Starting phenix.real_space_refine
on Tue Mar  3 17:26:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ktw_23032/03_2026/7ktw_23032.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ktw_23032/03_2026/7ktw_23032.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.27
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ktw_23032/03_2026/7ktw_23032.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ktw_23032/03_2026/7ktw_23032.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ktw_23032/03_2026/7ktw_23032.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ktw_23032/03_2026/7ktw_23032.map"
  }
  resolution = 4.27
  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=   0.032
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: 1.56, per 1000 atoms: 0.21
  Number of scatterers: 7577
  At special positions: 0
  Unit cell: (84.975, 97.35, 128.7, 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: 0.73
  Conformation dependent library (CDL) restraints added in 298.1 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:
      39 helices and 0 sheets defined
      86.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.622A  pdb=" N   GLU A  10 " --> pdb=" O   THR A   6 " (cutoff:3.500A)
      Proline residue:  A  15  - end of helix
      removed outlier: 3.578A  pdb=" N   LEU A  23 " --> pdb=" O   GLN A  19 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ILE A  25 " --> pdb=" O   SER A  21 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   MET A  26 " --> pdb=" O   HIS A  22 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   GLU A  29 " --> pdb=" O   ILE A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 65
      removed outlier: 3.783A  pdb=" N   VAL A  44 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   ALA A  45 " --> pdb=" O   THR A  41 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   ASN A  53 " --> pdb=" O   ALA A  49 " (cutoff:3.500A)
      removed outlier: 4.740A  pdb=" N   LEU A  54 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 98
      removed outlier: 4.145A  pdb=" N   ASP A  73 " --> pdb=" O   ILE A  69 " (cutoff:3.500A)
      Proline residue:  A  75  - end of helix
      removed outlier: 3.621A  pdb=" N   ILE A  79 " --> pdb=" O   PRO A  75 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   LYS A  80 " --> pdb=" O   PRO A  76 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   VAL A  81 " --> pdb=" O   ALA A  77 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   VAL A  89 " --> pdb=" O   CYS A  85 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   GLN A  90 " --> pdb=" O   THR A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 148
      removed outlier: 4.315A  pdb=" N   TYR A 107 " --> pdb=" O   PRO A 103 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ILE A 109 " --> pdb=" O   ARG A 105 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   GLY A 111 " --> pdb=" O   TYR A 107 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ARG A 113 " --> pdb=" O   ILE A 109 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   SER A 120 " --> pdb=" O   LEU A 116 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   ALA A 129 " --> pdb=" O   THR A 125 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLU A 130 " --> pdb=" O   PHE A 126 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LYS A 133 " --> pdb=" O   ALA A 129 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   ILE A 134 " --> pdb=" O   GLU A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 182
      removed outlier: 3.509A  pdb=" N   VAL A 158 " --> pdb=" O   MET A 154 " (cutoff:3.500A)
      Proline residue:  A 166  - end of helix
      removed outlier: 3.683A  pdb=" N   LYS A 173 " --> pdb=" O   THR A 169 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   MET A 174 " --> pdb=" O   LYS A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 218
      removed outlier: 3.629A  pdb=" N   MET A 190 " --> pdb=" O   GLU A 186 " (cutoff:3.500A)
      removed outlier: 4.565A  pdb=" N   THR A 197 " --> pdb=" O   ASN A 193 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   LEU A 202 " --> pdb=" O   VAL A 198 " (cutoff:3.500A)
      Proline residue:  A 203  - end of helix
      removed outlier: 3.535A  pdb=" N   THR A 214 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 249
      removed outlier: 4.243A  pdb=" N   GLU A 225 " --> pdb=" O   GLN A 221 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   PHE A 232 " --> pdb=" O   LYS A 228 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   THR A 233 " --> pdb=" O   ASN A 229 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   GLU A 240 " --> pdb=" O   LYS A 236 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ILE A 245 " --> pdb=" O   ILE A 241 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   ARG A 246 " --> pdb=" O   ASN A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 262
      removed outlier: 4.550A  pdb=" N   ALA A 259 " --> pdb=" O   GLU A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 286
      removed outlier: 3.946A  pdb=" N   LYS A 267 " --> pdb=" O   THR A 263 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ALA A 271 " --> pdb=" O   LYS A 267 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   ASP A 274 " --> pdb=" O   LEU A 270 " (cutoff:3.500A)
      removed outlier: 4.831A  pdb=" N   SER A 275 " --> pdb=" O   ALA A 271 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   ASN A 278 " --> pdb=" O   ASP A 274 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   GLN A 279 " --> pdb=" O   SER A 275 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ALA A 280 " --> pdb=" O   LYS A 276 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   TRP A 283 " --> pdb=" O   GLN A 279 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ASP A 286 " --> pdb=" O   GLY A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 313
      removed outlier: 3.536A  pdb=" N   VAL A 309 " --> pdb=" O   GLU A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 342
      removed outlier: 3.640A  pdb=" N   GLU A 320 " --> pdb=" O   LYS A 316 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LEU A 322 " --> pdb=" O   ARG A 318 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ALA A 340 " --> pdb=" O   ALA A 336 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ARG A 341 " --> pdb=" O   ASP A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 389
      removed outlier: 3.604A  pdb=" N   VAL A 367 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   GLU A 368 " --> pdb=" O   THR A 364 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   ARG A 372 " --> pdb=" O   GLU A 368 " (cutoff:3.500A)
      removed outlier: 5.499A  pdb=" N   MET A 377 " --> pdb=" O   LYS A 373 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   THR A 378 " --> pdb=" O   LEU A 374 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   LYS A 386 " --> pdb=" O   GLN A 382 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   LYS A 387 " --> pdb=" O   SER A 383 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ILE A 388 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   ASP A 389 " --> pdb=" O   ALA A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 397
      removed outlier: 3.896A  pdb=" N   TRP A 394 " --> pdb=" O   ALA A 390 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ASP A 397 " --> pdb=" O   ASN A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 424
      removed outlier: 3.580A  pdb=" N   ILE A 408 " --> pdb=" O   GLY A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 427
      No H-bonds generated for 'chain 'A' and resid 425 through 427'
    Processing helix  chain 'A' and resid 428 through 451
      removed outlier: 3.925A  pdb=" N   ARG A 433 " --> pdb=" O   ASP A 429 " (cutoff:3.500A)
