Starting phenix.real_space_refine
on Wed Feb  4 08:15:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xjz_33238/02_2026/7xjz_33238.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xjz_33238/02_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xjz_33238/02_2026/7xjz_33238.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xjz_33238/02_2026/7xjz_33238.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xjz_33238/02_2026/7xjz_33238.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xjz_33238/02_2026/7xjz_33238.map"
  }
  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-2.0-5952/lib/python3.9/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: 3.59, per 1000 atoms: 0.39
  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: 0.70
  Conformation dependent library (CDL) restraints added in 706.9 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: 1.02
  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: 1.78

  Time building geometry restraints manager: 0.94 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: 5582
       30.00 -    60.00: 244
       60.00 -    90.00: 66
       90.00 -   120.00: 2
      120.00 -   150.00: 1
  Dihedral angle restraints: 5895
    sinusoidal: 3037
      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 5892 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:             1.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     12.070
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
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  : 16.502 149.999   4047
  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
  covalent geometry    : bond        0.00366 ( 9614)
  covalent geometry    : angle       0.59082 (13391)
  hydrogen bonds       : bond        0.16244 (  369)
  hydrogen bonds       : angle       7.42555 ( 1013)
  Misc. bond           : bond        0.17590 (    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  : 0.266 
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: 0.1043
  time to fit residues: 15.5548
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  : 0.289 
-------------------------------------------------------------------------------
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:    9.9990
   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...

