Starting phenix.real_space_refine
on Tue Mar  3 17:26:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ktu_23030/03_2026/7ktu_23030.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ktu_23030/03_2026/7ktu_23030.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.15
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ktu_23030/03_2026/7ktu_23030.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ktu_23030/03_2026/7ktu_23030.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ktu_23030/03_2026/7ktu_23030.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ktu_23030/03_2026/7ktu_23030.map"
  }
  resolution = 4.15
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.031
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: 4
    Type Number    sf(0)   Gaussians
     S      43      5.16       5
     C    4671      2.51       5
     N    1373      2.21       5
     O    1490      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7577
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7577
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 995, 7577
          Classifications: {'peptide': 995}
          Link IDs: {'PTRANS': 35, 'TRANS': 959}
          Chain breaks: 1
  Time building chain proxies: 1.76, per 1000 atoms: 0.23
  Number of scatterers: 7577
  At special positions: 0
  Unit cell: (82.5, 98.175, 127.875, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      43     16.00
     O    1490      8.00
     N    1373      7.00
     C    4671      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.68
  Conformation dependent library (CDL) restraints added in 274.1 milliseconds
  

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1886

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 0 sheets defined
      86.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 30
      Proline residue:  A  15  - end of helix
      removed outlier: 3.601A  pdb=" N   HIS A  22 " --> pdb=" O   GLN A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 64
      removed outlier: 3.603A  pdb=" N   ALA A  46 " --> pdb=" O   ALA A  42 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ALA A  50 " --> pdb=" O   ALA A  46 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   VAL A  51 " --> pdb=" O   VAL A  47 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LEU A  54 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   VAL A  57 " --> pdb=" O   ASN A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 98
      removed outlier: 4.084A  pdb=" N   ASP A  73 " --> pdb=" O   ILE A  69 " (cutoff:3.500A)
      Proline residue:  A  75  - end of helix
      removed outlier: 3.771A  pdb=" N   ILE A  79 " --> pdb=" O   PRO A  75 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LYS A  80 " --> pdb=" O   PRO A  76 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   VAL A  81 " --> pdb=" O   ALA A  77 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLN A  90 " --> pdb=" O   THR A  86 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   GLN A  96 " --> pdb=" O   ALA A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 106
    Processing helix  chain 'A' and resid 108 through 151
      removed outlier: 3.610A  pdb=" N   ILE A 115 " --> pdb=" O   GLY A 111 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   LEU A 116 " --> pdb=" O   SER A 112 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   ALA A 129 " --> pdb=" O   THR A 125 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   ILE A 134 " --> pdb=" O   GLU A 130 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   ILE A 135 " --> pdb=" O   VAL A 131 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   ARG A 136 " --> pdb=" O   ARG A 132 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   VAL A 137 " --> pdb=" O   LYS A 133 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   VAL A 151 " --> pdb=" O   VAL A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 182
      removed outlier: 3.855A  pdb=" N   LEU A 157 " --> pdb=" O   THR A 153 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   VAL A 158 " --> pdb=" O   MET A 154 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   THR A 159 " --> pdb=" O   GLU A 155 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   GLY A 165 " --> pdb=" O   THR A 161 " (cutoff:3.500A)
      Proline residue:  A 166  - end of helix
      removed outlier: 3.759A  pdb=" N   LYS A 170 " --> pdb=" O   PRO A 166 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   GLU A 177 " --> pdb=" O   LYS A 173 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   GLN A 180 " --> pdb=" O   ASP A 176 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   GLU A 181 " --> pdb=" O   GLU A 177 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LEU A 182 " --> pdb=" O   ARG A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 201
      removed outlier: 3.847A  pdb=" N   MET A 190 " --> pdb=" O   GLU A 186 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   LEU A 191 " --> pdb=" O   HIS A 187 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   VAL A 192 " --> pdb=" O   ARG A 188 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   SER A 194 " --> pdb=" O   MET A 190 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   THR A 197 " --> pdb=" O   ASN A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 214
    Processing helix  chain 'A' and resid 215 through 217
      No H-bonds generated for 'chain 'A' and resid 215 through 217'
    Processing helix  chain 'A' and resid 224 through 250
      removed outlier: 4.290A  pdb=" N   LYS A 228 " --> pdb=" O   GLU A 224 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   ASN A 229 " --> pdb=" O   GLU A 225 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   THR A 233 " --> pdb=" O   ASN A 229 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ARG A 246 " --> pdb=" O   ASN A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 259
    Processing helix  chain 'A' and resid 260 through 286
      removed outlier: 4.270A  pdb=" N   SER A 272 " --> pdb=" O   ARG A 268 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ASP A 274 " --> pdb=" O   LEU A 270 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   SER A 275 " --> pdb=" O   ALA A 271 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   ASN A 278 " --> pdb=" O   ASP A 274 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   GLN A 279 " --> pdb=" O   SER A 275 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   GLY A 282 " --> pdb=" O   ASN A 278 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   TRP A 283 " --> pdb=" O   GLN A 279 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LEU A 284 " --> pdb=" O   ALA A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 310
      removed outlier: 3.867A  pdb=" N   GLN A 301 " --> pdb=" O   GLN A 297 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LEU A 303 " --> pdb=" O   ILE A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 342
      removed outlier: 3.785A  pdb=" N   ARG A 319 " --> pdb=" O   GLY A 315 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ILE A 321 " --> pdb=" O   GLU A 317 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   LEU A 322 " --> pdb=" O   ARG A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 358
    Processing helix  chain 'A' and resid 359 through 390
      removed outlier: 3.814A  pdb=" N   LEU A 363 " --> pdb=" O   GLY A 359 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   GLU A 368 " --> pdb=" O   THR A 364 " (cutoff:3.500A)
      removed outlier: 4.428A  pdb=" N   MET A 377 " --> pdb=" O   LYS A 373 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LYS A 381 " --> pdb=" O   MET A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 396
      removed outlier: 4.128A  pdb=" N   TRP A 394 " --> pdb=" O   ALA A 390 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   LEU A 395 " --> pdb=" O   ALA A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 416