      removed outlier: 4.784A  pdb=" N   SER A 439 " --> pdb=" O   LEU A 435 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   THR A 442 " --> pdb=" O   ILE A 438 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   LYS A 444 " --> pdb=" O   ALA A 440 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   LEU A 448 " --> pdb=" O   LYS A 444 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   ARG A 449 " --> pdb=" O   LEU A 445 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   ARG A 450 " --> pdb=" O   ALA A 446 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   GLN A 451 " --> pdb=" O   ASP A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 479
      removed outlier: 3.746A  pdb=" N   LYS A 464 " --> pdb=" O   ARG A 460 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   GLN A 465 " --> pdb=" O   ALA A 461 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   THR A 468 " --> pdb=" O   LYS A 464 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   GLN A 471 " --> pdb=" O   ALA A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 482
      No H-bonds generated for 'chain 'A' and resid 480 through 482'
    Processing helix  chain 'A' and resid 492 through 503
      removed outlier: 3.783A  pdb=" N   TRP A 503 " --> pdb=" O   GLN A 499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 531
      removed outlier: 3.634A  pdb=" N   GLU A 525 " --> pdb=" O   GLY A 521 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   GLY A 526 " --> pdb=" O   LEU A 522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 550
      removed outlier: 3.785A  pdb=" N   ASP A 540 " --> pdb=" O   PRO A 536 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   VAL A 548 " --> pdb=" O   LYS A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 550 through 555
      removed outlier: 3.926A  pdb=" N   GLN A 554 " --> pdb=" O   GLN A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 599
      removed outlier: 4.054A  pdb=" N   LEU A 572 " --> pdb=" O   GLN A 568 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   LEU A 576 " --> pdb=" O   LEU A 572 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   GLN A 577 " --> pdb=" O   ALA A 573 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   ASP A 578 " --> pdb=" O   SER A 574 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   SER A 579 " --> pdb=" O   GLN A 575 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   LEU A 583 " --> pdb=" O   SER A 579 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   LYS A 584 " --> pdb=" O   LEU A 580 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   ALA A 585 " --> pdb=" O   LYS A 581 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ARG A 586 " --> pdb=" O   ASP A 582 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   GLU A 594 " --> pdb=" O   ALA A 590 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   SER A 596 " --> pdb=" O   THR A 592 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 615
      removed outlier: 3.870A  pdb=" N   ALA A 615 " --> pdb=" O   VAL A 611 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 650
      removed outlier: 3.670A  pdb=" N   LYS A 639 " --> pdb=" O   ASN A 635 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   GLU A 645 " --> pdb=" O   GLY A 641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 654 through 685
      removed outlier: 3.624A  pdb=" N   VAL A 658 " --> pdb=" O   ASN A 654 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   GLN A 662 " --> pdb=" O   VAL A 658 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ALA A 663 " --> pdb=" O   GLU A 659 " (cutoff:3.500A)
      Proline residue:  A 673  - end of helix
    Processing helix  chain 'A' and resid 688 through 717
      removed outlier: 3.810A  pdb=" N   ASN A 700 " --> pdb=" O   GLU A 696 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ASN A 705 " --> pdb=" O   GLN A 701 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   GLU A 715 " --> pdb=" O   GLY A 711 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 718 through 743
      removed outlier: 3.852A  pdb=" N   ASP A 724 " --> pdb=" O   LYS A 720 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 745 through 774
      removed outlier: 3.506A  pdb=" N   LEU A 749 " --> pdb=" O   GLN A 745 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ARG A 762 " --> pdb=" O   ARG A 758 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   VAL A 771 " --> pdb=" O   ALA A 767 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 779 through 794
    Processing helix  chain 'A' and resid 794 through 805
      removed outlier: 3.887A  pdb=" N   VAL A 798 " --> pdb=" O   ILE A 794 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 812 through 836
      removed outlier: 3.510A  pdb=" N   ILE A 824 " --> pdb=" O   SER A 820 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLY A 826 " --> pdb=" O   TYR A 822 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA A 827 " --> pdb=" O   ARG A 823 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ARG A 832 " --> pdb=" O   VAL A 828 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLU A 833 " --> pdb=" O   ALA A 829 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ALA A 834 " --> pdb=" O   LYS A 830 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   PHE A 835 " --> pdb=" O   VAL A 831 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   GLN A 836 " --> pdb=" O   ARG A 832 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 965 through 976
      removed outlier: 3.808A  pdb=" N   LEU A 973 " --> pdb=" O   ALA A 969 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ARG A 975 " --> pdb=" O   GLN A 971 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 987 through 1005
      removed outlier: 3.738A  pdb=" N   ALA A 991 " --> pdb=" O   ILE A 987 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ARG A1003 " --> pdb=" O   ALA A 999 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1011 through 1040
      removed outlier: 3.879A  pdb=" N   LEU A1015 " --> pdb=" O   THR A1011 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ILE A1016 " --> pdb=" O   LYS A1012 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ALA A1019 " --> pdb=" O   LEU A1015 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ASP A1021 " --> pdb=" O   GLN A1017 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   SER A1026 " --> pdb=" O   ILE A1022 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   VAL A1029 " --> pdb=" O   ALA A1025 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   VAL A1036 " --> pdb=" O   LEU A1032 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1042 through 1054
    Processing helix  chain 'A' and resid 1054 through 1074
      removed outlier: 3.868A  pdb=" N   THR A1058 " --> pdb=" O   GLU A1054 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   THR A1061 " --> pdb=" O   PRO A1057 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   GLN A1062 " --> pdb=" O   THR A1058 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU A1063 " --> pdb=" O   ILE A1059 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   LYS A1064 " --> pdb=" O   SER A1060 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1080 through 1112
      removed outlier: 3.806A  pdb=" N   SER A1084 " --> pdb=" O   SER A1080 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ALA A1095 " --> pdb=" O   LEU A1091 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LYS A1103 " --> pdb=" O   MET A1099 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLU A1104 " --> pdb=" O   GLN A1100 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   THR A1105 " --> pdb=" O   SER A1101 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   GLU A1110 " --> pdb=" O   VAL A1106 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ALA A1112 " --> pdb=" O   GLU A1108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1113 through 1116
      removed outlier: 3.741A  pdb=" N   ILE A1116 " --> pdb=" O   SER A1113 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1113 through 1116'

    551 hydrogen bonds defined for protein.