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3670 r_free = 0.3670 target = 0.098355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.076382 restraints weight = 26354.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.077911 restraints weight = 13870.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.078597 restraints weight = 9806.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.079201 restraints weight = 7486.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.079273 restraints weight = 7230.827|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
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 |
|-----------------------------------------------------------------------------|
r_final: 0.3264
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.1276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9615  Z= 0.111
  Angle     :  0.554   8.559  13391  Z= 0.280
  Chirality :  0.040   0.149   1577
  Planarity :  0.004   0.040   1461
  Dihedral  : 17.738 150.025   2215
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 12.17 %
    Favored  : 85.06 %
  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: -0.97 (0.27), residues: 982
  helix:  0.15 (0.26), residues: 448
  sheet: -0.08 (0.53), residues: 110
  loop : -1.64 (0.27), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 144 
 TYR   0.012   0.001   TYR A 230 
 PHE   0.024   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
  covalent geometry    : bond        0.00234 ( 9614)
  covalent geometry    : angle       0.55370 (13391)
  hydrogen bonds       : bond        0.03987 (  369)
  hydrogen bonds       : angle       4.20693 ( 1013)
  Misc. bond           : bond        0.00099 (    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  : 0.281 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 MET cc_start: 0.7859 (mtm) cc_final: 0.7634 (mtp)
REVERT: A  237 MET cc_start: 0.8253 (ttt) cc_final: 0.8000 (ttt)
REVERT: A  263 ASN cc_start: 0.7890 (t0) cc_final: 0.7547 (t0)
REVERT: A  267 MET cc_start: 0.8974 (mmm) cc_final: 0.8722 (mmp)
REVERT: A  495 TYR cc_start: 0.4294 (OUTLIER) cc_final: 0.2740 (m-80)
REVERT: A  597 MET cc_start: 0.8664 (tmm) cc_final: 0.8456 (tmm)
REVERT: A  653 ASP cc_start: 0.7875 (p0) cc_final: 0.7584 (t0)
REVERT: A  714 MET cc_start: 0.8401 (tmm) cc_final: 0.8087 (tmm)
REVERT: A  726 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7665 (pp30)
REVERT: A  775 MET cc_start: 0.8104 (tmm) cc_final: 0.7896 (tmm)
REVERT: A  793 MET cc_start: 0.8762 (mmm) cc_final: 0.8451 (mmm)
REVERT: A  875 ASN cc_start: 0.9054 (OUTLIER) cc_final: 0.8792 (m-40)
REVERT: A  906 GLN cc_start: 0.8028 (tm-30) cc_final: 0.7766 (tm-30)
REVERT: A  963 TYR cc_start: 0.8748 (OUTLIER) cc_final: 0.8063 (t80)
  outliers start: 23
  outliers final: 8
  residues processed: 77
  average time/residue: 0.0771
  time to fit residues: 8.7691
Evaluate side-chains
  67 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 55
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 54 optimal weight:    0.7980
   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:    4.9990
   chunk 77 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 149 GLN
** A 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.096736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.075079 restraints weight = 26855.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.076193 restraints weight = 14195.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.076972 restraints weight = 10536.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.077201 restraints weight = 8324.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.077292 restraints weight = 7986.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3216
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3216 r_free = 0.3216    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3216 r_free = 0.3216    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3216
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.1629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9615  Z= 0.143
  Angle     :  0.554   7.257  13391  Z= 0.280
  Chirality :  0.040   0.169   1577
  Planarity :  0.004   0.046   1461
  Dihedral  : 17.611 148.639   2211
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 12.89 %
    Favored  : 84.70 %
  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: -0.92 (0.27), residues: 982
  helix:  0.23 (0.26), residues: 445
  sheet: -0.16 (0.53), residues: 112
  loop : -1.63 (0.27), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 144 
 TYR   0.018   0.001   TYR A 230 
 PHE   0.011   0.001   PHE A 544 
 TRP   0.007   0.001   TRP A 198 
 HIS   0.003   0.001   HIS A 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 9614)
  covalent geometry    : angle       0.55426 (13391)
  hydrogen bonds       : bond        0.03980 (  369)
  hydrogen bonds       : angle       4.19244 ( 1013)
  Misc. bond           : bond        0.00057 (    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
  72 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 52
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
REVERT: A  263 ASN cc_start: 0.8024 (t0) cc_final: 0.7779 (t0)
REVERT: A  267 MET cc_start: 0.9033 (mmm) cc_final: 0.8830 (mmp)
REVERT: A  495 TYR cc_start: 0.4319 (OUTLIER) cc_final: 0.2525 (m-80)
REVERT: A  597 MET cc_start: 0.8772 (tmm) cc_final: 0.8537 (tmm)
REVERT: A  653 ASP cc_start: 0.7899 (p0) cc_final: 0.7671 (t0)
REVERT: A  793 MET cc_start: 0.8899 (mmm) cc_final: 0.8548 (mmm)
REVERT: A  875 ASN cc_start: 0.9095 (OUTLIER) cc_final: 0.8807 (m-40)
REVERT: A  963 TYR cc_start: 0.8830 (OUTLIER) cc_final: 0.7931 (t80)
  outliers start: 20
  outliers final: 10
  residues processed: 67
  average time/residue: 0.0836
  time to fit residues: 8.4196
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  : 0.319 
-------------------------------------------------------------------------------
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  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:    0.7980
   chunk 19 optimal weight:    0.8980
   chunk 67 optimal weight:    4.9990
   chunk 77 optimal weight:    8.9990
   chunk 93 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9980
   chunk 1 optimal weight:    6.9990
   chunk 62 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 906 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 = 0.3642 r_free = 0.3642 target = 0.096809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.074027 restraints weight = 26685.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.075826 restraints weight = 14613.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.077068 restraints weight = 9606.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.077907 restraints weight = 7079.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.078372 restraints weight = 5714.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3258
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3258 r_free = 0.3258    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 = 0.3258 r_free = 0.3258    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3258
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.1819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.053   9615  Z= 0.111
  Angle     :  0.548  16.987  13391  Z= 0.269
  Chirality :  0.039   0.164   1577
  Planarity :  0.004   0.044   1461
  Dihedral  : 17.517 148.537   2210
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 13.49 %
    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: -0.88 (0.27), residues: 982
  helix:  0.29 (0.26), residues: 445
  sheet: -0.24 (0.53), residues: 112
  loop : -1.60 (0.27), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 144 
 TYR   0.014   0.001   TYR A 230 
 PHE   0.008   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
  covalent geometry    : bond        0.00249 ( 9614)
  covalent geometry    : angle       0.54812 (13391)
  hydrogen bonds       : bond        0.03426 (  369)
  hydrogen bonds       : angle       4.03417 ( 1013)
  Misc. bond           : bond        0.00052 (    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
  68 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 52
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
REVERT: A  263 ASN cc_start: 0.7781 (t0) cc_final: 0.7505 (t0)
REVERT: A  495 TYR cc_start: 0.4356 (OUTLIER) cc_final: 0.2659 (m-80)
REVERT: A  597 MET cc_start: 0.8731 (tmm) cc_final: 0.8514 (tmm)
REVERT: A  653 ASP cc_start: 0.7909 (p0) cc_final: 0.7688 (t0)
REVERT: A  726 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7705 (tm-30)
REVERT: A  743 MET cc_start: 0.8757 (mmt) cc_final: 0.8399 (mmm)
REVERT: A  793 MET cc_start: 0.8811 (mmm) cc_final: 0.8498 (mmm)
REVERT: A  875 ASN cc_start: 0.9098 (OUTLIER) cc_final: 0.8827 (m-40)
REVERT: A  963 TYR cc_start: 0.8832 (OUTLIER) cc_final: 0.7925 (t80)
  outliers start: 16
  outliers final: 8
  residues processed: 63
  average time/residue: 0.0849
  time to fit residues: 8.0778
Evaluate side-chains
  62 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 50
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
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  741 ASP
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:    1.9990
   chunk 68 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 71 optimal weight:    0.7980
   chunk 87 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   chunk 34 optimal weight:    0.5980
   chunk 97 optimal weight:    0.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3655 r_free = 0.3655 target = 0.097488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.074807 restraints weight = 26626.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.076667 restraints weight = 14648.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.077903 restraints weight = 9538.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.078720 restraints weight = 7052.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.079287 restraints weight = 5699.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3279
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3279 r_free = 0.3279    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 = 0.3279 r_free = 0.3279    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3279
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.2035