      removed outlier: 3.902A  pdb=" N   ARG A 409 " --> pdb=" O   GLU A 405 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ALA A 415 " --> pdb=" O   ALA A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 424
      removed outlier: 4.441A  pdb=" N   GLU A 420 " --> pdb=" O   ARG A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 433
      removed outlier: 3.673A  pdb=" N   ARG A 433 " --> pdb=" O   ASP A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 447
    Processing helix  chain 'A' and resid 448 through 453
    Processing helix  chain 'A' and resid 456 through 484
      removed outlier: 3.593A  pdb=" N   ARG A 460 " --> pdb=" O   SER A 456 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   THR A 475 " --> pdb=" O   GLN A 471 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   SER A 484 " --> pdb=" O   ALA A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 499
    Processing helix  chain 'A' and resid 500 through 506
    Processing helix  chain 'A' and resid 514 through 532
      removed outlier: 3.588A  pdb=" N   ILE A 519 " --> pdb=" O   GLY A 515 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ARG A 520 " --> pdb=" O   GLN A 516 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLY A 521 " --> pdb=" O   ALA A 517 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU A 522 " --> pdb=" O   ALA A 518 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   VAL A 532 " --> pdb=" O   ARG A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 556
      removed outlier: 3.926A  pdb=" N   GLN A 539 " --> pdb=" O   GLY A 535 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   ASP A 540 " --> pdb=" O   PRO A 536 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LYS A 544 " --> pdb=" O   ASP A 540 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   VAL A 548 " --> pdb=" O   LYS A 544 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   LEU A 551 " --> pdb=" O   ARG A 547 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   ALA A 553 " --> pdb=" O   ASP A 549 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   GLN A 554 " --> pdb=" O   GLN A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 571
    Processing helix  chain 'A' and resid 573 through 596
      removed outlier: 4.105A  pdb=" N   GLN A 577 " --> pdb=" O   ALA A 573 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ASP A 578 " --> pdb=" O   SER A 574 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   GLU A 589 " --> pdb=" O   ALA A 585 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   THR A 592 " --> pdb=" O   GLN A 588 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   GLN A 593 " --> pdb=" O   GLU A 589 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLU A 594 " --> pdb=" O   ALA A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 615
      removed outlier: 3.674A  pdb=" N   LEU A 608 " --> pdb=" O   THR A 604 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ALA A 615 " --> pdb=" O   VAL A 611 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 622 through 651
    Processing helix  chain 'A' and resid 654 through 683
      Proline residue:  A 673  - end of helix
      removed outlier: 3.518A  pdb=" N   VAL A 676 " --> pdb=" O   THR A 672 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   SER A 677 " --> pdb=" O   PRO A 673 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 688 through 717
      removed outlier: 3.632A  pdb=" N   GLU A 693 " --> pdb=" O   GLN A 689 " (cutoff:3.500A)
      removed outlier: 5.219A  pdb=" N   HIS A 694 " --> pdb=" O   ALA A 690 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   PHE A 695 " --> pdb=" O   ALA A 691 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   GLU A 696 " --> pdb=" O   TYR A 692 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ASN A 700 " --> pdb=" O   GLU A 696 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ASP A 704 " --> pdb=" O   ASN A 700 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU A 712 " --> pdb=" O   LYS A 708 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 718 through 743
      removed outlier: 3.567A  pdb=" N   ALA A 725 " --> pdb=" O   SER A 721 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 745 through 774
      removed outlier: 3.638A  pdb=" N   GLY A 752 " --> pdb=" O   MET A 748 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ALA A 757 " --> pdb=" O   ALA A 753 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ASN A 761 " --> pdb=" O   ALA A 757 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   ARG A 762 " --> pdb=" O   ARG A 758 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ASN A 773 " --> pdb=" O   ARG A 769 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 780 through 786
    Processing helix  chain 'A' and resid 786 through 807
      removed outlier: 3.666A  pdb=" N   LEU A 790 " --> pdb=" O   ALA A 786 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   THR A 793 " --> pdb=" O   GLU A 789 " (cutoff:3.500A)
      removed outlier: 4.729A  pdb=" N   SER A 795 " --> pdb=" O   SER A 791 " (cutoff:3.500A)
      Proline residue:  A 796  - end of helix
    Processing helix  chain 'A' and resid 812 through 823
      removed outlier: 3.610A  pdb=" N   ARG A 823 " --> pdb=" O   ASP A 819 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 824 through 836
      removed outlier: 3.602A  pdb=" N   ALA A 829 " --> pdb=" O   LEU A 825 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   LYS A 830 " --> pdb=" O   GLY A 826 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 965 through 979
      removed outlier: 3.814A  pdb=" N   SER A 972 " --> pdb=" O   ALA A 968 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   LEU A 973 " --> pdb=" O   ALA A 969 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   HIS A 974 " --> pdb=" O   ALA A 970 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 985 through 1005
      removed outlier: 3.568A  pdb=" N   ALA A 990 " --> pdb=" O   ASP A 986 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1006 through 1007
      No H-bonds generated for 'chain 'A' and resid 1006 through 1007'
    Processing helix  chain 'A' and resid 1008 through 1010
      No H-bonds generated for 'chain 'A' and resid 1008 through 1010'
    Processing helix  chain 'A' and resid 1011 through 1038
      removed outlier: 3.594A  pdb=" N   ILE A1016 " --> pdb=" O   LYS A1012 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   VAL A1036 " --> pdb=" O   LEU A1032 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LYS A1038 " --> pdb=" O   LYS A1034 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1042 through 1053
      removed outlier: 3.611A  pdb=" N   ARG A1046 " --> pdb=" O   ASP A1042 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1054 through 1074
      removed outlier: 3.845A  pdb=" N   THR A1058 " --> pdb=" O   GLU A1054 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   SER A1060 " --> pdb=" O   ILE A1056 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   THR A1061 " --> pdb=" O   PRO A1057 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   GLN A1062 " --> pdb=" O   THR A1058 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   THR A1068 " --> pdb=" O   LYS A1064 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1080 through 1114
      removed outlier: 3.534A  pdb=" N   SER A1084 " --> pdb=" O   SER A1080 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   MET A1090 " --> pdb=" O   GLN A1086 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LEU A1091 " --> pdb=" O   ALA A1087 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ARG A1107 " --> pdb=" O   LYS A1103 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   GLU A1110 " --> pdb=" O   VAL A1106 " (cutoff:3.500A)