    1653 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: 0.98

  Time building geometry restraints manager: 0.96 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2625
        1.34 -     1.46: 1040
        1.46 -     1.57: 3913
        1.57 -     1.69: 0
        1.69 -     1.81: 76
  Bond restraints: 7654
  Sorted by residual:
  bond pdb=" C   ILE A1056 "
       pdb=" N   PRO A1057 "
    ideal  model  delta    sigma   weight residual
    1.337  1.368 -0.031 1.24e-02 6.50e+03 6.38e+00
  bond pdb=" C   GLN A 964 "
       pdb=" N   PRO A 965 "
    ideal  model  delta    sigma   weight residual
    1.334  1.383 -0.049 2.34e-02 1.83e+03 4.34e+00
  bond pdb=" CA  THR A 710 "
       pdb=" C   THR A 710 "
    ideal  model  delta    sigma   weight residual
    1.524  1.499  0.024 1.27e-02 6.20e+03 3.64e+00
  bond pdb=" C   VAL A 102 "
       pdb=" N   PRO A 103 "
    ideal  model  delta    sigma   weight residual
    1.334  1.378 -0.044 2.34e-02 1.83e+03 3.58e+00
  bond pdb=" C   GLU A  14 "
       pdb=" N   PRO A  15 "
    ideal  model  delta    sigma   weight residual
    1.335  1.359 -0.024 1.30e-02 5.92e+03 3.32e+00
  ... (remaining 7649 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.29: 9841
        2.29 -     4.57: 417
        4.57 -     6.86: 47
        6.86 -     9.14: 15
        9.14 -    11.43: 5
  Bond angle restraints: 10325
  Sorted by residual:
  angle pdb=" C   ILE A 987 "
        pdb=" N   ILE A 988 "
        pdb=" CA  ILE A 988 "
      ideal   model   delta    sigma   weight residual
     120.53  130.49   -9.96 1.41e+00 5.03e-01 4.99e+01
  angle pdb=" C   LYS A 979 "
        pdb=" N   TRP A 980 "
        pdb=" CA  TRP A 980 "
      ideal   model   delta    sigma   weight residual
     121.54  131.89  -10.35 1.91e+00 2.74e-01 2.94e+01
  angle pdb=" N   GLY A 535 "
        pdb=" CA  GLY A 535 "
        pdb=" C   GLY A 535 "
      ideal   model   delta    sigma   weight residual
     112.34  120.46   -8.12 2.04e+00 2.40e-01 1.58e+01
  angle pdb=" N   GLY A 984 "
        pdb=" CA  GLY A 984 "
        pdb=" C   GLY A 984 "
      ideal   model   delta    sigma   weight residual
     111.42  116.78   -5.36 1.42e+00 4.96e-01 1.42e+01
  angle pdb=" N   THR A 697 "
        pdb=" CA  THR A 697 "
        pdb=" C   THR A 697 "
      ideal   model   delta    sigma   weight residual
     111.03  106.88    4.15 1.11e+00 8.12e-01 1.40e+01
  ... (remaining 10320 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.12: 4418
       15.12 -    30.24: 303
       30.24 -    45.35: 108
       45.35 -    60.47: 6
       60.47 -    75.59: 9
  Dihedral angle restraints: 4844
    sinusoidal: 1958
      harmonic: 2886
  Sorted by residual:
  dihedral pdb=" CA  ASP A 511 "
           pdb=" C   ASP A 511 "
           pdb=" N   ARG A 512 "
           pdb=" CA  ARG A 512 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.55  -24.45     0      5.00e+00 4.00e-02 2.39e+01
  dihedral pdb=" CA  ARG A1003 "
           pdb=" C   ARG A1003 "
           pdb=" N   LEU A1004 "
           pdb=" CA  LEU A1004 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.82  -23.18     0      5.00e+00 4.00e-02 2.15e+01
  dihedral pdb=" CA  ASN A 963 "
           pdb=" C   ASN A 963 "
           pdb=" N   GLN A 964 "
           pdb=" CA  GLN A 964 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.09   22.91     0      5.00e+00 4.00e-02 2.10e+01
  ... (remaining 4841 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 844
       0.051 -    0.102: 294
       0.102 -    0.153: 63
       0.153 -    0.204: 11
       0.204 -    0.255: 3
  Chirality restraints: 1215
  Sorted by residual:
  chirality pdb=" CG  LEU A 250 "
            pdb=" CB  LEU A 250 "
            pdb=" CD1 LEU A 250 "
            pdb=" CD2 LEU A 250 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.33   -0.26 2.00e-01 2.50e+01 1.63e+00
  chirality pdb=" CG  LEU A 322 "
            pdb=" CB  LEU A 322 "
            pdb=" CD1 LEU A 322 "
            pdb=" CD2 LEU A 322 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.34   -0.25 2.00e-01 2.50e+01 1.58e+00
  chirality pdb=" CB  VAL A   3 "
            pdb=" CA  VAL A   3 "
            pdb=" CG1 VAL A   3 "
            pdb=" CG2 VAL A   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.13e+00
  ... (remaining 1212 not shown)

  Planarity restraints: 1358
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 346 "   -0.054 5.00e-02 4.00e+02   8.03e-02 1.03e+01
        pdb=" N   PRO A 347 "    0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO A 347 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A 347 "   -0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 964 "   -0.039 5.00e-02 4.00e+02   5.78e-02 5.34e+00
        pdb=" N   PRO A 965 "    0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A 965 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 965 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A  42 "    0.038 5.00e-02 4.00e+02   5.75e-02 5.29e+00
        pdb=" N   PRO A  43 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A  43 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A  43 "    0.033 5.00e-02 4.00e+02
  ... (remaining 1355 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1348
        2.75 -     3.29: 8626
        3.29 -     3.83: 13765
        3.83 -     4.36: 16773
        4.36 -     4.90: 24654
  Nonbonded interactions: 65166
  Sorted by model distance:
  nonbonded pdb=" O   ASP A 121 "
            pdb=" OG1 THR A 125 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" O   HIS A 694 "
            pdb=" OG1 THR A 697 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O   GLU A 143 "
