.094
  Angle     :  0.539   9.063  26677  Z= 0.263
  Chirality :  0.039   0.149   3140
  Planarity :  0.004   0.046   2916
  Dihedral  : 17.996 173.720   4365
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  0.06 %
    Favored  : 99.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.20), residues: 1964
  helix:  0.67 (0.18), residues: 897
  sheet: -0.44 (0.37), residues: 213
  loop : -1.06 (0.22), residues: 854

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 186 
 HIS   0.003   0.001   HIS A 244 
 PHE   0.009   0.001   PHE B 284 
 TYR   0.013   0.001   TYR A 705 
 ARG   0.004   0.000   ARG B 426 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02801 (  619)
  hydrogen bonds       : angle       3.82496 ( 1660)
  covalent geometry    : bond        0.00205 (19155)
  covalent geometry    : angle       0.53866 (26677)
  Misc. bond           : bond        0.00044 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5733.11 seconds
wall clock time: 100 minutes 59.27 seconds (6059.27 seconds total)