    535 hydrogen bonds defined for protein.
    1602 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.16

  Time building geometry restraints manager: 0.87 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1736
        1.33 -     1.45: 1313
        1.45 -     1.57: 4529
        1.57 -     1.69: 0
        1.69 -     1.81: 76
  Bond restraints: 7654
  Sorted by residual:
  bond pdb=" C   SER A 456 "
       pdb=" N   PRO A 457 "
    ideal  model  delta    sigma   weight residual
    1.336  1.387 -0.052 1.23e-02 6.61e+03 1.77e+01
  bond pdb=" C   ASP A 424 "
       pdb=" N   PRO A 425 "
    ideal  model  delta    sigma   weight residual
    1.337  1.382 -0.046 1.11e-02 8.12e+03 1.68e+01
  bond pdb=" CA  THR A 215 "
       pdb=" C   THR A 215 "
    ideal  model  delta    sigma   weight residual
    1.523  1.470  0.052 1.41e-02 5.03e+03 1.38e+01
  bond pdb=" C   THR A 215 "
       pdb=" O   THR A 215 "
    ideal  model  delta    sigma   weight residual
    1.236  1.207  0.028 1.35e-02 5.49e+03 4.40e+00
  bond pdb=" C   ASP A 505 "
       pdb=" N   ASN A 506 "
    ideal  model  delta    sigma   weight residual
    1.332  1.316  0.016 8.60e-03 1.35e+04 3.58e+00
  ... (remaining 7649 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 9639
        1.91 -     3.81: 583
        3.81 -     5.72: 74
        5.72 -     7.63: 22
        7.63 -     9.53: 7
  Bond angle restraints: 10325
  Sorted by residual:
  angle pdb=" C   LYS A 639 "
        pdb=" N   LEU A 640 "
        pdb=" CA  LEU A 640 "
      ideal   model   delta    sigma   weight residual
     120.54  127.14   -6.60 1.35e+00 5.49e-01 2.39e+01
  angle pdb=" N   VAL A 713 "
        pdb=" CA  VAL A 713 "
        pdb=" C   VAL A 713 "
      ideal   model   delta    sigma   weight residual
     110.72  106.66    4.06 1.01e+00 9.80e-01 1.62e+01
  angle pdb=" N   GLY A 401 "
        pdb=" CA  GLY A 401 "
        pdb=" C   GLY A 401 "
      ideal   model   delta    sigma   weight residual
     112.34  119.70   -7.36 2.04e+00 2.40e-01 1.30e+01
  angle pdb=" C   THR A 710 "
        pdb=" N   GLY A 711 "
        pdb=" CA  GLY A 711 "
      ideal   model   delta    sigma   weight residual
     120.13  124.50   -4.37 1.26e+00 6.30e-01 1.20e+01
  angle pdb=" N   GLN A 964 "
        pdb=" CA  GLN A 964 "
        pdb=" C   GLN A 964 "
      ideal   model   delta    sigma   weight residual
     109.81  117.43   -7.62 2.21e+00 2.05e-01 1.19e+01
  ... (remaining 10320 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.88: 4449
       15.88 -    31.75: 300
       31.75 -    47.63: 81
       47.63 -    63.50: 3
       63.50 -    79.38: 11
  Dihedral angle restraints: 4844
    sinusoidal: 1958
      harmonic: 2886
  Sorted by residual:
  dihedral pdb=" CA  ASN A1094 "
           pdb=" C   ASN A1094 "
           pdb=" N   ALA A1095 "
           pdb=" CA  ALA A1095 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.02   29.98     0      5.00e+00 4.00e-02 3.59e+01
  dihedral pdb=" CA  ALA A 615 "
           pdb=" C   ALA A 615 "
           pdb=" N   PRO A 616 "
           pdb=" CA  PRO A 616 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.28   26.72     0      5.00e+00 4.00e-02 2.86e+01
  dihedral pdb=" CA  ASP A 106 "
           pdb=" C   ASP A 106 "
           pdb=" N   TYR A 107 "
           pdb=" CA  TYR A 107 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.43   26.57     0      5.00e+00 4.00e-02 2.82e+01
  ... (remaining 4841 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 769
       0.043 -    0.085: 321
       0.085 -    0.128: 101
       0.128 -    0.171: 15
       0.171 -    0.213: 9
  Chirality restraints: 1215
  Sorted by residual:
  chirality pdb=" CB  ILE A 808 "
            pdb=" CA  ILE A 808 "
            pdb=" CG1 ILE A 808 "
            pdb=" CG2 ILE A 808 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.21 2.00e-01 2.50e+01 1.14e+00
  chirality pdb=" CB  ILE A 519 "
            pdb=" CA  ILE A 519 "
            pdb=" CG1 ILE A 519 "
            pdb=" CG2 ILE A 519 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.86   -0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" CB  ILE A 730 "
            pdb=" CA  ILE A 730 "
            pdb=" CG1 ILE A 730 "
            pdb=" CG2 ILE A 730 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.71e-01
  ... (remaining 1212 not shown)

  Planarity restraints: 1358
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A  42 "    0.050 5.00e-02 4.00e+02   7.59e-02 9.22e+00
        pdb=" N   PRO A  43 "   -0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO A  43 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A  43 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A  75 "   -0.044 5.00e-02 4.00e+02   6.55e-02 6.87e+00
        pdb=" N   PRO A  76 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO A  76 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A  76 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 615 "    0.043 5.00e-02 4.00e+02   6.55e-02 6.85e+00
        pdb=" N   PRO A 616 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO A 616 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 616 "    0.036 5.00e-02 4.00e+02
  ... (remaining 1355 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2010
        2.79 -     3.32: 8345
        3.32 -     3.84: 13479
        3.84 -     4.37: 16454
        4.37 -     4.90: 24124
  Nonbonded interactions: 64412
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 661 "
            pdb=" OG  SER A 664 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" O   ILE A 211 "
            pdb=" OG1 THR A 214 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" O   HIS A 694 "
            pdb=" OG1 THR A 697 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" O   ILE A1065 "
            pdb=" OG1 THR A1068 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" O   ALA A 440 "
            pdb=" OG  SER A 443 "
     model   vdw
     2.289 3.040
  ... (remaining 64407 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.790
  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:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
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      :  0.006   0.058   7654  Z= 0.293
  Angle     :  1.047   9.532  10325  Z= 0.603
  Chirality :  0.052   0.213   1215
  Planarity :  0.007   0.076   1358
  Dihedral  : 12.608  79.380   2958
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 12.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  4.06 %
    Favored  : 95.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -5.35 (0.18), residues: 991
  helix: -3.49 (0.12), residues: 745
  sheet:  None (None), residues: 0
  loop : -2.82 (0.33), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 780 
 TYR   0.021   0.003   TYR A 160 
 PHE   0.025   0.004   PHE A  78 
 TRP   0.026   0.005   TRP A 980 
 HIS   0.008   0.003   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00621 ( 7654)
  covalent geometry    : angle       1.04749 (10325)
  hydrogen bonds       : bond        0.30528 (  535)
  hydrogen bonds       : angle       9.83579 ( 1602)