            pdb=" OG1 THR A 146 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O   LEU A 191 "
            pdb=" OG  SER A 194 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" O   VAL A1069 "
            pdb=" OG1 THR A1072 "
     model   vdw
     2.277 3.040
  ... (remaining 65161 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:             1.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     7.980
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
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      :  0.007   0.071   7654  Z= 0.332
  Angle     :  1.121  11.429  10325  Z= 0.644
  Chirality :  0.054   0.255   1215
  Planarity :  0.007   0.080   1358
  Dihedral  : 12.461  75.590   2958
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 14.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.69 %
    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: -4.61 (0.20), residues: 991
  helix: -2.98 (0.13), residues: 745
  sheet:  None (None), residues: 0
  loop : -2.47 (0.35), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.002   ARG A 758 
 TYR   0.022   0.003   TYR A 107 
 PHE   0.029   0.004   PHE A   4 
 TRP   0.017   0.004   TRP A 702 
 HIS   0.018   0.004   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00712 ( 7654)
  covalent geometry    : angle       1.12065 (10325)
  hydrogen bonds       : bond        0.30358 (  551)
  hydrogen bonds       : angle       9.24224 ( 1653)

*********************** 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
  231 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 230
  time to evaluate  : 0.297 
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: 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   72 ARG cc_start: 0.8532 (tpm170) cc_final: 0.8268 (tpm170)
REVERT: A  113 ARG cc_start: 0.9219 (ptm160) cc_final: 0.8717 (ptp-170)
REVERT: A  137 VAL cc_start: 0.9530 (t) cc_final: 0.9222 (t)
REVERT: A  174 MET cc_start: 0.8746 (mmm) cc_final: 0.8395 (mmm)
REVERT: A  181 GLU cc_start: 0.9294 (mm-30) cc_final: 0.8433 (mm-30)
REVERT: A  190 MET cc_start: 0.9301 (mtt) cc_final: 0.9003 (mtt)
REVERT: A  199 LYS cc_start: 0.8947 (tptp) cc_final: 0.8717 (tptp)
REVERT: A  201 LEU cc_start: 0.9649 (tp) cc_final: 0.9361 (tp)
REVERT: A  205 LEU cc_start: 0.9770 (tt) cc_final: 0.9504 (tp)
REVERT: A  237 MET cc_start: 0.9499 (mtm) cc_final: 0.8901 (ttm)
REVERT: A  245 ILE cc_start: 0.9249 (mt) cc_final: 0.8923 (mt)
REVERT: A  416 ARG cc_start: 0.7894 (mtp180) cc_final: 0.7365 (mtp180)
REVERT: A  471 GLN cc_start: 0.8739 (pt0) cc_final: 0.8012 (pt0)
REVERT: A  498 GLU cc_start: 0.9394 (mm-30) cc_final: 0.9037 (mm-30)
REVERT: A  502 ARG cc_start: 0.9104 (ttp80) cc_final: 0.8692 (ttt-90)
REVERT: A  533 MET cc_start: 0.9493 (mtm) cc_final: 0.8977 (mtp)
REVERT: A  591 MET cc_start: 0.9096 (tpt) cc_final: 0.8728 (tpt)
REVERT: A  635 ASN cc_start: 0.9219 (m-40) cc_final: 0.8952 (m110)
REVERT: A  646 LYS cc_start: 0.9313 (mtmm) cc_final: 0.8910 (mtmm)
REVERT: A  701 GLN cc_start: 0.9372 (tp-100) cc_final: 0.9132 (tp-100)
REVERT: A  707 GLU cc_start: 0.9441 (mm-30) cc_final: 0.8967 (tp30)
REVERT: A  748 MET cc_start: 0.9247 (mmp) cc_final: 0.9019 (mmm)
REVERT: A  784 LYS cc_start: 0.9666 (ttmm) cc_final: 0.9439 (tppt)
REVERT: A  797 MET cc_start: 0.9275 (mmm) cc_final: 0.9028 (mmp)
REVERT: A  799 MET cc_start: 0.9476 (mtt) cc_final: 0.9006 (tpt)
REVERT: A  823 ARG cc_start: 0.9272 (mpp80) cc_final: 0.8851 (mtt180)
REVERT: A  836 GLN cc_start: 0.8696 (mm110) cc_final: 0.8410 (mp10)
REVERT: A 1028 GLU cc_start: 0.9667 (tt0) cc_final: 0.9402 (tm-30)
REVERT: A 1046 ARG cc_start: 0.9239 (ttm110) cc_final: 0.8709 (mtm110)
REVERT: A 1073 MET cc_start: 0.9216 (mmt) cc_final: 0.8959 (mmm)
REVERT: A 1083 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8429 (mm-30)
REVERT: A 1090 MET cc_start: 0.9116 (mmt) cc_final: 0.8799 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 230
  average time/residue: 0.1178
  time to fit residues: 33.8542
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  : 0.302 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    7.9990
   chunk 45 optimal weight:    0.4980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A  48 GLN
A  93 GLN
A 179 GLN
A 279 GLN
A 471 GLN
A 575 GLN
A 814 GLN
A1086 GLN
A1093 HIS
A1094 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.087050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.068550 restraints weight = 33296.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.070488 restraints weight = 24116.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.071942 restraints weight = 18827.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.073074 restraints weight = 15471.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.073977 restraints weight = 13168.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.2938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7654  Z= 0.167
  Angle     :  0.719   7.301  10325  Z= 0.383
  Chirality :  0.041   0.143   1215
  Planarity :  0.005   0.050   1358
  Dihedral  :  5.769  19.917   1060
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 17.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  :  3.20 %
    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: -2.62 (0.23), residues: 991
  helix: -1.40 (0.15), residues: 812
  sheet:  None (None), residues: 0
  loop : -2.42 (0.44), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 759 
 TYR   0.020   0.002   TYR A 107 
 PHE   0.018   0.003   PHE A 126 
 TRP   0.012   0.002   TRP A 258 
 HIS   0.010   0.002   HIS A 694 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 7654)
  covalent geometry    : angle       0.71924 (10325)
