Starting phenix.real_space_refine
on Thu Jul  2 18:22:05 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7xjz_33238/07_2026/7xjz_33238.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xjz_33238/07_2026/7xjz_33238.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xjz_33238/07_2026/7xjz_33238.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xjz_33238/07_2026/7xjz_33238.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7xjz_33238/07_2026/7xjz_33238.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7xjz_33238/07_2026/7xjz_33238.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xjz_33238/07_2026/7xjz_33238.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xjz_33238/07_2026/7xjz_33238.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.073
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      75      5.49       5
     S      31      5.16       5
     C    5618      2.51       5
     N    1594      2.21       5
     O    1958      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9276
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7716
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 983, 7711
          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 non-hydrogen bonds: 76
          Unresolved non-hydrogen angles: 91
          Unresolved non-hydrogen dihedrals: 61
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 7, 'ASP:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 58
      Conformer: "B"
        Number of residues, atoms: 983, 7711
          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 non-hydrogen bonds: 76
          Unresolved non-hydrogen angles: 91
          Unresolved non-hydrogen dihedrals: 61
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 7, 'ASP:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 58
          bond proxies already assigned to first conformer: 7862
    Chain: "B"
      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 B   1 "
              pdbres="  C B   2 "
  Residues with excluded nonbonded symmetry interactions: 1
    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: 2.70, per 1000 atoms: 0.29
  Number of scatterers: 9276
  At special positions: 0
  Unit cell: (123.2, 107.8, 106.7, 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      31     16.00
     P      75     15.00
     O    1958      8.00
     N    1594      7.00
     C    5618      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.67
  Conformation dependent library (CDL) restraints added in 342.7 milliseconds
  

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1848

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 8 sheets defined
      52.0% alpha, 13.1% beta
      16 base pairs and 36 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 73 through 89
      removed outlier: 3.814A  pdb=" N   ILE A  78 " --> pdb=" O   PHE A  74 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   GLN A  79 " --> pdb=" O   GLN A  75 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ASP A  83 " --> pdb=" O   GLN A  79 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   TYR A  84 " --> pdb=" O   ARG A  80 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   TRP A  85 " --> pdb=" O   LEU A  81 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   SER A  87 " --> pdb=" O   ASP A  83 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   GLY A  89 " --> pdb=" O   TRP A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 133
    Processing helix  chain 'A' and resid 158 through 171
      removed outlier: 3.997A  pdb=" N   PHE A 163 " --> pdb=" O   SER A 159 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   LEU A 164 " --> pdb=" O   GLN A 160 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   GLY A 171 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 240
      removed outlier: 4.122A  pdb=" N   LEU A 236 " --> pdb=" O   LEU A 232 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   MET A 237 " --> pdb=" O   GLU A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 274
      removed outlier: 3.985A  pdb=" N   GLU A 266 " --> pdb=" O   GLU A 262 " (cutoff:3.500A)
      removed outlier: 4.752A  pdb=" N   MET A 267 " --> pdb=" O   ASN A 263 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   HIS A 274 " --> pdb=" O   TYR A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 296
      removed outlier: 4.111A  pdb=" N   ILE A 280 " --> pdb=" O   ASN A 276 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   GLN A 281 " --> pdb=" O   VAL A 277 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   LYS A 282 " --> pdb=" O   ASP A 278 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   ASP A 285 " --> pdb=" O   GLN A 281 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ASP A 286 " --> pdb=" O   LYS A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 321
      removed outlier: 3.501A  pdb=" N   ALA A 303 " --> pdb=" O   LEU A 299 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   VAL A 307 " --> pdb=" O   ALA A 303 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU A 308 " --> pdb=" O   TYR A 304 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   LYS A 309 " --> pdb=" O   ASP A 305 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ALA A 313 " --> pdb=" O   LYS A 309 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   PHE A 314 " --> pdb=" O   ALA A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 352
      removed outlier: 4.153A  pdb=" N   ARG A 330 " --> pdb=" O   THR A 326 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   LEU A 345 " --> pdb=" O   GLN A 341 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   TRP A 346 " --> pdb=" O   CYS A 342 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   VAL A 347 " --> pdb=" O   ALA A 343 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   LYS A 348 " --> pdb=" O   GLN A 344 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   ASN A 352 " --> pdb=" O   LYS A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 418
      removed outlier: 3.538A  pdb=" N   LYS A 405 " --> pdb=" O   ILE A 401 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   GLU A 408 " --> pdb=" O   THR A 404 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   SER A 410 " --> pdb=" O   GLN A 406 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   GLN A 413 " --> pdb=" O   LYS A 409 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ILE A 414 " --> pdb=" O   SER A 410 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   LEU A 415 " --> pdb=" O   LEU A 411 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   GLU A 416 " --> pdb=" O   ILE A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 456 through 461
    Processing helix  chain 'A' and resid 468 through 479
      removed outlier: 3.636A  pdb=" N   GLU A 472 " --> pdb=" O   THR A 468 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 485
    Processing helix  chain 'A' and resid 508 through 521
      Proline residue:  A 516  - end of helix
      removed outlier: 3.643A  pdb=" N   SER A 520 " --> pdb=" O   PRO A 516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 584 through 591
      removed outlier: 3.572A  pdb=" N   GLU A 589 " --> pdb=" O   LEU A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 613
      removed outlier: 3.875A  pdb=" N   HIS A 606 " --> pdb=" O   GLN A 602 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ASP A 607 " --> pdb=" O   ARG A 603 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   SER A 609 " --> pdb=" O   LEU A 605 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ILE A 610 " --> pdb=" O   HIS A 606 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   GLU A 613 " --> pdb=" O   SER A 609 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 622 through 631
      removed outlier: 4.119A  pdb=" N   GLU A 628 " --> pdb=" O   SER A 624 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   ASN A 631 " --> pdb=" O   GLN A 627 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 644 through 650