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= 0.096
  Angle     :  0.516  11.714  13391  Z= 0.253
  Chirality :  0.038   0.166   1577
  Planarity :  0.004   0.041   1461
  Dihedral  : 17.425 148.895   2210
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 13.01 %
    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: -0.75 (0.27), residues: 982
  helix:  0.39 (0.26), residues: 447
  sheet: -0.15 (0.53), residues: 111
  loop : -1.54 (0.27), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 144 
 TYR   0.012   0.001   TYR A 230 
 PHE   0.008   0.001   PHE A 950 
 TRP   0.008   0.001   TRP A 542 
 HIS   0.002   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 ( 9614)
  covalent geometry    : angle       0.51632 (13391)
  hydrogen bonds       : bond        0.03193 (  369)
  hydrogen bonds       : angle       3.89339 ( 1013)
  Misc. bond           : bond        0.00054 (    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
  75 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 55
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
REVERT: A  495 TYR cc_start: 0.4386 (OUTLIER) cc_final: 0.2643 (m-80)
REVERT: A  597 MET cc_start: 0.8738 (tmm) cc_final: 0.8479 (tmm)
REVERT: A  726 GLN cc_start: 0.7961 (pp30) cc_final: 0.7650 (tm-30)
REVERT: A  793 MET cc_start: 0.8776 (mmm) cc_final: 0.8468 (mmm)
REVERT: A  875 ASN cc_start: 0.9093 (OUTLIER) cc_final: 0.8844 (m-40)
REVERT: A  906 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7624 (tm-30)
REVERT: A  963 TYR cc_start: 0.8832 (OUTLIER) cc_final: 0.7896 (t80)
REVERT: A 1052 VAL cc_start: 0.8124 (t) cc_final: 0.7880 (t)
  outliers start: 20
  outliers final: 11
  residues processed: 70
  average time/residue: 0.0885
  time to fit residues: 9.1457
Evaluate side-chains
  64 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 49
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
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  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  875 ASN
Chi-restraints excluded: chain A residue  906 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 90 optimal weight:    0.1980
   chunk 81 optimal weight:    0.6980
   chunk 20 optimal weight:    3.9990
   chunk 80 optimal weight:    6.9990
   chunk 35 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 102 optimal weight:   10.0000
   chunk 72 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 244 HIS
A 263 ASN
A 906 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.096803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.075114 restraints weight = 26449.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.076531 restraints weight = 14234.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.076982 restraints weight = 10584.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.077404 restraints weight = 8417.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.077534 restraints weight = 7902.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3240
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3240 r_free = 0.3240    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 = 0.3240 r_free = 0.3240    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3240
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.2139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9615  Z= 0.110
  Angle     :  0.525  11.129  13391  Z= 0.258
  Chirality :  0.039   0.162   1577
  Planarity :  0.004   0.043   1461
  Dihedral  : 17.390 148.826   2208
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 13.25 %
    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: -0.69 (0.27), residues: 982
  helix:  0.44 (0.26), residues: 446
  sheet: -0.13 (0.52), residues: 111
  loop : -1.51 (0.27), residues: 425