  hydrogen bonds       : bond        0.05567 (  551)
  hydrogen bonds       : angle       5.32979 ( 1653)

*********************** 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
  236 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 231
  time to evaluate  : 0.309 
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: 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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 THR cc_start: 0.9557 (p) cc_final: 0.9323 (t)
REVERT: A  113 ARG cc_start: 0.9070 (ptm160) cc_final: 0.8182 (ptm160)
REVERT: A  174 MET cc_start: 0.8993 (mmm) cc_final: 0.8273 (mmm)
REVERT: A  176 ASP cc_start: 0.9527 (t0) cc_final: 0.9103 (t0)
REVERT: A  180 GLN cc_start: 0.9347 (mt0) cc_final: 0.9006 (mm-40)
REVERT: A  205 LEU cc_start: 0.9746 (tt) cc_final: 0.9487 (tt)
REVERT: A  237 MET cc_start: 0.9537 (mtm) cc_final: 0.9080 (mtm)
REVERT: A  253 TRP cc_start: 0.4328 (m100) cc_final: 0.3591 (m100)
REVERT: A  331 MET cc_start: 0.8825 (ttt) cc_final: 0.8487 (ttt)
REVERT: A  424 ASP cc_start: 0.8919 (t0) cc_final: 0.8623 (m-30)
REVERT: A  431 ILE cc_start: 0.8529 (mm) cc_final: 0.8274 (mm)
REVERT: A  471 GLN cc_start: 0.8847 (pt0) cc_final: 0.8370 (pt0)
REVERT: A  533 MET cc_start: 0.9417 (mtm) cc_final: 0.9153 (mtp)
REVERT: A  645 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8919 (mt-10)
REVERT: A  662 GLN cc_start: 0.9461 (mt0) cc_final: 0.9024 (mp10)
REVERT: A  748 MET cc_start: 0.9300 (mmp) cc_final: 0.9051 (mpp)
REVERT: A  749 LEU cc_start: 0.8856 (mt) cc_final: 0.8487 (mt)
REVERT: A  792 LYS cc_start: 0.9579 (mmtm) cc_final: 0.9379 (mmmm)
REVERT: A  799 MET cc_start: 0.9506 (mtt) cc_final: 0.9177 (tpt)
REVERT: A  823 ARG cc_start: 0.9196 (mpp80) cc_final: 0.8733 (mtt180)
REVERT: A  998 MET cc_start: 0.8455 (tpp) cc_final: 0.8094 (tpp)
REVERT: A 1029 VAL cc_start: 0.9596 (t) cc_final: 0.9345 (t)
REVERT: A 1046 ARG cc_start: 0.9310 (ttm110) cc_final: 0.8697 (mtm110)
REVERT: A 1083 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8229 (mm-30)
REVERT: A 1090 MET cc_start: 0.9156 (mmt) cc_final: 0.8815 (mmm)
  outliers start: 5
  outliers final: 0
  residues processed: 232
  average time/residue: 0.1119
  time to fit residues: 32.8079
Evaluate side-chains
  174 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
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:    0.0970
   chunk 46 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 92 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 43 optimal weight:    4.9990
   chunk 97 optimal weight:    0.9990
   chunk 44 optimal weight:    9.9990
   chunk 58 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 68 optimal weight:   20.0000
   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  48 GLN
** A 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 279 GLN
A 379 ASN
** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 701 GLN
A 745 GLN
A 814 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.087423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.068785 restraints weight = 34268.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.070671 restraints weight = 25399.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.072125 restraints weight = 20122.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.073258 restraints weight = 16638.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.074148 restraints weight = 14277.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.3755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7654  Z= 0.145
  Angle     :  0.658   7.896  10325  Z= 0.341
  Chirality :  0.040   0.119   1215
  Planarity :  0.004   0.044   1358
  Dihedral  :  5.265  19.169   1060
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 16.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  3.82 %
    Favored  : 95.81 %
  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: -1.37 (0.25), residues: 991
  helix: -0.53 (0.17), residues: 818
  sheet:  None (None), residues: 0
  loop : -2.01 (0.47), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 769 
 TYR   0.025   0.002   TYR A 107 
 PHE   0.018   0.003   PHE A  78 
 TRP   0.011   0.002   TRP A 253 
 HIS   0.010   0.001   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 7654)
  covalent geometry    : angle       0.65816 (10325)
  hydrogen bonds       : bond        0.04420 (  551)
  hydrogen bonds       : angle       4.71521 ( 1653)

*********************** 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
  227 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 224
  time to evaluate  : 0.269 
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: 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: symmetry clash
   revert: symmetry clash
REVERT: A  174 MET cc_start: 0.9242 (mmm) cc_final: 0.8501 (mmm)
REVERT: A  181 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8378 (mm-30)
REVERT: A  201 LEU cc_start: 0.9642 (tp) cc_final: 0.9160 (tp)
REVERT: A  205 LEU cc_start: 0.9715 (tt) cc_final: 0.9374 (tt)
REVERT: A  216 LYS cc_start: 0.9261 (mmmt) cc_final: 0.9038 (tmtt)
REVERT: A  224 GLU cc_start: 0.9480 (mt-10) cc_final: 0.9261 (mt-10)
REVERT: A  227 LEU cc_start: 0.9723 (tp) cc_final: 0.9427 (pp)
REVERT: A  237 MET cc_start: 0.9627 (mtm) cc_final: 0.8989 (mtm)
REVERT: A  240 GLU cc_start: 0.9224 (mp0) cc_final: 0.8996 (mp0)
REVERT: A  245 ILE cc_start: 0.9468 (mt) cc_final: 0.8994 (mt)
REVERT: A  252 SER cc_start: 0.9226 (t) cc_final: 0.9023 (t)
REVERT: A  253 TRP cc_start: 0.4374 (m100) cc_final: 0.3694 (m100)
REVERT: A  416 ARG cc_start: 0.7768 (mtp180) cc_final: 0.7047 (mtp180)
REVERT: A  496 LYS cc_start: 0.9361 (mtmm) cc_final: 0.9090 (mttt)
REVERT: A  533 MET cc_start: 0.9446 (mtm) cc_final: 0.9201 (mtp)