      removed outlier: 3.835A  pdb=" N   PHE A 647 " --> pdb=" O   ASP A 644 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ALA A 649 " --> pdb=" O   SER A 646 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   LEU A 650 " --> pdb=" O   PHE A 647 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 651 through 662
      removed outlier: 3.684A  pdb=" N   LEU A 655 " --> pdb=" O   PRO A 651 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ILE A 656 " --> pdb=" O   LYS A 652 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   THR A 657 " --> pdb=" O   ASP A 653 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   HIS A 662 " --> pdb=" O   VAL A 658 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 689 through 716
      removed outlier: 3.764A  pdb=" N   VAL A 693 " --> pdb=" O   LYS A 689 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ARG A 694 " --> pdb=" O   GLU A 690 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   ALA A 699 " --> pdb=" O   LYS A 695 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   VAL A 700 " --> pdb=" O   GLY A 696 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ALA A 703 " --> pdb=" O   ALA A 699 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   TYR A 705 " --> pdb=" O   LEU A 701 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   GLU A 706 " --> pdb=" O   ARG A 702 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ASP A 707 " --> pdb=" O   ALA A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 719 through 729
      removed outlier: 4.403A  pdb=" N   LEU A 727 " --> pdb=" O   ARG A 724 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   SER A 728 " --> pdb=" O   ASP A 725 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   SER A 729 " --> pdb=" O   GLN A 726 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 739 through 757
      removed outlier: 5.065A  pdb=" N   ALA A 751 " --> pdb=" O   GLU A 747 " (cutoff:3.500A)
      removed outlier: 5.435A  pdb=" N   GLU A 752 " --> pdb=" O   ASN A 748 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   VAL A 753 " --> pdb=" O   THR A 749 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 760 through 762
      No H-bonds generated for 'chain 'A' and resid 760 through 762'
    Processing helix  chain 'A' and resid 763 through 771
      removed outlier: 3.663A  pdb=" N   ILE A 767 " --> pdb=" O   MET A 763 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 776 through 780
      removed outlier: 3.709A  pdb=" N   ALA A 779 " --> pdb=" O   SER A 776 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 781 through 786
      removed outlier: 4.254A  pdb=" N   GLU A 785 " --> pdb=" O   ASN A 781 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   PHE A 786 " --> pdb=" O   ILE A 782 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 781 through 786'
    Processing helix  chain 'A' and resid 787 through 790
    Processing helix  chain 'A' and resid 792 through 802
      removed outlier: 3.517A  pdb=" N   GLY A 802 " --> pdb=" O   ALA A 798 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 804 through 813
      removed outlier: 3.735A  pdb=" N   ALA A 808 " --> pdb=" O   SER A 804 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   GLU A 809 " --> pdb=" O   GLU A 805 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   ALA A 810 " --> pdb=" O   GLN A 806 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 827 through 848
      removed outlier: 3.620A  pdb=" N   VAL A 832 " --> pdb=" O   ASP A 828 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LEU A 833 " --> pdb=" O   PRO A 829 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ALA A 848 " --> pdb=" O   GLY A 844 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 860 through 874
    Processing helix  chain 'A' and resid 880 through 891
      removed outlier: 4.097A  pdb=" N   THR A 886 " --> pdb=" O   THR A 882 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   LEU A 887 " --> pdb=" O   LYS A 883 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   GLU A 891 " --> pdb=" O   LEU A 887 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 897 through 917
      removed outlier: 4.424A  pdb=" N   ILE A 901 " --> pdb=" O   ASP A 897 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   ASP A 902 " --> pdb=" O   SER A 898 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 922 through 930
      removed outlier: 3.580A  pdb=" N   SER A 928 " --> pdb=" O   GLU A 924 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 936 through 951
      removed outlier: 4.004A  pdb=" N   GLU A 946 " --> pdb=" O   GLN A 942 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   GLU A 948 " --> pdb=" O   ALA A 944 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   ALA A 949 " --> pdb=" O   ILE A 945 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 955 through 964
      removed outlier: 3.754A  pdb=" N   SER A 964 " --> pdb=" O   VAL A 960 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 966 through 971
      removed outlier: 3.545A  pdb=" N   ILE A 970 " --> pdb=" O   PRO A 966 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ARG A 971 " --> pdb=" O   THR A 967 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 966 through 971'
    Processing helix  chain 'A' and resid 974 through 978
    Processing helix  chain 'A' and resid 988 through 1003
      removed outlier: 3.906A  pdb=" N   ARG A 992 " --> pdb=" O   LYS A 988 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   ASP A1003 " --> pdb=" O   LEU A 999 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1013 through 1019
    Processing helix  chain 'A' and resid 1021 through 1032
      removed outlier: 3.804A  pdb=" N   LEU A1025 " --> pdb=" O   LEU A1021 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   GLU A1026 " --> pdb=" O   LEU A1022 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   ASP A1027 " --> pdb=" O   GLN A1023 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1038 through 1054
    Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 92
      removed outlier: 3.802A  pdb=" N   ALA A 122 " --> pdb=" O   ALA A  91 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   ILE A 207 " --> pdb=" O   GLY A 231 " (cutoff:3.500A)
      removed outlier: 5.731A  pdb=" N   GLU A 206 " --> pdb=" O   MET A 202 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   MET A 202 " --> pdb=" O   GLU A 206 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   THR A 208 " --> pdb=" O   VAL A 200 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   TRP A 194 " --> pdb=" O   GLN A 214 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 179 through 183
      removed outlier: 6.582A  pdb=" N   TRP A 194 " --> pdb=" O   GLN A 214 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   THR A 208 " --> pdb=" O   VAL A 200 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   MET A 202 " --> pdb=" O   GLU A 206 " (cutoff:3.500A)
      removed outlier: 5.731A  pdb=" N   GLU A 206 " --> pdb=" O   MET A 202 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 425 through 430
      removed outlier: 3.775A  pdb=" N   LEU A 434 " --> pdb=" O   ILE A 390 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   ILE A 390 " --> pdb=" O   LEU A 434 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   ASN A 440 " --> pdb=" O   ARG A 384 " (cutoff:3.500A)
      removed outlier: 5.836A  pdb=" N   ARG A 384 " --> pdb=" O   ASN A 440 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 450 through 451
    Processing sheet with id=AA5, first strand: chain 'A' and resid 555 through 556
    Processing sheet with id=AA6, first strand: chain 'A' and resid 564 through 565
    Processing sheet with id=AA7, first strand: chain 'A' and resid 617 through 619
      removed outlier: 7.056A  pdb=" N   PHE A 666 " --> pdb=" O   CYS A 679 " (cutoff:3.500A)
      removed outlier: 7.190A  pdb=" N   CYS A 679 " --> pdb=" O   PHE A 666 " (cutoff:3.500A)
      removed outlier: 5.171A  pdb=" N   VAL A 668 " --> pdb=" O   LEU A 677 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   MET A 637 " --> pdb=" O   ALA A 684 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 731 through 733
      removed outlier: 6.322A  pdb=" N   GLY A 737 " --> pdb=" O   PHE A 732 " (cutoff:3.500A)

    331 hydrogen bonds defined for protein.