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   0.017   0.001   PHE A 907 
 TRP   0.008   0.001   TRP A 542 
 HIS   0.002   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 9614)
  covalent geometry    : angle       0.52524 (13391)
  hydrogen bonds       : bond        0.03288 (  369)
  hydrogen bonds       : angle       3.88378 ( 1013)
  Misc. bond           : bond        0.00055 (    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
  74 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 51
  time to evaluate  : 0.327 
Fit side-chains
REVERT: A   93 MET cc_start: 0.8127 (pmm) cc_final: 0.7900 (ptp)
REVERT: A  160 GLN cc_start: 0.8552 (pt0) cc_final: 0.8173 (pt0)
REVERT: A  495 TYR cc_start: 0.4474 (OUTLIER) cc_final: 0.2704 (m-80)
REVERT: A  597 MET cc_start: 0.8737 (tmm) cc_final: 0.8490 (tmm)
REVERT: A  726 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7732 (tm-30)
REVERT: A  743 MET cc_start: 0.8807 (mmt) cc_final: 0.8399 (mmm)
REVERT: A  775 MET cc_start: 0.8579 (tmm) cc_final: 0.8358 (tmm)
REVERT: A  793 MET cc_start: 0.8845 (mmm) cc_final: 0.8594 (mmm)
REVERT: A  875 ASN cc_start: 0.9027 (OUTLIER) cc_final: 0.8815 (m-40)
REVERT: A  963 TYR cc_start: 0.8869 (OUTLIER) cc_final: 0.7943 (t80)
  outliers start: 23
  outliers final: 12
  residues processed: 67
  average time/residue: 0.0785
  time to fit residues: 8.1282
Evaluate side-chains
  66 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 50
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
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  263 ASN
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  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 1029 PHE
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:    0.0050
   chunk 5 optimal weight:    7.9990
   chunk 86 optimal weight:    9.9990
   chunk 82 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   chunk 52 optimal weight:    7.9990
   chunk 77 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.6596

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

Flipped N/Q/H residues before XYZ refinement:
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 263 ASN
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 = 0.098014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.075369 restraints weight = 26685.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.077247 restraints weight = 14598.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.078485 restraints weight = 9488.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.079279 restraints weight = 7001.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.079854 restraints weight = 5671.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3289
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3289 r_free = 0.3289    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 = 0.3289 r_free = 0.3289    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3289
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.2315

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= 0.090
  Angle     :  0.518   9.642  13391  Z= 0.253
  Chirality :  0.038   0.162   1577
  Planarity :  0.004   0.039   1461
  Dihedral  : 17.344 149.181   2208
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 14.46 %
    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: -0.54 (0.27), residues: 982
  helix:  0.60 (0.26), residues: 446
  sheet: -0.06 (0.52), residues: 111
  loop : -1.47 (0.28), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 144 
 TYR   0.011   0.001   TYR A 230 
 PHE   0.033   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
  covalent geometry    : bond        0.00193 ( 9614)
  covalent geometry    : angle       0.51793 (13391)
  hydrogen bonds       : bond        0.03019 (  369)
  hydrogen bonds       : angle       3.78815 ( 1013)
  Misc. bond           : bond        0.00056 (    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
  70 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 53
  time to evaluate  : 0.344 
Fit side-chains
REVERT: A  160 GLN cc_start: 0.8530 (pt0) cc_final: 0.8284 (pt0)
REVERT: A  495 TYR cc_start: 0.4276 (OUTLIER) cc_final: 0.2612 (m-80)
REVERT: A  597 MET cc_start: 0.8730 (tmm) cc_final: 0.8477 (tmm)
REVERT: A  726 GLN cc_start: 0.7946 (pp30) cc_final: 0.7701 (tm-30)
REVERT: A  743 MET cc_start: 0.8752 (mmt) cc_final: 0.8353 (mmm)
REVERT: A  775 MET cc_start: 0.8521 (tmm) cc_final: 0.8308 (tmm)
REVERT: A  875 ASN cc_start: 0.9070 (OUTLIER) cc_final: 0.8869 (m-40)
REVERT: A  963 TYR cc_start: 0.8907 (OUTLIER) cc_final: 0.7859 (t80)
  outliers start: 17
  outliers final: 12
  residues processed: 66
  average time/residue: 0.0828
  time to fit residues: 8.3098
Evaluate side-chains
  65 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 50
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
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  263 ASN
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  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:    2.9990
   chunk 32 optimal weight:    0.2980
   chunk 2 optimal weight:    0.0000
   chunk 44 optimal weight:    0.9980
   chunk 101 optimal weight:   10.0000
   chunk 26 optimal weight:    3.9990
   chunk 73 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 6 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   overall best weight:    0.6586

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
A 263 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.098670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.076996 restraints weight = 26701.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.078528 restraints weight = 14241.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.079000 restraints weight = 10299.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.079218 restraints weight = 8048.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.079317 restraints weight = 7765.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3257
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3257 r_free = 0.3257    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 = 0.3257 r_free = 0.3257    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3257
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.2417