REVERT: A  591 MET cc_start: 0.9558 (mmm) cc_final: 0.9280 (mmm)
REVERT: A  633 PHE cc_start: 0.9298 (t80) cc_final: 0.8812 (t80)
REVERT: A  634 GLU cc_start: 0.9434 (mp0) cc_final: 0.9068 (mp0)
REVERT: A  635 ASN cc_start: 0.9263 (m110) cc_final: 0.9012 (m110)
REVERT: A  645 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8914 (mt-10)
REVERT: A  662 GLN cc_start: 0.9488 (mt0) cc_final: 0.9040 (mp10)
REVERT: A  792 LYS cc_start: 0.9599 (mmtm) cc_final: 0.9399 (mmmm)
REVERT: A  799 MET cc_start: 0.9538 (mtt) cc_final: 0.9176 (tpt)
REVERT: A  832 ARG cc_start: 0.8707 (tpm170) cc_final: 0.8115 (tpp-160)
REVERT: A 1046 ARG cc_start: 0.9293 (ttm110) cc_final: 0.8776 (mtm110)
REVERT: A 1083 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8124 (mm-30)
REVERT: A 1090 MET cc_start: 0.9125 (mmt) cc_final: 0.8783 (mmm)
REVERT: A 1110 GLU cc_start: 0.9357 (mp0) cc_final: 0.9044 (mp0)
  outliers start: 3
  outliers final: 2
  residues processed: 225
  average time/residue: 0.1040
  time to fit residues: 29.8652
Evaluate side-chains
  171 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 169
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 53 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 27 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   chunk 1 optimal weight:    7.9990
   chunk 51 optimal weight:    6.9990
   chunk 60 optimal weight:    0.5980
   chunk 21 optimal weight:    8.9990
   chunk 75 optimal weight:    0.9990
   chunk 73 optimal weight:    0.7980
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
A 184 HIS
A 279 GLN
** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 701 GLN
A 773 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.087669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.068803 restraints weight = 34964.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.070729 restraints weight = 25913.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.072134 restraints weight = 20537.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.073292 restraints weight = 17187.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.074207 restraints weight = 14731.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.4171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7654  Z= 0.149
  Angle     :  0.661   7.089  10325  Z= 0.344
  Chirality :  0.040   0.173   1215
  Planarity :  0.004   0.059   1358
  Dihedral  :  5.035  17.587   1060
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 17.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  3.69 %
    Favored  : 95.94 %
  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: -0.60 (0.26), residues: 991
  helix: -0.02 (0.17), residues: 809
  sheet:  None (None), residues: 0
  loop : -1.58 (0.47), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 409 
 TYR   0.019   0.001   TYR A 107 
 PHE   0.016   0.003   PHE A  78 
 TRP   0.016   0.002   TRP A 980 
 HIS   0.009   0.002   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 7654)
  covalent geometry    : angle       0.66096 (10325)
  hydrogen bonds       : bond        0.04006 (  551)
  hydrogen bonds       : angle       4.50739 ( 1653)

*********************** 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
  219 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 216
  time to evaluate  : 0.301 
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: 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: symmetry clash
REVERT: A   74 MET cc_start: 0.9282 (tpp) cc_final: 0.9035 (tpt)
REVERT: A  174 MET cc_start: 0.9023 (mmm) cc_final: 0.8731 (mmm)
REVERT: A  177 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8957 (mp0)
REVERT: A  205 LEU cc_start: 0.9697 (tt) cc_final: 0.9352 (tt)
REVERT: A  224 GLU cc_start: 0.9478 (mt-10) cc_final: 0.9264 (mt-10)
REVERT: A  227 LEU cc_start: 0.9717 (tp) cc_final: 0.9443 (pp)
REVERT: A  237 MET cc_start: 0.9568 (mtm) cc_final: 0.9240 (mtt)
REVERT: A  253 TRP cc_start: 0.4536 (m100) cc_final: 0.3940 (m100)
REVERT: A  416 ARG cc_start: 0.7637 (mtp180) cc_final: 0.6952 (mtp180)
REVERT: A  496 LYS cc_start: 0.9391 (mtmm) cc_final: 0.9051 (mttt)
REVERT: A  525 GLU cc_start: 0.9284 (mm-30) cc_final: 0.8896 (mm-30)
REVERT: A  533 MET cc_start: 0.9423 (mtm) cc_final: 0.9189 (mtp)
REVERT: A  593 GLN cc_start: 0.9381 (mt0) cc_final: 0.9110 (mm-40)
REVERT: A  633 PHE cc_start: 0.9191 (t80) cc_final: 0.8920 (t80)
REVERT: A  635 ASN cc_start: 0.9265 (m110) cc_final: 0.8944 (m110)
REVERT: A  645 GLU cc_start: 0.9199 (mt-10) cc_final: 0.8842 (mp0)
REVERT: A  646 LYS cc_start: 0.9345 (mttt) cc_final: 0.9117 (mttt)
REVERT: A  662 GLN cc_start: 0.9452 (mt0) cc_final: 0.9213 (mp10)
REVERT: A  709 MET cc_start: 0.9023 (mmt) cc_final: 0.8821 (mmt)
REVERT: A  799 MET cc_start: 0.9532 (mtt) cc_final: 0.9177 (tpt)
REVERT: A  832 ARG cc_start: 0.8603 (tpm170) cc_final: 0.8071 (tpp-160)
REVERT: A  998 MET cc_start: 0.8332 (tpp) cc_final: 0.8115 (tpp)
REVERT: A 1004 LEU cc_start: 0.9689 (tp) cc_final: 0.9364 (mt)
REVERT: A 1046 ARG cc_start: 0.9258 (ttm110) cc_final: 0.8752 (ttm110)
REVERT: A 1059 ILE cc_start: 0.9172 (mp) cc_final: 0.8965 (mp)
REVERT: A 1083 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8018 (mm-30)
REVERT: A 1090 MET cc_start: 0.9058 (mmt) cc_final: 0.8733 (mmm)
REVERT: A 1110 GLU cc_start: 0.9338 (mp0) cc_final: 0.8971 (mp0)
  outliers start: 3
  outliers final: 1
  residues processed: 216
  average time/residue: 0.1046
  time to fit residues: 29.0016
Evaluate side-chains
  166 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 164
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 94 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 22 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9990