    925 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      44 hydrogen bonds
      88 hydrogen bond angles
      0 basepair planarities
      16 basepair parallelities
      36 stacking parallelities
  Total time for adding SS restraints: 1.49

  Time building geometry restraints manager: 0.88 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1408
        1.31 -     1.44: 2901
        1.44 -     1.56: 5105
        1.56 -     1.68: 148
        1.68 -     1.81: 52
  Bond restraints: 9614
  Sorted by residual:
  bond pdb=" C2  GTP B   1 "
       pdb=" N2  GTP B   1 "
    ideal  model  delta    sigma   weight residual
    1.330  1.454 -0.124 2.00e-02 2.50e+03 3.84e+01
  bond pdb=" N   THR A 967 "
       pdb=" CA  THR A 967 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.039 1.21e-02 6.83e+03 1.03e+01
  bond pdb=" N   ARG A 965 "
       pdb=" CA  ARG A 965 "
    ideal  model  delta    sigma   weight residual
    1.461  1.488 -0.027 9.20e-03 1.18e+04 8.71e+00
  bond pdb=" N   ASN A 697 "
       pdb=" CA  ASN A 697 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.037 1.29e-02 6.01e+03 8.18e+00
  bond pdb=" N   ILE A 945 "
       pdb=" CA  ILE A 945 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.33e-02 5.65e+03 8.00e+00
  ... (remaining 9609 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.83: 13156
        1.83 -     3.66: 191
        3.66 -     5.49: 30
        5.49 -     7.32: 8
        7.32 -     9.15: 6
  Bond angle restraints: 13391
  Sorted by residual:
  angle pdb=" N   ARG A 965 "
        pdb=" CA  ARG A 965 "
        pdb=" C   ARG A 965 "
      ideal   model   delta    sigma   weight residual
     112.75  103.96    8.79 1.36e+00 5.41e-01 4.18e+01
  angle pdb=" C   PRO A 966 "
        pdb=" CA  PRO A 966 "
        pdb=" CB  PRO A 966 "
      ideal   model   delta    sigma   weight residual
     112.64  105.72    6.92 1.74e+00 3.30e-01 1.58e+01
  angle pdb=" CA  ALA A 962 "
        pdb=" C   ALA A 962 "
        pdb=" O   ALA A 962 "
      ideal   model   delta    sigma   weight residual
     120.90  117.03    3.87 1.03e+00 9.43e-01 1.41e+01
  angle pdb=" CA  GLY A1067 "
        pdb=" C   GLY A1067 "
        pdb=" O   GLY A1067 "
      ideal   model   delta    sigma   weight residual
     120.80  117.50    3.30 9.80e-01 1.04e+00 1.13e+01
  angle pdb=" CA  THR A 967 "
        pdb=" C   THR A 967 "
        pdb=" O   THR A 967 "
      ideal   model   delta    sigma   weight residual
     120.55  117.06    3.49 1.06e+00 8.90e-01 1.08e+01
  ... (remaining 13386 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.00: 5482
       30.00 -    60.00: 146
       60.00 -    90.00: 8
       90.00 -   120.00: 2
      120.00 -   150.00: 1
  Dihedral angle restraints: 5639
    sinusoidal: 2781
      harmonic: 2858
  Sorted by residual:
  dihedral pdb=" O4'   U B  19 "
           pdb=" C1'   U B  19 "
           pdb=" N1    U B  19 "
           pdb=" C2    U B  19 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   50.00  150.00     1      1.50e+01 4.44e-03 7.96e+01
  dihedral pdb=" C8  GTP B   1 "
           pdb=" C1' GTP B   1 "
           pdb=" N9  GTP B   1 "
           pdb=" O4' GTP B   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59    6.23   98.37     1      2.00e+01 2.50e-03 2.75e+01
  dihedral pdb=" O2G GTP B   1 "
           pdb=" O3B GTP B   1 "
           pdb=" PG  GTP B   1 "
           pdb=" PB  GTP B   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     177.30  -86.23  -96.47     1      2.00e+01 2.50e-03 2.67e+01
  ... (remaining 5636 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 1220
       0.043 -    0.087: 274
       0.087 -    0.130: 72
       0.130 -    0.174: 8
       0.174 -    0.217: 3
  Chirality restraints: 1577
  Sorted by residual:
  chirality pdb=" CA  SER A 964 "
            pdb=" N   SER A 964 "
            pdb=" C   SER A 964 "
            pdb=" CB  SER A 964 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.18e+00
  chirality pdb=" C2'   C B   2 "
            pdb=" C3'   C B   2 "
            pdb=" O2'   C B   2 "
            pdb=" C1'   C B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.58   -0.18 2.00e-01 2.50e+01 7.82e-01
  chirality pdb=" C3' GTP B   1 "
            pdb=" C2' GTP B   1 "
            pdb=" C4' GTP B   1 "
            pdb=" O3' GTP B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.65    0.17 2.00e-01 2.50e+01 7.56e-01
  ... (remaining 1574 not shown)

  Planarity restraints: 1461
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 637 "   -0.028 5.00e-02 4.00e+02   4.31e-02 2.97e+00
        pdb=" N   PRO A 638 "    0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO A 638 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 638 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A1063 "    0.008 2.00e-02 2.50e+03   1.56e-02 2.42e+00
        pdb=" C   SER A1063 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   SER A1063 "    0.010 2.00e-02 2.50e+03
        pdb=" N   VAL A1064 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 969 "    0.007 2.00e-02 2.50e+03   1.51e-02 2.29e+00
        pdb=" C   ILE A 969 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   ILE A 969 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ILE A 970 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1458 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1359
        2.75 -     3.29: 8903
        3.29 -     3.83: 15407
        3.83 -     4.36: 17335
        4.36 -     4.90: 28389
  Nonbonded interactions: 71393
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 950 "
            pdb=" OG1 THR A 953 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" OG1 THR A 855 "
            pdb=" OP1   G B  69 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" O   GLU A 206 "
            pdb=" NH1 ARG A 234 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" OE1 GLU A 389 "
            pdb=" OH  TYR A 584 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" OG1 THR A 255 "
            pdb=" OE1 GLU A 258 "
     model   vdw
     2.248 3.040
  ... (remaining 71388 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             1.110
  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:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     9.870
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.176   9615  Z= 0.265
  Angle     :  0.591   9.148  13391  Z= 0.321
  Chirality :  0.040   0.217   1577
  Planarity :  0.004   0.043   1461
  Dihedral  : 12.644 149.999   3791
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  :  8.19 %
    Favored  : 88.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.22 (0.27), residues: 982
  helix: -0.15 (0.26), residues: 439
  sheet: -0.34 (0.52), residues: 119
  loop : -1.59 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1045 
 TYR   0.012   0.001   TYR A 230 
 PHE   0.010   0.001   PHE A 544 
 TRP   0.008   0.001   TRP A 194 
 HIS   0.004   0.001   HIS A 145 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00366 /  0.20 ( 9614)