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= 0.090
  Angle     :  0.514   9.099  13391  Z= 0.251
  Chirality :  0.038   0.164   1577
  Planarity :  0.004   0.040   1461
  Dihedral  : 17.315 149.461   2208
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 14.70 %
    Favored  : 83.13 %
  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:  0.69 (0.26), residues: 446
  sheet: -0.00 (0.52), residues: 111
  loop : -1.44 (0.28), 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   0.030   0.001   PHE A 986 
 TRP   0.008   0.001   TRP A 542 
 HIS   0.002   0.000   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00194 ( 9614)
  covalent geometry    : angle       0.51394 (13391)
  hydrogen bonds       : bond        0.02990 (  369)
  hydrogen bonds       : angle       3.73303 ( 1013)
  Misc. bond           : bond        0.00056 (    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
  72 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 54
  time to evaluate  : 0.272 
Fit side-chains
REVERT: A  160 GLN cc_start: 0.8590 (pt0) cc_final: 0.8243 (pt0)
REVERT: A  495 TYR cc_start: 0.4189 (OUTLIER) cc_final: 0.2536 (m-80)
REVERT: A  597 MET cc_start: 0.8754 (tmm) cc_final: 0.8488 (tmm)
REVERT: A  726 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7915 (tm-30)
REVERT: A  741 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.7785 (p0)
REVERT: A  743 MET cc_start: 0.8789 (mmt) cc_final: 0.8370 (mmm)
REVERT: A  775 MET cc_start: 0.8509 (tmm) cc_final: 0.8295 (tmm)
REVERT: A  875 ASN cc_start: 0.9094 (OUTLIER) cc_final: 0.8882 (m-40)
REVERT: A  963 TYR cc_start: 0.8900 (OUTLIER) cc_final: 0.7860 (t80)
  outliers start: 18
  outliers final: 10
  residues processed: 65
  average time/residue: 0.0851
  time to fit residues: 8.2138
Evaluate side-chains
  65 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 50
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
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  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  741 ASP
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 94 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9980
   chunk 34 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0040
   chunk 86 optimal weight:    0.9990
   overall best weight:    0.7392

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

Flipped N/Q/H residues before XYZ refinement:
A 263 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.097727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.076118 restraints weight = 26274.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.078185 restraints weight = 14189.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.078540 restraints weight = 8366.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.078677 restraints weight = 7463.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.078752 restraints weight = 7085.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
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 |
|-----------------------------------------------------------------------------|
r_final: 0.3264
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.2518