   chunk 18 optimal weight:    5.9990
   chunk 65 optimal weight:    0.0770
   chunk 56 optimal weight:   10.0000
   overall best weight:    0.7942

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

Flipped N/Q/H residues before XYZ refinement:
A 279 GLN
** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 701 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.087678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.069073 restraints weight = 35131.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.071077 restraints weight = 25781.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.072648 restraints weight = 20214.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.073872 restraints weight = 16592.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.074836 restraints weight = 14095.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.4613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7654  Z= 0.136
  Angle     :  0.657   6.830  10325  Z= 0.337
  Chirality :  0.040   0.169   1215
  Planarity :  0.004   0.051   1358
  Dihedral  :  4.843  17.766   1060
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 17.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  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: -0.29 (0.26), residues: 991
  helix:  0.20 (0.18), residues: 810
  sheet:  None (None), residues: 0
  loop : -1.49 (0.47), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 188 
 TYR   0.016   0.001   TYR A 107 
 PHE   0.019   0.002   PHE A  78 
 TRP   0.044   0.003   TRP A 394 
 HIS   0.009   0.001   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 7654)
  covalent geometry    : angle       0.65730 (10325)
  hydrogen bonds       : bond        0.03675 (  551)
  hydrogen bonds       : angle       4.30600 ( 1653)

*********************** 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
  214 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 0.312 
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: 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  113 ARG cc_start: 0.9170 (ptm-80) cc_final: 0.8189 (ptp-110)
REVERT: A  174 MET cc_start: 0.9094 (mmm) cc_final: 0.8676 (mmm)
REVERT: A  176 ASP cc_start: 0.9460 (t70) cc_final: 0.8963 (t70)
REVERT: A  227 LEU cc_start: 0.9725 (tp) cc_final: 0.9440 (pp)
REVERT: A  237 MET cc_start: 0.9342 (mtm) cc_final: 0.9009 (mmm)
REVERT: A  252 SER cc_start: 0.9285 (m) cc_final: 0.9076 (t)
REVERT: A  407 GLN cc_start: 0.8793 (tm-30) cc_final: 0.8589 (tm-30)
REVERT: A  416 ARG cc_start: 0.7645 (mtp180) cc_final: 0.7079 (mtp180)
REVERT: A  496 LYS cc_start: 0.9366 (mtmm) cc_final: 0.9084 (mttt)
REVERT: A  533 MET cc_start: 0.9408 (mtm) cc_final: 0.9162 (mtp)
REVERT: A  589 GLU cc_start: 0.9461 (tm-30) cc_final: 0.9207 (pt0)
REVERT: A  591 MET cc_start: 0.9408 (mmm) cc_final: 0.9099 (mmm)
REVERT: A  618 ASP cc_start: 0.8825 (t0) cc_final: 0.8472 (m-30)
REVERT: A  633 PHE cc_start: 0.9109 (t80) cc_final: 0.8848 (t80)
REVERT: A  635 ASN cc_start: 0.9132 (m110) cc_final: 0.8895 (m110)
REVERT: A  645 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8897 (mp0)
REVERT: A  646 LYS cc_start: 0.9282 (mttt) cc_final: 0.9033 (mttt)
REVERT: A  662 GLN cc_start: 0.9435 (mt0) cc_final: 0.8946 (mp10)
REVERT: A  702 TRP cc_start: 0.9150 (t60) cc_final: 0.8751 (t60)
REVERT: A  735 ASP cc_start: 0.9387 (m-30) cc_final: 0.9134 (m-30)
REVERT: A  799 MET cc_start: 0.9533 (mtt) cc_final: 0.9155 (tpt)
REVERT: A 1046 ARG cc_start: 0.9284 (ttm110) cc_final: 0.8772 (ttm110)
REVERT: A 1090 MET cc_start: 0.9045 (mmt) cc_final: 0.8675 (mmm)
REVERT: A 1110 GLU cc_start: 0.9078 (mp0) cc_final: 0.8664 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 214
  average time/residue: 0.1021
  time to fit residues: 28.0533
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  : 0.203 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 44 optimal weight:    6.9990
   chunk 12 optimal weight:    0.8980
   chunk 91 optimal weight:    0.5980
   chunk 2 optimal weight:    6.9990
   chunk 84 optimal weight:    7.9990
   chunk 26 optimal weight:    0.3980
   chunk 28 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 81 optimal weight:    1.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 279 GLN
** A 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 685 ASN
** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 701 GLN
A 773 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.088599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.069616 restraints weight = 34821.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.071551 restraints weight = 25813.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.073051 restraints weight = 20461.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.074218 restraints weight = 16950.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.075099 restraints weight = 14570.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.4922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7654  Z= 0.150
  Angle     :  0.696   7.696  10325  Z= 0.354
  Chirality :  0.041   0.155   1215
  Planarity :  0.004   0.047   1358
  Dihedral  :  4.824  21.963   1060
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 16.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.20 %
    Favored  : 96.67 %
  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: -0.05 (0.27), residues: 991
  helix:  0.36 (0.18), residues: 811
  sheet:  None (None), residues: 0
  loop : -1.42 (0.48), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 188 
 TYR   0.015   0.001   TYR A 107 
 PHE   0.017   0.002   PHE A  78 