  covalent geometry    : angle       0.59082 /  0.32 (13391)
  hydrogen bonds       : bond        0.16244 / 10.76 (  369)
  hydrogen bonds       : angle       7.42555 /  4.98 ( 1013)
  Misc. bond           : bond        0.17590 /  9.26 (    1)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 92
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
REVERT: A  263 ASN cc_start: 0.7814 (t0) cc_final: 0.7556 (t0)
REVERT: A  267 MET cc_start: 0.9033 (mmm) cc_final: 0.8695 (mmp)
REVERT: A  495 TYR cc_start: 0.4079 (OUTLIER) cc_final: 0.2605 (m-80)
REVERT: A  597 MET cc_start: 0.8677 (tmm) cc_final: 0.8469 (tmm)
REVERT: A  653 ASP cc_start: 0.8157 (p0) cc_final: 0.7515 (t0)
REVERT: A  714 MET cc_start: 0.8508 (tmm) cc_final: 0.8173 (tmm)
REVERT: A  775 MET cc_start: 0.8274 (tmm) cc_final: 0.7898 (tmm)
REVERT: A  793 MET cc_start: 0.8824 (mmm) cc_final: 0.8494 (mmm)
REVERT: A  875 ASN cc_start: 0.8994 (OUTLIER) cc_final: 0.8726 (m-40)
REVERT: A  963 TYR cc_start: 0.8811 (OUTLIER) cc_final: 0.7770 (t80)
  outliers start: 26
  outliers final: 7
  residues processed: 113
  average time/residue: 0.1022
  time to fit residues: 15.5474
Evaluate side-chains
  62 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 ASP
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  741 ASP
Chi-restraints excluded: chain A residue  875 ASN
Chi-restraints excluded: chain A residue  963 TYR
Chi-restraints excluded: chain A residue  967 THR
Chi-restraints excluded: chain A residue 1064 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.0070
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:   10.0000
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.7198

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.098363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.076402 restraints weight = 26311.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.077908 restraints weight = 13787.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.078660 restraints weight = 9793.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.079132 restraints weight = 7461.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.079229 restraints weight = 7177.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3264
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3264
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.1271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9615  Z= 0.109
  Angle     :  0.545   8.409  13391  Z= 0.277
  Chirality :  0.039   0.156   1577
  Planarity :  0.004   0.040   1461
  Dihedral  : 10.804 149.895   1959
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 12.29 %
    Favored  : 84.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.98 (0.27), residues: 982
  helix:  0.15 (0.26), residues: 448
  sheet: -0.08 (0.53), residues: 110
  loop : -1.65 (0.27), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 927 
 TYR   0.012   0.001   TYR A 230 
 PHE   0.022   0.001   PHE A 260 
 TRP   0.007   0.001   TRP A 542 
 HIS   0.003   0.001   HIS A 145 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00233 /  0.11 ( 9614)
  covalent geometry    : angle       0.54542 /  0.28 (13391)
  hydrogen bonds       : bond        0.04034 /  2.59 (  369)
  hydrogen bonds       : angle       4.20378 /  2.97 ( 1013)
  Misc. bond           : bond        0.00114 /  0.06 (    1)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 59
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 MET cc_start: 0.7822 (mtm) cc_final: 0.7595 (mtp)
REVERT: A  237 MET cc_start: 0.8210 (ttt) cc_final: 0.7883 (ttt)
REVERT: A  263 ASN cc_start: 0.7878 (t0) cc_final: 0.7530 (t0)
REVERT: A  267 MET cc_start: 0.8954 (mmm) cc_final: 0.8698 (mmp)
REVERT: A  495 TYR cc_start: 0.4289 (OUTLIER) cc_final: 0.2737 (m-80)
REVERT: A  597 MET cc_start: 0.8651 (tmm) cc_final: 0.8440 (tmm)
REVERT: A  653 ASP cc_start: 0.7858 (p0) cc_final: 0.7585 (t0)
REVERT: A  714 MET cc_start: 0.8377 (tmm) cc_final: 0.8074 (tmm)
REVERT: A  726 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7626 (pp30)
REVERT: A  793 MET cc_start: 0.8758 (mmm) cc_final: 0.8447 (mmm)
REVERT: A  875 ASN cc_start: 0.9041 (OUTLIER) cc_final: 0.8790 (m-40)
REVERT: A  906 GLN cc_start: 0.8022 (tm-30) cc_final: 0.7789 (tm-30)
REVERT: A  963 TYR cc_start: 0.8749 (OUTLIER) cc_final: 0.8065 (t80)
  outliers start: 23
  outliers final: 8
  residues processed: 77
  average time/residue: 0.0711
  time to fit residues: 8.1796
Evaluate side-chains
  66 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 54
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  266 GLU
Chi-restraints excluded: chain A residue  414 ILE
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  726 GLN
Chi-restraints excluded: chain A residue  741 ASP
Chi-restraints excluded: chain A residue  875 ASN
Chi-restraints excluded: chain A residue  963 TYR
Chi-restraints excluded: chain A residue  967 THR
Chi-restraints excluded: chain A residue 1064 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 54 optimal weight:    0.5980
   chunk 16 optimal weight:    5.9990
   chunk 90 optimal weight:    3.9990
   chunk 98 optimal weight:   10.0000
   chunk 75 optimal weight:    3.9990
   chunk 95 optimal weight:    6.9990
   chunk 77 optimal weight:    1.9990
   chunk 44 optimal weight:    0.2980
   chunk 9 optimal weight:    0.8980
   overall best weight:    1.5584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 149 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.096237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.074731 restraints weight = 26186.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.076336 restraints weight = 14132.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.076803 restraints weight = 8891.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.077068 restraints weight = 7705.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.077116 restraints weight = 7189.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3231
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3231 r_free = 0.3231    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3231 r_free = 0.3231    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3231
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.1594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9615  Z= 0.135
  Angle     :  0.555   9.197  13391  Z= 0.278
  Chirality :  0.040   0.172   1577
  Planarity :  0.004   0.046   1461
  Dihedral  : 10.759 148.809   1955
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 12.65 %
    Favored  : 84.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.91 (0.27), residues: 982
  helix:  0.26 (0.26), residues: 444
  sheet: -0.15 (0.53), residues: 112
  loop : -1.64 (0.27), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 144 
 TYR   0.017   0.001   TYR A 230 
 PHE   0.010   0.001   PHE A 544 
 TRP   0.007   0.001   TRP A 542 
 HIS   0.003   0.001   HIS A 312 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.13 ( 9614)