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 206
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 MET cc_start: 0.7823 (mmm) cc_final: 0.7318 (mmm)
REVERT: A  195 MET cc_start: 0.8341 (tmt) cc_final: 0.8107 (tmt)
REVERT: A  209 MET cc_start: 0.9218 (mmt) cc_final: 0.8928 (mmm)
REVERT: A  246 ARG cc_start: 0.9182 (mpt-90) cc_final: 0.8851 (mmt90)
REVERT: A  305 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8439 (mm-30)
REVERT: A  377 MET cc_start: 0.7705 (ttt) cc_final: 0.6987 (tpp)
REVERT: A  498 GLU cc_start: 0.9327 (mm-30) cc_final: 0.8873 (mp0)
REVERT: A  550 GLN cc_start: 0.9096 (pt0) cc_final: 0.8896 (pt0)
REVERT: A  578 ASP cc_start: 0.8660 (m-30) cc_final: 0.8345 (t0)
REVERT: A  640 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8926 (mm)
REVERT: A  655 LYS cc_start: 0.8997 (tptp) cc_final: 0.8670 (pttp)
REVERT: A  666 LYS cc_start: 0.9524 (mtmt) cc_final: 0.9177 (mtpt)
REVERT: A  669 ARG cc_start: 0.8665 (ttp-110) cc_final: 0.8396 (ttp-110)
REVERT: A  799 MET cc_start: 0.9133 (mmt) cc_final: 0.8779 (mmp)
REVERT: A 1090 MET cc_start: 0.8415 (mmt) cc_final: 0.8022 (mmt)
REVERT: A 1103 LYS cc_start: 0.9107 (mtpt) cc_final: 0.8600 (mttt)
  outliers start: 3
  outliers final: 0
  residues processed: 209
  average time/residue: 0.1010
  time to fit residues: 27.5934
Evaluate side-chains
  137 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 136
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    9.9990
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:    8.9990
   chunk 45 optimal weight:    9.9990
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 334 GLN
A 382 GLN
A 527 HIS
A 550 GLN
** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 632 ASN
A 701 GLN
A1086 GLN
A1093 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.087130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.069022 restraints weight = 35479.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.070946 restraints weight = 25646.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.072345 restraints weight = 19989.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.073358 restraints weight = 16488.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.074171 restraints weight = 14212.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.2837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   7654  Z= 0.192
  Angle     :  0.739   8.782  10325  Z= 0.396
  Chirality :  0.041   0.144   1215
  Planarity :  0.005   0.046   1358
  Dihedral  :  6.207  23.772   1060
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 16.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  3.33 %
    Favored  : 96.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.40 (0.22), residues: 991
  helix: -1.86 (0.15), residues: 813
  sheet:  None (None), residues: 0
  loop : -3.10 (0.40), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 409 
 TYR   0.013   0.002   TYR A 822 
 PHE   0.019   0.003   PHE A 232 
 TRP   0.019   0.003   TRP A 258 
 HIS   0.006   0.001   HIS A1093 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 7654)
  covalent geometry    : angle       0.73908 (10325)
  hydrogen bonds       : bond        0.05981 (  535)
  hydrogen bonds       : angle       5.85984 ( 1602)

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 189
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 MET cc_start: 0.8099 (mmm) cc_final: 0.7610 (mmm)
REVERT: A  209 MET cc_start: 0.9113 (mmt) cc_final: 0.8913 (mmm)
REVERT: A  241 ILE cc_start: 0.9409 (mt) cc_final: 0.9076 (tt)
REVERT: A  246 ARG cc_start: 0.9397 (mpt-90) cc_final: 0.8896 (mpt180)
REVERT: A  258 TRP cc_start: 0.8385 (m-90) cc_final: 0.8074 (m-90)
REVERT: A  462 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7248 (pt)
REVERT: A  578 ASP cc_start: 0.8842 (m-30) cc_final: 0.8417 (t0)
REVERT: A  655 LYS cc_start: 0.9142 (tptp) cc_final: 0.8855 (pttm)
REVERT: A  659 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8697 (pt0)
REVERT: A  666 LYS cc_start: 0.9442 (mtmt) cc_final: 0.9014 (mtmt)
REVERT: A  669 ARG cc_start: 0.8550 (ttp-110) cc_final: 0.8341 (ttp-110)
REVERT: A  698 MET cc_start: 0.9150 (mmm) cc_final: 0.8903 (mmm)
REVERT: A  709 MET cc_start: 0.8959 (ttm) cc_final: 0.8630 (ttm)
REVERT: A  975 ARG cc_start: 0.8103 (mpt180) cc_final: 0.7265 (mmt180)
REVERT: A 1004 LEU cc_start: 0.9633 (mp) cc_final: 0.9333 (mt)
REVERT: A 1083 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8217 (mp0)
REVERT: A 1094 ASN cc_start: 0.8677 (m110) cc_final: 0.8435 (p0)
  outliers start: 4
  outliers final: 0
  residues processed: 192
  average time/residue: 0.0960
  time to fit residues: 24.0988
Evaluate side-chains
  136 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 135
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 46 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9980
   chunk 0 optimal weight:    9.9990
   chunk 43 optimal weight:    9.9990
   chunk 97 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 68 optimal weight:   10.0000
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:
** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 382 GLN
A 451 GLN
A 492 HIS
A 550 GLN
** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 705 ASN
A1078 ASN
A1096 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.089974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.071614 restraints weight = 34767.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.073500 restraints weight = 25252.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.074911 restraints weight = 19744.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.075974 restraints weight = 16352.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.076738 restraints weight = 14079.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.3667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7654  Z= 0.144
  Angle     :  0.673   7.760  10325  Z= 0.350
  Chirality :  0.041   0.139   1215
  Planarity :  0.004   0.044   1358
  Dihedral  :  5.675  24.790   1060
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 14.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.57 %
    Favored  : 96.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.19 (0.24), residues: 991
  helix: -0.99 (0.17), residues: 824
  sheet:  None (None), residues: 0
  loop : -2.99 (0.43), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 832 
 TYR   0.010   0.001   TYR A 822 
 PHE   0.020   0.002   PHE A 232 
 TRP   0.020   0.002   TRP A 980 
 HIS   0.005   0.001   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 7654)
  covalent geometry    : angle       0.67250 (10325)
  hydrogen bonds       : bond        0.04562 (  535)
  hydrogen bonds       : angle       5.20471 ( 1602)