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= 0.094
  Angle     :  0.520   8.960  13391  Z= 0.255
  Chirality :  0.038   0.155   1577
  Planarity :  0.004   0.040   1461
  Dihedral  : 17.291 149.733   2208
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 15.18 %
    Favored  : 82.77 %
  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: -0.41 (0.27), residues: 982
  helix:  0.75 (0.26), residues: 449
  sheet:  0.02 (0.52), residues: 111
  loop : -1.46 (0.28), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 330 
 TYR   0.012   0.001   TYR A 212 
 PHE   0.023   0.001   PHE A 986 
 TRP   0.008   0.001   TRP A 542 
 HIS   0.002   0.000   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 ( 9614)
  covalent geometry    : angle       0.51997 (13391)
  hydrogen bonds       : bond        0.03023 (  369)
  hydrogen bonds       : angle       3.76055 ( 1013)
  Misc. bond           : bond        0.00057 (    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
  69 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 52
  time to evaluate  : 0.333 
Fit side-chains
REVERT: A  160 GLN cc_start: 0.8466 (pt0) cc_final: 0.8219 (pt0)
REVERT: A  495 TYR cc_start: 0.4391 (OUTLIER) cc_final: 0.2820 (m-80)
REVERT: A  597 MET cc_start: 0.8702 (tmm) cc_final: 0.8413 (tmm)
REVERT: A  726 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7754 (tm-30)
REVERT: A  741 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7642 (p0)
REVERT: A  743 MET cc_start: 0.8771 (mmt) cc_final: 0.8568 (mmt)
REVERT: A  775 MET cc_start: 0.8321 (tmm) cc_final: 0.7798 (tmm)
REVERT: A  963 TYR cc_start: 0.8967 (OUTLIER) cc_final: 0.7938 (t80)
  outliers start: 17
  outliers final: 11
  residues processed: 63
  average time/residue: 0.0767
  time to fit residues: 7.4616
Evaluate side-chains
  65 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 50
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
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  263 ASN
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  726 GLN
Chi-restraints excluded: chain A residue  741 ASP
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:    7.9990
   chunk 97 optimal weight:    0.5980
   chunk 93 optimal weight:    0.9980
   chunk 100 optimal weight:   10.0000
   chunk 50 optimal weight:    2.9990
   chunk 73 optimal weight:    0.7980
   chunk 96 optimal weight:    1.9990
   chunk 89 optimal weight:    6.9990
   chunk 48 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
A 263 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.097197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.075419 restraints weight = 26531.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.077119 restraints weight = 14823.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.077533 restraints weight = 9412.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.077742 restraints weight = 8367.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.077812 restraints weight = 7606.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3232
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3232 r_free = 0.3232    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 = 0.3232 r_free = 0.3232    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3232
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.2518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9615  Z= 0.126
  Angle     :  0.548   8.780  13391  Z= 0.270
  Chirality :  0.039   0.153   1577
  Planarity :  0.004   0.045   1461
  Dihedral  : 17.304 149.062   2206
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 15.18 %
    Favored  : 82.77 %
  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: -0.36 (0.27), residues: 982
  helix:  0.82 (0.26), residues: 447
  sheet: -0.01 (0.53), residues: 111
  loop : -1.45 (0.28), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 330 
 TYR   0.015   0.001   TYR A 230 
 PHE   0.026   0.001   PHE A 986 
 TRP   0.007   0.001   TRP A 542 
 HIS   0.002   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 9614)
  covalent geometry    : angle       0.54845 (13391)
  hydrogen bonds       : bond        0.03345 (  369)
  hydrogen bonds       : angle       3.80876 ( 1013)
  Misc. bond           : bond        0.00054 (    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
  64 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 47
  time to evaluate  : 0.340 
Fit side-chains
REVERT: A  160 GLN cc_start: 0.8484 (pt0) cc_final: 0.8229 (pt0)
REVERT: A  495 TYR cc_start: 0.4409 (OUTLIER) cc_final: 0.2638 (m-80)
REVERT: A  597 MET cc_start: 0.8712 (tmm) cc_final: 0.8456 (tmm)
REVERT: A  726 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7816 (tm-30)
REVERT: A  947 MET cc_start: 0.8008 (ttp) cc_final: 0.7803 (ttp)
REVERT: A  963 TYR cc_start: 0.9004 (OUTLIER) cc_final: 0.7970 (t80)
  outliers start: 17
  outliers final: 12
  residues processed: 58
  average time/residue: 0.0781
  time to fit residues: 7.1118
Evaluate side-chains
  62 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 47
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
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  263 ASN
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  726 GLN
Chi-restraints excluded: chain A residue  741 ASP
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:    0.0470
   chunk 100 optimal weight:   10.0000
   chunk 17 optimal weight:    7.9990
   chunk 18 optimal weight:    3.9990
   chunk 93 optimal weight:    0.2980
   chunk 7 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 104 optimal weight:   10.0000
   overall best weight:    1.0282

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

Flipped N/Q/H residues before XYZ refinement:
A 263 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.096854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.075020 restraints weight = 26127.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.077101 restraints weight = 14343.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.077529 restraints weight = 8394.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.077625 restraints weight = 7386.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.077693 restraints weight = 7101.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3240
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3240 r_free = 0.3240    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 = 0.3240 r_free = 0.3240    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3240
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.2552

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= 0.107
  Angle     :  0.556  15.582  13391  Z= 0.270
  Chirality :  0.039   0.153   1577
  Planarity :  0.004   0.045   1461
  Dihedral  : 17.301 148.961   2206
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 15.30 %
    Favored  : 82.89 %
  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: -0.33 (0.27), residues: 982
  helix:  0.84 (0.26), residues: 448
  sheet:  0.01 (0.53), residues: 111
  loop : -1.44 (0.28), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 330 
 TYR   0.014   0.001   TYR A 230 
 PHE   0.023   0.001   PHE A 986 
 TRP   0.007   0.001   TRP A 542 
 HIS   0.002   0.001   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 9614)
  covalent geometry    : angle       0.55635 (13391)
  hydrogen bonds       : bond        0.03233 (  369)
  hydrogen bonds       : angle       3.80660 ( 1013)
  Misc. bond           : bond        0.00055 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1488.58 seconds
wall clock time: 26 minutes 20.38 seconds (1580.38 seconds total)