  covalent geometry    : angle       0.55504 /  0.28 (13391)
  hydrogen bonds       : bond        0.03882 /  2.53 (  369)
  hydrogen bonds       : angle       4.16401 /  2.92 ( 1013)
  Misc. bond           : bond        0.00063 /  0.03 (    1)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 52
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
REVERT: A  263 ASN cc_start: 0.7985 (t0) cc_final: 0.7715 (t0)
REVERT: A  267 MET cc_start: 0.9005 (mmm) cc_final: 0.8774 (mmp)
REVERT: A  495 TYR cc_start: 0.4335 (OUTLIER) cc_final: 0.2620 (m-80)
REVERT: A  597 MET cc_start: 0.8721 (tmm) cc_final: 0.8465 (tmm)
REVERT: A  793 MET cc_start: 0.8866 (mmm) cc_final: 0.8539 (mmm)
REVERT: A  875 ASN cc_start: 0.9075 (OUTLIER) cc_final: 0.8815 (m-40)
REVERT: A  906 GLN cc_start: 0.7966 (tm-30) cc_final: 0.7270 (tm-30)
REVERT: A  910 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7279 (tpp-160)
REVERT: A  947 MET cc_start: 0.7972 (ttp) cc_final: 0.7733 (ttp)
REVERT: A  963 TYR cc_start: 0.8817 (OUTLIER) cc_final: 0.8017 (t80)
  outliers start: 21
  outliers final: 10
  residues processed: 68
  average time/residue: 0.0761
  time to fit residues: 7.8713
Evaluate side-chains
  63 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 49
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  266 GLU
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  414 ILE
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  493 THR
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  741 ASP
Chi-restraints excluded: chain A residue  875 ASN
Chi-restraints excluded: chain A residue  910 ARG
Chi-restraints excluded: chain A residue  963 TYR
Chi-restraints excluded: chain A residue 1064 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 77 optimal weight:    0.9980
   chunk 93 optimal weight:    0.3980
   chunk 74 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0000
   chunk 62 optimal weight:    0.8980
   chunk 20 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.5584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.097916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.074810 restraints weight = 26769.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.076772 restraints weight = 14178.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.078064 restraints weight = 9041.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.078922 restraints weight = 6618.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.079488 restraints weight = 5323.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3294
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3294 r_free = 0.3294    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3294 r_free = 0.3294    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3294
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.1911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9615  Z= 0.091
  Angle     :  0.513   9.440  13391  Z= 0.254
  Chirality :  0.038   0.169   1577
  Planarity :  0.004   0.039   1461
  Dihedral  : 10.602 149.427   1954
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 13.37 %
    Favored  : 84.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.79 (0.27), residues: 982
  helix:  0.38 (0.26), residues: 446
  sheet: -0.21 (0.53), residues: 110
  loop : -1.57 (0.27), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  80 
 TYR   0.010   0.001   TYR A 230 
 PHE   0.007   0.001   PHE A 950 
 TRP   0.009   0.001   TRP A 542 
 HIS   0.002   0.000   HIS A 145 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00192 /  0.09 ( 9614)
  covalent geometry    : angle       0.51320 /  0.25 (13391)
  hydrogen bonds       : bond        0.03036 /  1.95 (  369)
  hydrogen bonds       : angle       3.87824 /  2.71 ( 1013)
  Misc. bond           : bond        0.00057 /  0.03 (    1)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 59
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
REVERT: A  160 GLN cc_start: 0.8584 (pt0) cc_final: 0.8343 (pt0)
REVERT: A  237 MET cc_start: 0.8175 (ttt) cc_final: 0.7934 (ttt)
REVERT: A  263 ASN cc_start: 0.7789 (t0) cc_final: 0.7528 (t0)
REVERT: A  267 MET cc_start: 0.8997 (mmm) cc_final: 0.8783 (mmp)
REVERT: A  278 ASP cc_start: 0.7170 (p0) cc_final: 0.6759 (p0)
REVERT: A  495 TYR cc_start: 0.4127 (OUTLIER) cc_final: 0.2597 (m-80)
REVERT: A  597 MET cc_start: 0.8721 (tmm) cc_final: 0.8441 (tmm)
REVERT: A  726 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7676 (tm-30)
REVERT: A  875 ASN cc_start: 0.9078 (OUTLIER) cc_final: 0.8831 (m-40)
REVERT: A  963 TYR cc_start: 0.8787 (OUTLIER) cc_final: 0.7943 (t80)
REVERT: A 1052 VAL cc_start: 0.8148 (t) cc_final: 0.7920 (t)
  outliers start: 17
  outliers final: 7
  residues processed: 69
  average time/residue: 0.0763
  time to fit residues: 7.7557
Evaluate side-chains
  64 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  266 GLU
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  493 THR
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  726 GLN
Chi-restraints excluded: chain A residue  875 ASN
Chi-restraints excluded: chain A residue  963 TYR
Chi-restraints excluded: chain A residue 1064 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 68 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 71 optimal weight:    4.9990
   chunk 87 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9980
   chunk 97 optimal weight:    4.9990
   overall best weight:    1.3986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 906 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.096151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.072798 restraints weight = 26804.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.074712 restraints weight = 14382.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.075975 restraints weight = 9333.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.076801 restraints weight = 6890.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.077400 restraints weight = 5561.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3250
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3250 r_free = 0.3250    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3250 r_free = 0.3250    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3250
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.2017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9615  Z= 0.124
  Angle     :  0.534  10.216  13391  Z= 0.264
  Chirality :  0.039   0.166   1577
  Planarity :  0.004   0.043   1461
  Dihedral  : 10.633 148.913   1952
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 13.25 %
    Favored  : 84.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.76 (0.27), residues: 982
  helix:  0.40 (0.26), residues: 444
  sheet: -0.11 (0.53), residues: 111
  loop : -1.56 (0.27), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 144 
 TYR   0.015   0.001   TYR A 230 
 PHE   0.009   0.001   PHE A 544 
 TRP   0.007   0.001   TRP A 542 