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 192
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 MET cc_start: 0.8086 (mmm) cc_final: 0.7598 (mmm)
REVERT: A  241 ILE cc_start: 0.9433 (mt) cc_final: 0.9104 (tt)
REVERT: A  246 ARG cc_start: 0.9361 (mpt-90) cc_final: 0.8901 (mmt-90)
REVERT: A  254 ASP cc_start: 0.8041 (p0) cc_final: 0.7675 (p0)
REVERT: A  258 TRP cc_start: 0.8174 (m-90) cc_final: 0.7911 (m-90)
REVERT: A  451 GLN cc_start: 0.7135 (tp40) cc_final: 0.5430 (mm-40)
REVERT: A  578 ASP cc_start: 0.8825 (m-30) cc_final: 0.8451 (t0)
REVERT: A  618 ASP cc_start: 0.7817 (m-30) cc_final: 0.7569 (m-30)
REVERT: A  655 LYS cc_start: 0.9183 (tptp) cc_final: 0.8806 (pttm)
REVERT: A  659 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8734 (pt0)
REVERT: A  666 LYS cc_start: 0.9402 (mtmt) cc_final: 0.8869 (mtpt)
REVERT: A  669 ARG cc_start: 0.8591 (ttp-110) cc_final: 0.8150 (ttp-110)
REVERT: A  697 THR cc_start: 0.8937 (p) cc_final: 0.8717 (t)
REVERT: A  709 MET cc_start: 0.8968 (ttm) cc_final: 0.8516 (ttm)
REVERT: A 1004 LEU cc_start: 0.9620 (mp) cc_final: 0.9133 (mt)
REVERT: A 1043 LYS cc_start: 0.9131 (mttp) cc_final: 0.8898 (mttt)
REVERT: A 1083 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8150 (mp0)
REVERT: A 1094 ASN cc_start: 0.8671 (m110) cc_final: 0.8425 (p0)
REVERT: A 1103 LYS cc_start: 0.9056 (mtpt) cc_final: 0.8521 (ttmm)
  outliers start: 1
  outliers final: 0
  residues processed: 192
  average time/residue: 0.0928
  time to fit residues: 23.2741
Evaluate side-chains
  143 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 98 optimal weight:    0.5980
   chunk 53 optimal weight:    7.9990
   chunk 71 optimal weight:    0.2980
   chunk 27 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 51 optimal weight:    9.9990
   chunk 60 optimal weight:    1.9990
   chunk 21 optimal weight:    5.9990
   chunk 75 optimal weight:    6.9990
   chunk 73 optimal weight:    3.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 382 GLN
A 492 HIS
A 550 GLN
** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 705 ASN
A1051 GLN
** A1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.090563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.072926 restraints weight = 35815.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.074741 restraints weight = 26209.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.076124 restraints weight = 20630.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.077172 restraints weight = 17153.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.077907 restraints weight = 14787.282|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.4319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7654  Z= 0.138
  Angle     :  0.666   8.913  10325  Z= 0.341
  Chirality :  0.041   0.140   1215
  Planarity :  0.004   0.043   1358
  Dihedral  :  5.453  25.195   1060
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 13.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  2.46 %
    Favored  : 97.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.62 (0.25), residues: 991
  helix: -0.57 (0.17), residues: 822
  sheet:  None (None), residues: 0
  loop : -2.93 (0.42), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 832 
 TYR   0.009   0.001   TYR A 144 
 PHE   0.021   0.002   PHE A 232 
 TRP   0.025   0.002   TRP A 980 
 HIS   0.006   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 7654)
  covalent geometry    : angle       0.66620 (10325)
  hydrogen bonds       : bond        0.04099 (  535)
  hydrogen bonds       : angle       4.88873 ( 1602)

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 179
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 SER cc_start: 0.8882 (p) cc_final: 0.8582 (p)
REVERT: A  174 MET cc_start: 0.8006 (mmm) cc_final: 0.7558 (mmm)
REVERT: A  180 GLN cc_start: 0.9074 (pm20) cc_final: 0.8727 (mm-40)
REVERT: A  241 ILE cc_start: 0.9405 (mt) cc_final: 0.9060 (tt)
REVERT: A  246 ARG cc_start: 0.9354 (mpt-90) cc_final: 0.8852 (mmt-90)
REVERT: A  254 ASP cc_start: 0.7953 (p0) cc_final: 0.7574 (p0)
REVERT: A  258 TRP cc_start: 0.8025 (m-90) cc_final: 0.7784 (m-90)
REVERT: A  451 GLN cc_start: 0.6911 (tp40) cc_final: 0.5614 (mm-40)
REVERT: A  578 ASP cc_start: 0.8799 (m-30) cc_final: 0.8423 (t0)
REVERT: A  618 ASP cc_start: 0.7760 (m-30) cc_final: 0.7511 (m-30)
REVERT: A  655 LYS cc_start: 0.9101 (tptp) cc_final: 0.8775 (pttp)
REVERT: A  666 LYS cc_start: 0.9344 (mtmt) cc_final: 0.9073 (mtpt)
REVERT: A  669 ARG cc_start: 0.8476 (ttp-110) cc_final: 0.8206 (ttp-110)
REVERT: A  697 THR cc_start: 0.8889 (p) cc_final: 0.8662 (p)
REVERT: A  698 MET cc_start: 0.8807 (mmm) cc_final: 0.8233 (mmm)
REVERT: A  709 MET cc_start: 0.8824 (ttm) cc_final: 0.8560 (ttm)
REVERT: A 1043 LYS cc_start: 0.9085 (mttp) cc_final: 0.8858 (mttt)
REVERT: A 1073 MET cc_start: 0.8227 (mmm) cc_final: 0.7818 (tpt)
REVERT: A 1083 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8067 (mp0)
REVERT: A 1103 LYS cc_start: 0.9089 (mtpt) cc_final: 0.8657 (ttmm)
  outliers start: 1
  outliers final: 0
  residues processed: 180
  average time/residue: 0.0823
  time to fit residues: 20.0612
Evaluate side-chains
  136 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 74 optimal weight:    7.9990
   chunk 3 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9990
   chunk 24 optimal weight:    6.9990
   chunk 64 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 22 optimal weight:   10.0000
   chunk 37 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
A 179 GLN
** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 382 GLN
A 492 HIS
A 550 GLN
** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1051 GLN
A1094 ASN
** A1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.090799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.072528 restraints weight = 34889.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.074408 restraints weight = 25449.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.075779 restraints weight = 20057.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.076813 restraints weight = 16717.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.077584 restraints weight = 14521.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.4629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7654  Z= 0.133
  Angle     :  0.643   8.356  10325  Z= 0.331
  Chirality :  0.040   0.140   1215
  Planarity :  0.004   0.041   1358
  Dihedral  :  5.270  24.345   1060
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 13.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.07 (0.25), residues: 991
  helix: -0.19 (0.17), residues: 819
  sheet:  None (None), residues: 0
  loop : -2.68 (0.42), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 409 
 TYR   0.007   0.001   TYR A 144 
 PHE   0.018   0.002   PHE A 232 
 TRP   0.009   0.001   TRP A 258 
 HIS   0.010   0.002   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 7654)
  covalent geometry    : angle       0.64302 (10325)
  hydrogen bonds       : bond        0.03875 (  535)
  hydrogen bonds       : angle       4.67278 ( 1602)

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 MET cc_start: 0.8058 (mmm) cc_final: 0.7625 (mmm)
REVERT: A  241 ILE cc_start: 0.9413 (mt) cc_final: 0.9076 (tt)
REVERT: A  246 ARG cc_start: 0.9398 (mpt-90) cc_final: 0.8909 (mmt-90)
REVERT: A  254 ASP cc_start: 0.7942 (p0) cc_final: 0.7527 (p0)
REVERT: A  258 TRP cc_start: 0.8099 (m-90) cc_final: 0.7757 (m-90)
REVERT: A  305 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8722 (mm-30)
REVERT: A  386 LYS cc_start: 0.9138 (pttt) cc_final: 0.8903 (tttt)
REVERT: A  451 GLN cc_start: 0.7073 (tp40) cc_final: 0.5434 (mm-40)
REVERT: A  578 ASP cc_start: 0.8829 (m-30) cc_final: 0.8448 (t0)
REVERT: A  618 ASP cc_start: 0.7865 (m-30) cc_final: 0.7616 (m-30)
REVERT: A  655 LYS cc_start: 0.9167 (tptp) cc_final: 0.8821 (pttp)
REVERT: A  659 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8814 (mt-10)
REVERT: A  662 GLN cc_start: 0.8614 (pp30) cc_final: 0.7987 (tm-30)
REVERT: A  666 LYS cc_start: 0.9361 (mtmt) cc_final: 0.8800 (ptpt)
REVERT: A  697 THR cc_start: 0.9034 (p) cc_final: 0.8672 (t)
REVERT: A  698 MET cc_start: 0.8857 (mmm) cc_final: 0.8380 (mmm)
REVERT: A  709 MET cc_start: 0.8923 (ttm) cc_final: 0.8329 (ttm)
REVERT: A  748 MET cc_start: 0.8262 (mmt) cc_final: 0.7848 (mmp)
REVERT: A  799 MET cc_start: 0.9031 (mmt) cc_final: 0.8730 (mmt)
REVERT: A 1083 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8057 (mp0)
REVERT: A 1103 LYS cc_start: 0.9063 (mtpt) cc_final: 0.8536 (ttmm)
  outliers start: 0
  outliers final: 0
  residues processed: 170
  average time/residue: 0.0723
  time to fit residues: 17.0216
Evaluate side-chains
  135 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 91 optimal weight:    6.9990
   chunk 2 optimal weight:   10.0000
   chunk 84 optimal weight:    0.0010
   chunk 26 optimal weight:   10.0000
   chunk 28 optimal weight:    9.9990
   chunk 96 optimal weight:    5.9990
   chunk 10 optimal weight:    9.9990
   chunk 81 optimal weight:    0.0270
   overall best weight:    2.0050

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

Flipped N/Q/H residues before XYZ refinement:
** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 382 GLN
A 492 HIS
A 550 GLN
** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1051 GLN
** A1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.090229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.072124 restraints weight = 36307.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.073945 restraints weight = 26929.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.075307 restraints weight = 21363.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.076334 restraints weight = 17874.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.076814 restraints weight = 15507.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.4787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7654  Z= 0.148
  Angle     :  0.672   9.361  10325  Z= 0.342
  Chirality :  0.041   0.184   1215
  Planarity :  0.004   0.047   1358
  Dihedral  :  5.233  24.216   1060
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 15.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.81 (0.26), residues: 991
  helix: -0.01 (0.18), residues: 823
  sheet:  None (None), residues: 0
  loop : -2.68 (0.41), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 416 
 TYR   0.008   0.001   TYR A 144 
 PHE   0.016   0.002   PHE A 232 
 TRP   0.033   0.002   TRP A 503 
 HIS   0.006   0.002   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 7654)
  covalent geometry    : angle       0.67227 (10325)
  hydrogen bonds       : bond        0.03926 (  535)
  hydrogen bonds       : angle       4.66822 ( 1602)

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 MET cc_start: 0.7978 (mmm) cc_final: 0.7612 (mmm)
REVERT: A  241 ILE cc_start: 0.9384 (mt) cc_final: 0.9044 (tt)
REVERT: A  246 ARG cc_start: 0.9355 (mpt-90) cc_final: 0.8896 (mmt-90)
REVERT: A  254 ASP cc_start: 0.7889 (p0) cc_final: 0.7417 (p0)
REVERT: A  258 TRP cc_start: 0.8141 (m-90) cc_final: 0.7804 (m-90)
REVERT: A  266 MET cc_start: 0.7714 (mmt) cc_final: 0.7368 (mmt)
REVERT: A  386 LYS cc_start: 0.9105 (pttt) cc_final: 0.8867 (tttt)
REVERT: A  451 GLN cc_start: 0.7176 (tp40) cc_final: 0.5487 (mm-40)
REVERT: A  578 ASP cc_start: 0.8817 (m-30) cc_final: 0.8450 (t0)
REVERT: A  618 ASP cc_start: 0.7938 (m-30) cc_final: 0.7718 (m-30)
REVERT: A  655 LYS cc_start: 0.9186 (tptp) cc_final: 0.8834 (pttp)
REVERT: A  659 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8782 (mt-10)
REVERT: A  662 GLN cc_start: 0.8594 (pp30) cc_final: 0.8002 (tm-30)
REVERT: A  666 LYS cc_start: 0.9442 (mtmt) cc_final: 0.8819 (ptpt)
REVERT: A  697 THR cc_start: 0.8988 (p) cc_final: 0.8518 (t)
REVERT: A  698 MET cc_start: 0.8794 (mmm) cc_final: 0.8277 (mmm)
REVERT: A  709 MET cc_start: 0.8865 (ttm) cc_final: 0.8596 (ttm)
REVERT: A  748 MET cc_start: 0.8305 (mmt) cc_final: 0.7998 (mmp)
REVERT: A 1083 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8100 (mp0)
REVERT: A 1103 LYS cc_start: 0.9069 (mtpt) cc_final: 0.8623 (ttmm)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.0817
  time to fit residues: 18.4533
Evaluate side-chains
  142 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 57 optimal weight:    9.9990
   chunk 69 optimal weight:    5.9990
   chunk 92 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 58 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 26 optimal weight:    8.9990
   chunk 87 optimal weight:    0.9980
   chunk 67 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 355 GLN
A 382 GLN
A 492 HIS
** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1051 GLN
** A1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.090669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.072379 restraints weight = 34899.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.074238 restraints weight = 25596.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.075674 restraints weight = 20161.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.076755 restraints weight = 16661.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.077515 restraints weight = 14378.498|
|-----------------------------------------------------------------------------|
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.5130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7654  Z= 0.129
  Angle     :  0.662  10.448  10325  Z= 0.334
  Chirality :  0.041   0.157   1215
  Planarity :  0.004   0.044   1358
  Dihedral  :  5.131  24.697   1060
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 14.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.55 (0.26), residues: 991
  helix:  0.15 (0.18), residues: 824
  sheet:  None (None), residues: 0
  loop : -2.54 (0.42), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 669 
 TYR   0.008   0.001   TYR A 144 
 PHE   0.021   0.002   PHE A 599 
 TRP   0.051   0.003   TRP A 503 
 HIS   0.006   0.001   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 7654)
  covalent geometry    : angle       0.66168 (10325)
  hydrogen bonds       : bond        0.03653 (  535)
  hydrogen bonds       : angle       4.55384 ( 1602)