 HIS   0.003   0.001   HIS A 312 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.12 ( 9614)
  covalent geometry    : angle       0.53441 /  0.26 (13391)
  hydrogen bonds       : bond        0.03520 /  2.28 (  369)
  hydrogen bonds       : angle       3.95767 /  2.77 ( 1013)
  Misc. bond           : bond        0.00058 /  0.03 (    1)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 52
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A  160 GLN cc_start: 0.8594 (pt0) cc_final: 0.8332 (pt0)
REVERT: A  263 ASN cc_start: 0.7877 (t0) cc_final: 0.7582 (t0)
REVERT: A  267 MET cc_start: 0.9052 (mmm) cc_final: 0.8798 (mmp)
REVERT: A  495 TYR cc_start: 0.4381 (OUTLIER) cc_final: 0.2664 (m-80)
REVERT: A  597 MET cc_start: 0.8751 (tmm) cc_final: 0.8486 (tmm)
REVERT: A  726 GLN cc_start: 0.7991 (pp30) cc_final: 0.7690 (tm-30)
REVERT: A  743 MET cc_start: 0.8918 (mmt) cc_final: 0.8375 (mmm)
REVERT: A  875 ASN cc_start: 0.9109 (OUTLIER) cc_final: 0.8834 (m-40)
REVERT: A  963 TYR cc_start: 0.8843 (OUTLIER) cc_final: 0.7900 (t80)
  outliers start: 19
  outliers final: 9
  residues processed: 65
  average time/residue: 0.0748
  time to fit residues: 7.4415
Evaluate side-chains
  61 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  266 GLU
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  493 THR
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  875 ASN
Chi-restraints excluded: chain A residue  963 TYR
Chi-restraints excluded: chain A residue 1029 PHE
Chi-restraints excluded: chain A residue 1064 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 90 optimal weight:    0.6980
   chunk 81 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 80 optimal weight:    1.9990
   chunk 35 optimal weight:    5.9990
   chunk 0 optimal weight:    6.9990
   chunk 102 optimal weight:   10.0000
   chunk 72 optimal weight:    0.9980
   chunk 57 optimal weight:    0.1980
   chunk 5 optimal weight:    5.9990
   chunk 8 optimal weight:    4.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 244 HIS
A 341 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.097848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.075170 restraints weight = 26675.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.077021 restraints weight = 14608.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.078241 restraints weight = 9526.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.079052 restraints weight = 7057.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.079595 restraints weight = 5714.721|
|-----------------------------------------------------------------------------|
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3284
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3284 r_free = 0.3284    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3284 r_free = 0.3284    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3284
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.2213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9615  Z= 0.092
  Angle     :  0.521  13.109  13391  Z= 0.254
  Chirality :  0.038   0.167   1577
  Planarity :  0.004   0.040   1461
  Dihedral  : 10.550 149.071   1952
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 13.86 %
    Favored  : 83.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.61 (0.27), residues: 982
  helix:  0.53 (0.26), residues: 446
  sheet: -0.10 (0.52), residues: 111
  loop : -1.49 (0.27), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 144 
 TYR   0.011   0.001   TYR A 230 
 PHE   0.008   0.001   PHE A 950 
 TRP   0.009   0.001   TRP A 542 
 HIS   0.002   0.000   HIS A 145 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00200 /  0.09 ( 9614)
  covalent geometry    : angle       0.52070 /  0.25 (13391)
  hydrogen bonds       : bond        0.03047 /  1.96 (  369)
  hydrogen bonds       : angle       3.82407 /  2.68 ( 1013)
  Misc. bond           : bond        0.00058 /  0.03 (    1)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 55
  time to evaluate  : 0.265 
Fit side-chains
REVERT: A  160 GLN cc_start: 0.8515 (pt0) cc_final: 0.8280 (pt0)
REVERT: A  263 ASN cc_start: 0.7864 (t0) cc_final: 0.7585 (t0)
REVERT: A  495 TYR cc_start: 0.4283 (OUTLIER) cc_final: 0.2587 (m-80)
REVERT: A  597 MET cc_start: 0.8716 (tmm) cc_final: 0.8446 (tmm)
REVERT: A  726 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7713 (tm-30)
REVERT: A  743 MET cc_start: 0.8813 (mmt) cc_final: 0.8402 (mmm)
REVERT: A  963 TYR cc_start: 0.8820 (OUTLIER) cc_final: 0.7874 (t80)
REVERT: A 1052 VAL cc_start: 0.8095 (t) cc_final: 0.7861 (t)
  outliers start: 18
  outliers final: 6
  residues processed: 66
  average time/residue: 0.0631
  time to fit residues: 6.3065
Evaluate side-chains
  60 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  266 GLU
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  493 THR
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  726 GLN
Chi-restraints excluded: chain A residue  963 TYR
Chi-restraints excluded: chain A residue 1064 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 86 optimal weight:    5.9990
   chunk 82 optimal weight:    0.9990
   chunk 27 optimal weight:    0.1980
   chunk 32 optimal weight:    0.6980
   chunk 52 optimal weight:    7.9990
   chunk 77 optimal weight:    5.9990
   chunk 7 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.7182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.097954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.075245 restraints weight = 26470.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.077071 restraints weight = 14544.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.078302 restraints weight = 9560.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.079087 restraints weight = 7071.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.079648 restraints weight = 5754.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3285
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3285 r_free = 0.3285    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3285 r_free = 0.3285    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3285
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.2369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9615  Z= 0.092
  Angle     :  0.521  14.235  13391  Z= 0.253
  Chirality :  0.038   0.163   1577
  Planarity :  0.004   0.040   1461
  Dihedral  : 10.453 149.442   1948
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 14.34 %
    Favored  : 84.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.45 (0.27), residues: 982
  helix:  0.70 (0.26), residues: 447
  sheet: -0.00 (0.52), residues: 111
  loop : -1.46 (0.27), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 144 
 TYR   0.011   0.001   TYR A 230 
 PHE   0.009   0.001   PHE A 986 
 TRP   0.008   0.001   TRP A 542 
 HIS   0.003   0.000   HIS A1006 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00201 /  0.09 ( 9614)
  covalent geometry    : angle       0.52065 /  0.25 (13391)
  hydrogen bonds       : bond        0.03012 /  1.96 (  369)