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 MET cc_start: 0.7966 (mmm) cc_final: 0.7574 (mmm)
REVERT: A  241 ILE cc_start: 0.9396 (mt) cc_final: 0.8943 (tt)
REVERT: A  246 ARG cc_start: 0.9355 (mpt-90) cc_final: 0.8931 (mpt180)
REVERT: A  254 ASP cc_start: 0.7894 (p0) cc_final: 0.7470 (p0)
REVERT: A  258 TRP cc_start: 0.7989 (m-90) cc_final: 0.7652 (m-90)
REVERT: A  386 LYS cc_start: 0.9081 (pttt) cc_final: 0.8845 (pttp)
REVERT: A  451 GLN cc_start: 0.6989 (tp40) cc_final: 0.5235 (mm-40)
REVERT: A  498 GLU cc_start: 0.9347 (mp0) cc_final: 0.8951 (mp0)
REVERT: A  533 MET cc_start: 0.7560 (mpp) cc_final: 0.7293 (mpp)
REVERT: A  578 ASP cc_start: 0.8825 (m-30) cc_final: 0.8438 (t0)
REVERT: A  587 MET cc_start: 0.2682 (mmm) cc_final: 0.1638 (mmt)
REVERT: A  662 GLN cc_start: 0.8569 (pp30) cc_final: 0.8106 (tm-30)
REVERT: A  666 LYS cc_start: 0.9407 (mtmt) cc_final: 0.8768 (ptpt)
REVERT: A  697 THR cc_start: 0.8989 (p) cc_final: 0.8574 (t)
REVERT: A  698 MET cc_start: 0.8796 (mmm) cc_final: 0.8304 (mmm)
REVERT: A  748 MET cc_start: 0.8303 (mmt) cc_final: 0.7988 (mmp)
REVERT: A  799 MET cc_start: 0.9001 (mmt) cc_final: 0.8701 (mmt)
REVERT: A 1083 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8153 (mp0)
REVERT: A 1090 MET cc_start: 0.7347 (mpp) cc_final: 0.7082 (mpp)
REVERT: A 1099 MET cc_start: 0.8603 (mmt) cc_final: 0.8375 (mmt)
REVERT: A 1103 LYS cc_start: 0.9091 (mtpt) cc_final: 0.8614 (ttmm)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.0803
  time to fit residues: 18.8827
Evaluate side-chains
  140 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 7 optimal weight:    0.8980
   chunk 10 optimal weight:    5.9990
   chunk 4 optimal weight:    0.0010
   chunk 32 optimal weight:    0.6980
   chunk 68 optimal weight:    7.9990
   chunk 94 optimal weight:    0.7980
   chunk 3 optimal weight:    0.2980
   chunk 93 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 47 optimal weight:    8.9990
   overall best weight:    0.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 382 GLN
A 492 HIS
A 685 ASN
A1051 GLN
** A1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.092819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.074567 restraints weight = 34822.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.076503 restraints weight = 25561.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.077940 restraints weight = 20077.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.079031 restraints weight = 16549.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.079899 restraints weight = 14262.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.5489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7654  Z= 0.124
  Angle     :  0.665  10.163  10325  Z= 0.334
  Chirality :  0.041   0.201   1215
  Planarity :  0.004   0.051   1358
  Dihedral  :  5.066  25.035   1060
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 13.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.26), residues: 991
  helix:  0.26 (0.18), residues: 826
  sheet:  None (None), residues: 0
  loop : -2.57 (0.41), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 669 
 TYR   0.012   0.001   TYR A 692 
 PHE   0.014   0.002   PHE A 232 
 TRP   0.055   0.003   TRP A 503 
 HIS   0.006   0.001   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 7654)
  covalent geometry    : angle       0.66548 (10325)
  hydrogen bonds       : bond        0.03558 (  535)
  hydrogen bonds       : angle       4.43371 ( 1602)

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 MET cc_start: 0.7908 (mmm) cc_final: 0.7495 (mmm)
REVERT: A  195 MET cc_start: 0.8251 (tmm) cc_final: 0.7639 (tmm)
REVERT: A  241 ILE cc_start: 0.9348 (mt) cc_final: 0.8963 (tt)
REVERT: A  246 ARG cc_start: 0.9342 (mpt-90) cc_final: 0.8950 (mpt180)
REVERT: A  254 ASP cc_start: 0.7923 (p0) cc_final: 0.7383 (p0)
REVERT: A  258 TRP cc_start: 0.7968 (m-90) cc_final: 0.7656 (m-90)
REVERT: A  386 LYS cc_start: 0.9090 (pttt) cc_final: 0.8854 (pttp)
REVERT: A  451 GLN cc_start: 0.6860 (tp40) cc_final: 0.5123 (mm-40)
REVERT: A  498 GLU cc_start: 0.9345 (mp0) cc_final: 0.8937 (mp0)
REVERT: A  578 ASP cc_start: 0.8852 (m-30) cc_final: 0.8454 (t0)
REVERT: A  662 GLN cc_start: 0.8506 (pp30) cc_final: 0.8120 (tm-30)
REVERT: A  666 LYS cc_start: 0.9426 (mtmt) cc_final: 0.8815 (ptpt)
REVERT: A  697 THR cc_start: 0.8994 (p) cc_final: 0.8671 (t)
REVERT: A  698 MET cc_start: 0.8762 (mmm) cc_final: 0.8390 (mmm)
REVERT: A  748 MET cc_start: 0.8295 (mmt) cc_final: 0.7981 (mmp)
REVERT: A  799 MET cc_start: 0.8965 (mmt) cc_final: 0.8657 (mmt)
REVERT: A 1043 LYS cc_start: 0.9029 (mttp) cc_final: 0.8763 (mttt)
REVERT: A 1083 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8106 (mp0)
REVERT: A 1103 LYS cc_start: 0.9044 (mtpt) cc_final: 0.8569 (ttmm)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.0867
  time to fit residues: 20.5559
Evaluate side-chains
  149 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 37 optimal weight:    6.9990
   chunk 72 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 82 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 43 optimal weight:    7.9990
   chunk 65 optimal weight:    0.1980
   chunk 50 optimal weight:    7.9990
   chunk 94 optimal weight:    0.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 382 GLN
A 492 HIS
A 685 ASN
A1051 GLN
A1078 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.093350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.075137 restraints weight = 34836.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.077037 restraints weight = 25616.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.078537 restraints weight = 20137.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.079638 restraints weight = 16618.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.080412 restraints weight = 14311.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.5749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7654  Z= 0.121
  Angle     :  0.664   9.741  10325  Z= 0.329
  Chirality :  0.041   0.185   1215
  Planarity :  0.004   0.063   1358
  Dihedral  :  4.942  25.089   1060
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 14.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.23 (0.26), residues: 991
  helix:  0.38 (0.18), residues: 823
  sheet:  None (None), residues: 0
  loop : -2.43 (0.42), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 762 
 TYR   0.008   0.001   TYR A 692 
 PHE   0.014   0.002   PHE A 817 
 TRP   0.007   0.001   TRP A 394 
 HIS   0.006   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 7654)
  covalent geometry    : angle       0.66422 (10325)
  hydrogen bonds       : bond        0.03547 (  535)
  hydrogen bonds       : angle       4.32183 ( 1602)

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 ASP cc_start: 0.8293 (p0) cc_final: 0.8009 (t70)
REVERT: A  174 MET cc_start: 0.7869 (mmm) cc_final: 0.7530 (mmm)
REVERT: A  195 MET cc_start: 0.8245 (tmm) cc_final: 0.7658 (tmm)
REVERT: A  241 ILE cc_start: 0.9362 (mt) cc_final: 0.8959 (tt)
REVERT: A  246 ARG cc_start: 0.9337 (mpt-90) cc_final: 0.8950 (mpt180)
REVERT: A  254 ASP cc_start: 0.7837 (p0) cc_final: 0.7467 (p0)
REVERT: A  258 TRP cc_start: 0.7944 (m-90) cc_final: 0.7651 (m-90)
REVERT: A  386 LYS cc_start: 0.9084 (pttt) cc_final: 0.8833 (tttt)
REVERT: A  451 GLN cc_start: 0.6846 (tp40) cc_final: 0.5114 (mm-40)
REVERT: A  510 ASP cc_start: 0.8718 (p0) cc_final: 0.7899 (p0)
REVERT: A  578 ASP cc_start: 0.8825 (m-30) cc_final: 0.8433 (t0)
REVERT: A  587 MET cc_start: 0.2386 (mmm) cc_final: 0.1914 (mmt)
REVERT: A  645 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8712 (mt-10)
REVERT: A  659 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8848 (pt0)
REVERT: A  662 GLN cc_start: 0.8466 (pp30) cc_final: 0.8172 (tm-30)
REVERT: A  666 LYS cc_start: 0.9420 (mtmt) cc_final: 0.8803 (ptpt)
REVERT: A  697 THR cc_start: 0.9041 (p) cc_final: 0.8695 (t)
REVERT: A  698 MET cc_start: 0.8837 (mmm) cc_final: 0.8424 (mmm)
REVERT: A  748 MET cc_start: 0.8303 (mmt) cc_final: 0.7973 (mmp)
REVERT: A  799 MET cc_start: 0.8974 (mmt) cc_final: 0.8679 (mmt)
REVERT: A 1043 LYS cc_start: 0.9013 (mttp) cc_final: 0.8748 (mttt)
REVERT: A 1083 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8115 (mp0)
REVERT: A 1103 LYS cc_start: 0.9049 (mtpt) cc_final: 0.8530 (ttmm)
  outliers start: 0
  outliers final: 0
  residues processed: 178
  average time/residue: 0.0922
  time to fit residues: 21.9254
Evaluate side-chains
  142 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 68 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9980
   chunk 41 optimal weight:    7.9990
   chunk 14 optimal weight:    0.9980
   chunk 77 optimal weight:    9.9990
   chunk 62 optimal weight:    0.7980
   chunk 71 optimal weight:    8.9990
   chunk 27 optimal weight:    9.9990
   chunk 12 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   chunk 34 optimal weight:    9.9990
   overall best weight:    2.5584

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

Flipped N/Q/H residues before XYZ refinement:
** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 382 GLN
A 492 HIS
** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1051 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.090796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.072650 restraints weight = 35201.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.074518 restraints weight = 25824.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.075937 restraints weight = 20242.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.076992 restraints weight = 16745.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.077799 restraints weight = 14453.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.5660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7654  Z= 0.168
  Angle     :  0.715  10.787  10325  Z= 0.364
  Chirality :  0.043   0.258   1215
  Planarity :  0.004   0.046   1358
  Dihedral  :  5.029  25.872   1060
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 16.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.18 (0.26), residues: 991
  helix:  0.35 (0.18), residues: 827
  sheet:  None (None), residues: 0
  loop : -2.13 (0.44), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 832 
 TYR   0.009   0.001   TYR A 692 
 PHE   0.015   0.002   PHE A 232 
 TRP   0.071   0.003   TRP A 503 
 HIS   0.006   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 7654)
  covalent geometry    : angle       0.71488 (10325)
  hydrogen bonds       : bond        0.03923 (  535)
  hydrogen bonds       : angle       4.47499 ( 1602)

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

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

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1982 Ramachandran restraints generated.
    991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 MET cc_start: 0.7975 (mmm) cc_final: 0.7628 (mmm)
REVERT: A  190 MET cc_start: 0.7713 (ptt) cc_final: 0.7190 (ptt)
REVERT: A  241 ILE cc_start: 0.9389 (mt) cc_final: 0.9006 (tt)
REVERT: A  246 ARG cc_start: 0.9371 (mpt-90) cc_final: 0.8936 (mmt-90)
REVERT: A  254 ASP cc_start: 0.7922 (p0) cc_final: 0.7404 (p0)
REVERT: A  382 GLN cc_start: 0.8824 (mp10) cc_final: 0.8323 (mp-120)
REVERT: A  578 ASP cc_start: 0.8833 (m-30) cc_final: 0.8461 (t0)
REVERT: A  645 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8840 (mt-10)
REVERT: A  659 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8823 (mt-10)
REVERT: A  666 LYS cc_start: 0.9458 (mtmt) cc_final: 0.8769 (mtmm)
REVERT: A  697 THR cc_start: 0.9103 (p) cc_final: 0.8760 (p)
REVERT: A  698 MET cc_start: 0.8940 (mmm) cc_final: 0.8388 (mmm)
REVERT: A  709 MET cc_start: 0.8830 (ttm) cc_final: 0.8587 (ttm)
REVERT: A  748 MET cc_start: 0.8300 (mmt) cc_final: 0.7957 (mmp)
REVERT: A  759 ARG cc_start: 0.9203 (mpt180) cc_final: 0.8648 (mmt-90)
REVERT: A  799 MET cc_start: 0.8951 (mmt) cc_final: 0.8653 (mmt)
REVERT: A 1083 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8133 (mp0)
REVERT: A 1103 LYS cc_start: 0.9163 (mtpt) cc_final: 0.8612 (ttmm)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.0785
  time to fit residues: 17.8124
Evaluate side-chains
  137 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 74 optimal weight:   10.0000
   chunk 48 optimal weight:    0.1980
   chunk 98 optimal weight:    0.7980
   chunk 93 optimal weight:    8.9990
   chunk 92 optimal weight:    5.9990
   chunk 94 optimal weight:    0.9980
   chunk 6 optimal weight:    4.9990
   chunk 39 optimal weight:    0.5980
   chunk 67 optimal weight:    0.2980
   chunk 36 optimal weight:    0.9990
   chunk 97 optimal weight:    6.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 451 GLN
A 492 HIS
** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1051 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.094231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.075712 restraints weight = 34126.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.077670 restraints weight = 24897.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.079137 restraints weight = 19536.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.080229 restraints weight = 16121.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.081051 restraints weight = 13896.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.6044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   7654  Z= 0.131
  Angle     :  0.682  11.088  10325  Z= 0.343
  Chirality :  0.042   0.221   1215
  Planarity :  0.004   0.053   1358
  Dihedral  :  4.968  25.804   1060
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 14.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.04 (0.27), residues: 991
  helix:  0.49 (0.18), residues: 820
  sheet:  None (None), residues: 0
  loop : -2.18 (0.43), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 832 
 TYR   0.005   0.001   TYR A 144 
 PHE   0.012   0.001   PHE A 232 
 TRP   0.057   0.005   TRP A 503 
 HIS   0.006   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 7654)
  covalent geometry    : angle       0.68212 (10325)
  hydrogen bonds       : bond        0.03677 (  535)
  hydrogen bonds       : angle       4.38635 ( 1602)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1296.03 seconds
wall clock time: 23 minutes 9.65 seconds (1389.65 seconds total)