  hydrogen bonds       : angle       3.73148 /  2.60 ( 1013)
  Misc. bond           : bond        0.00058 /  0.03 (    1)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 54
  time to evaluate  : 0.280 
Fit side-chains
REVERT: A  160 GLN cc_start: 0.8515 (pt0) cc_final: 0.8197 (pt0)
REVERT: A  263 ASN cc_start: 0.7740 (t0) cc_final: 0.7525 (t0)
REVERT: A  495 TYR cc_start: 0.4285 (OUTLIER) cc_final: 0.2691 (m-80)
REVERT: A  597 MET cc_start: 0.8709 (tmm) cc_final: 0.8428 (tmm)
REVERT: A  726 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7739 (tm-30)
REVERT: A  743 MET cc_start: 0.8830 (mmt) cc_final: 0.8382 (mmm)
REVERT: A  947 MET cc_start: 0.7960 (ttp) cc_final: 0.7644 (ttp)
REVERT: A  963 TYR cc_start: 0.8895 (OUTLIER) cc_final: 0.7869 (t80)
REVERT: A 1052 VAL cc_start: 0.8061 (t) cc_final: 0.7805 (t)
  outliers start: 12
  outliers final: 9
  residues processed: 60
  average time/residue: 0.0623
  time to fit residues: 5.7151
Evaluate side-chains
  61 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  266 GLU
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  493 THR
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  726 GLN
Chi-restraints excluded: chain A residue  963 TYR
Chi-restraints excluded: chain A residue 1029 PHE
Chi-restraints excluded: chain A residue 1064 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 3 optimal weight:    7.9990
   chunk 32 optimal weight:    1.9990
   chunk 2 optimal weight:    8.9990
   chunk 44 optimal weight:    0.7980
   chunk 101 optimal weight:   10.0000
   chunk 26 optimal weight:    3.9990
   chunk 73 optimal weight:    0.0980
   chunk 57 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 80 optimal weight:    4.9990
   overall best weight:    2.1786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  76 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.094847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.072831 restraints weight = 26153.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.074707 restraints weight = 14460.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.075178 restraints weight = 8712.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.075359 restraints weight = 7938.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.075416 restraints weight = 7275.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3193
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3193 r_free = 0.3193    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3193 r_free = 0.3193    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3193
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.2401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9615  Z= 0.170
  Angle     :  0.584  14.236  13391  Z= 0.289
  Chirality :  0.041   0.153   1577
  Planarity :  0.004   0.050   1461
  Dihedral  : 10.641 147.372   1948
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 14.70 %
    Favored  : 83.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.54 (0.27), residues: 982
  helix:  0.62 (0.26), residues: 446
  sheet: -0.17 (0.53), residues: 113
  loop : -1.47 (0.28), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 144 
 TYR   0.022   0.002   TYR A 230 
 PHE   0.012   0.001   PHE A 544 
 TRP   0.008   0.001   TRP A 198 
 HIS   0.003   0.001   HIS A 312 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00394 /  0.17 ( 9614)
  covalent geometry    : angle       0.58417 /  0.29 (13391)
  hydrogen bonds       : bond        0.03939 /  2.58 (  369)
  hydrogen bonds       : angle       4.02943 /  2.82 ( 1013)
  Misc. bond           : bond        0.00054 /  0.03 (    1)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 49
  time to evaluate  : 0.308 
Fit side-chains
REVERT: A  160 GLN cc_start: 0.8541 (pt0) cc_final: 0.8278 (pt0)
REVERT: A  263 ASN cc_start: 0.7935 (t0) cc_final: 0.7720 (t0)
REVERT: A  278 ASP cc_start: 0.7536 (p0) cc_final: 0.7136 (p0)
REVERT: A  495 TYR cc_start: 0.4997 (OUTLIER) cc_final: 0.3097 (m-80)
REVERT: A  597 MET cc_start: 0.8796 (tmm) cc_final: 0.8552 (tmm)
REVERT: A  726 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7830 (tm-30)
REVERT: A  743 MET cc_start: 0.8913 (mmt) cc_final: 0.8369 (mmm)
REVERT: A  947 MET cc_start: 0.8109 (ttp) cc_final: 0.7838 (ttp)
REVERT: A  963 TYR cc_start: 0.9049 (OUTLIER) cc_final: 0.7908 (t80)
  outliers start: 13
  outliers final: 8
  residues processed: 56
  average time/residue: 0.0683
  time to fit residues: 5.9393
Evaluate side-chains
  59 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  414 ILE
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  493 THR
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  726 GLN
Chi-restraints excluded: chain A residue  963 TYR
Chi-restraints excluded: chain A residue 1064 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 94 optimal weight:    0.9990
   chunk 78 optimal weight:    2.9990
   chunk 34 optimal weight:    0.3980
   chunk 62 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   chunk 81 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 86 optimal weight:    6.9990
   overall best weight:    0.6380

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.097359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.075542 restraints weight = 26424.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.077683 restraints weight = 14677.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.078188 restraints weight = 8693.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.078263 restraints weight = 7683.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.078315 restraints weight = 7295.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3250
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3250 r_free = 0.3250    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3250 r_free = 0.3250    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3250
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
moved from start:          0.2509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9615  Z= 0.093
  Angle     :  0.533  15.283  13391  Z= 0.261
  Chirality :  0.038   0.158   1577
  Planarity :  0.004   0.043   1461
  Dihedral  : 10.512 147.561   1948
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 15.18 %
    Favored  : 83.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.42 (0.27), residues: 982
  helix:  0.72 (0.26), residues: 448
  sheet: -0.01 (0.53), residues: 109
  loop : -1.43 (0.28), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 144 
 TYR   0.012   0.001   TYR A 230 
 PHE   0.010   0.001   PHE A 986 
 TRP   0.008   0.001   TRP A 542 
 HIS   0.002   0.000   HIS A 312 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00200 /  0.09 ( 9614)
  covalent geometry    : angle       0.53321 /  0.26 (13391)
  hydrogen bonds       : bond        0.03155 /  2.01 (  369)
  hydrogen bonds       : angle       3.85123 /  2.69 ( 1013)
  Misc. bond           : bond        0.00059 /  0.03 (    1)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.294 
Fit side-chains
REVERT: A  160 GLN cc_start: 0.8562 (pt0) cc_final: 0.8194 (pt0)
REVERT: A  263 ASN cc_start: 0.7846 (t0) cc_final: 0.7620 (t0)
REVERT: A  495 TYR cc_start: 0.4667 (OUTLIER) cc_final: 0.2812 (m-80)
REVERT: A  597 MET cc_start: 0.8818 (tmm) cc_final: 0.8556 (tmm)
REVERT: A  726 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7916 (tm-30)
REVERT: A  743 MET cc_start: 0.8827 (mmt) cc_final: 0.8371 (mmm)
REVERT: A  947 MET cc_start: 0.8101 (ttp) cc_final: 0.7826 (ttp)
REVERT: A  963 TYR cc_start: 0.9001 (OUTLIER) cc_final: 0.7830 (t80)
  outliers start: 12
  outliers final: 9
  residues processed: 56
  average time/residue: 0.0637
  time to fit residues: 5.7077
Evaluate side-chains
  60 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  493 THR
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  726 GLN
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain A residue  963 TYR
Chi-restraints excluded: chain A residue 1029 PHE
Chi-restraints excluded: chain A residue 1064 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 47 optimal weight:    6.9990
   chunk 97 optimal weight:    0.0970
   chunk 93 optimal weight:    2.9990
   chunk 100 optimal weight:   10.0000
   chunk 50 optimal weight:    0.0370
   chunk 73 optimal weight:    2.9990
   chunk 96 optimal weight:    6.9990
   chunk 89 optimal weight:    8.9990
   chunk 48 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   overall best weight:    1.1460

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.096479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.074623 restraints weight = 26095.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.076057 restraints weight = 14351.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.076724 restraints weight = 10383.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.076960 restraints weight = 8095.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.077059 restraints weight = 7924.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3229
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3229 r_free = 0.3229    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3229 r_free = 0.3229    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3229
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.2548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9615  Z= 0.109
  Angle     :  0.540  15.500  13391  Z= 0.263
  Chirality :  0.039   0.152   1577
  Planarity :  0.004   0.045   1461
  Dihedral  : 10.519 147.669   1948
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 14.94 %
    Favored  : 83.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.39 (0.27), residues: 982
  helix:  0.78 (0.26), residues: 448
  sheet: -0.02 (0.53), residues: 111
  loop : -1.46 (0.28), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 144 
 TYR   0.014   0.001   TYR A 230 
 PHE   0.010   0.001   PHE A 986 
 TRP   0.008   0.001   TRP A 542 
 HIS   0.003   0.001   HIS A 145 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.11 ( 9614)
  covalent geometry    : angle       0.53974 /  0.26 (13391)
  hydrogen bonds       : bond        0.03274 /  2.10 (  369)
  hydrogen bonds       : angle       3.84640 /  2.69 ( 1013)
  Misc. bond           : bond        0.00056 /  0.03 (    1)

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

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

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1964 Ramachandran restraints generated.
    982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 50
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A  160 GLN cc_start: 0.8505 (pt0) cc_final: 0.8262 (pt0)
REVERT: A  263 ASN cc_start: 0.7814 (t0) cc_final: 0.7493 (t0)
REVERT: A  495 TYR cc_start: 0.4822 (OUTLIER) cc_final: 0.2919 (m-80)
REVERT: A  597 MET cc_start: 0.8774 (tmm) cc_final: 0.8518 (tmm)
REVERT: A  726 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7848 (tm-30)
REVERT: A  743 MET cc_start: 0.8819 (mmt) cc_final: 0.8348 (mmm)
REVERT: A  963 TYR cc_start: 0.9045 (OUTLIER) cc_final: 0.7904 (t80)
  outliers start: 13
  outliers final: 10
  residues processed: 58
  average time/residue: 0.0654
  time to fit residues: 6.0662
Evaluate side-chains
  61 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 48
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  414 ILE
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  493 THR
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  726 GLN
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain A residue  963 TYR
Chi-restraints excluded: chain A residue 1029 PHE
Chi-restraints excluded: chain A residue 1064 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 100 optimal weight:   10.0000
   chunk 17 optimal weight:    6.9990
   chunk 18 optimal weight:    3.9990
   chunk 93 optimal weight:    0.0070
   chunk 7 optimal weight:    0.9980
   chunk 79 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9990
   chunk 91 optimal weight:    0.8980
   chunk 104 optimal weight:   10.0000
   overall best weight:    0.6798

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.098355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.076893 restraints weight = 26510.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.078786 restraints weight = 14212.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.079282 restraints weight = 8857.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.079401 restraints weight = 7610.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.079453 restraints weight = 7230.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3286
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3286 r_free = 0.3286    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3286 r_free = 0.3286    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3286
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.2680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9615  Z= 0.092
  Angle     :  0.538  15.783  13391  Z= 0.261
  Chirality :  0.038   0.152   1577
  Planarity :  0.004   0.042   1461
  Dihedral  : 10.457 148.282   1948
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 15.06 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.30 (0.27), residues: 982
  helix:  0.88 (0.26), residues: 451
  sheet: -0.00 (0.53), residues: 111
  loop : -1.46 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 144 
 TYR   0.013   0.001   TYR A 212 
 PHE   0.010   0.001   PHE A 986 
 TRP   0.009   0.001   TRP A 542 
 HIS   0.002   0.000   HIS A 145 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00202 /  0.09 ( 9614)
  covalent geometry    : angle       0.53762 /  0.26 (13391)
  hydrogen bonds       : bond        0.02962 /  1.90 (  369)
  hydrogen bonds       : angle       3.75306 /  2.62 ( 1013)
  Misc. bond           : bond        0.00057 /  0.03 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1248.66 seconds
wall clock time: 22 minutes 9.58 seconds (1329.58 seconds total)