 TRP   0.031   0.003   TRP A 253 
 HIS   0.008   0.002   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 7654)
  covalent geometry    : angle       0.69571 (10325)
  hydrogen bonds       : bond        0.03694 (  551)
  hydrogen bonds       : angle       4.29813 ( 1653)

*********************** 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
  214 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 213
  time to evaluate  : 0.294 
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: 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: symmetry clash
REVERT: A   74 MET cc_start: 0.9348 (mmm) cc_final: 0.9069 (mmm)
REVERT: A  113 ARG cc_start: 0.8994 (ptm-80) cc_final: 0.8268 (ptp-110)
REVERT: A  174 MET cc_start: 0.9146 (mmm) cc_final: 0.8716 (mmm)
REVERT: A  190 MET cc_start: 0.9464 (pmm) cc_final: 0.9246 (pmm)
REVERT: A  227 LEU cc_start: 0.9739 (tp) cc_final: 0.9484 (pp)
REVERT: A  237 MET cc_start: 0.9386 (mtm) cc_final: 0.9011 (mmm)
REVERT: A  331 MET cc_start: 0.8882 (mtp) cc_final: 0.8546 (mmm)
REVERT: A  407 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8572 (tm-30)
REVERT: A  416 ARG cc_start: 0.7743 (mtp180) cc_final: 0.7204 (mtp180)
REVERT: A  533 MET cc_start: 0.9374 (mtm) cc_final: 0.8919 (mtm)
REVERT: A  618 ASP cc_start: 0.8845 (t0) cc_final: 0.8509 (m-30)
REVERT: A  633 PHE cc_start: 0.9214 (t80) cc_final: 0.8926 (t80)
REVERT: A  635 ASN cc_start: 0.9164 (m110) cc_final: 0.8924 (m110)
REVERT: A  645 GLU cc_start: 0.9246 (mt-10) cc_final: 0.9017 (mt-10)
REVERT: A  646 LYS cc_start: 0.9432 (mttt) cc_final: 0.9201 (mttt)
REVERT: A  662 GLN cc_start: 0.9421 (mt0) cc_final: 0.8928 (mp10)
REVERT: A  694 HIS cc_start: 0.8994 (t-170) cc_final: 0.8693 (t-170)
REVERT: A  698 MET cc_start: 0.9100 (mmm) cc_final: 0.8729 (mmm)
REVERT: A  702 TRP cc_start: 0.9237 (t60) cc_final: 0.8937 (t60)
REVERT: A  735 ASP cc_start: 0.9431 (m-30) cc_final: 0.9189 (m-30)
REVERT: A  799 MET cc_start: 0.9576 (mtt) cc_final: 0.9202 (tpt)
REVERT: A  832 ARG cc_start: 0.8686 (tpm170) cc_final: 0.8134 (tpp-160)
REVERT: A  994 MET cc_start: 0.9128 (ppp) cc_final: 0.8911 (ppp)
REVERT: A 1001 MET cc_start: 0.8760 (ppp) cc_final: 0.8486 (ppp)
REVERT: A 1011 THR cc_start: 0.9013 (m) cc_final: 0.8687 (p)
REVERT: A 1046 ARG cc_start: 0.9311 (ttm110) cc_final: 0.8835 (ttm110)
REVERT: A 1090 MET cc_start: 0.9050 (mmt) cc_final: 0.8673 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 213
  average time/residue: 0.1036
  time to fit residues: 28.1363
Evaluate side-chains
  163 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
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:    0.0870
   chunk 57 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   chunk 92 optimal weight:    0.9980
   chunk 0 optimal weight:    8.9990
   chunk 58 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 26 optimal weight:    6.9990
   chunk 87 optimal weight:    0.7980
   chunk 67 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   overall best weight:    0.7158

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

Flipped N/Q/H residues before XYZ refinement:
A 180 GLN
** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 701 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.089025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.069852 restraints weight = 34271.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.071760 restraints weight = 25586.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.073276 restraints weight = 20361.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.074416 restraints weight = 16898.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.075349 restraints weight = 14559.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.5258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7654  Z= 0.141
  Angle     :  0.699   6.960  10325  Z= 0.360
  Chirality :  0.041   0.164   1215
  Planarity :  0.004   0.045   1358
  Dihedral  :  4.806  20.253   1060
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 16.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  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:  0.36 (0.18), residues: 811
  sheet:  None (None), residues: 0
  loop : -1.34 (0.49), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 547 
 TYR   0.015   0.001   TYR A 107 
 PHE   0.019   0.002   PHE A  78 
 TRP   0.052   0.004   TRP A 980 
 HIS   0.005   0.001   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 7654)
  covalent geometry    : angle       0.69901 (10325)
  hydrogen bonds       : bond        0.03433 (  551)
  hydrogen bonds       : angle       4.27676 ( 1653)

*********************** 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
  205 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 0.227 
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: 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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 HIS cc_start: 0.8851 (t-90) cc_final: 0.8549 (t-90)
REVERT: A  174 MET cc_start: 0.9076 (mmm) cc_final: 0.8433 (mmm)
REVERT: A  190 MET cc_start: 0.9454 (pmm) cc_final: 0.9200 (pmm)
REVERT: A  227 LEU cc_start: 0.9667 (tp) cc_final: 0.9324 (pp)
REVERT: A  237 MET cc_start: 0.9360 (mtm) cc_final: 0.9039 (mmm)
REVERT: A  407 GLN cc_start: 0.8769 (tm-30) cc_final: 0.8560 (tm-30)
REVERT: A  416 ARG cc_start: 0.7648 (mtp180) cc_final: 0.7157 (mtp180)
REVERT: A  533 MET cc_start: 0.9406 (mtm) cc_final: 0.8956 (mtm)
REVERT: A  633 PHE cc_start: 0.9161 (t80) cc_final: 0.8898 (t80)
REVERT: A  635 ASN cc_start: 0.9126 (m110) cc_final: 0.8888 (m110)
REVERT: A  662 GLN cc_start: 0.9414 (mt0) cc_final: 0.9156 (mp10)
REVERT: A  694 HIS cc_start: 0.8982 (t-170) cc_final: 0.8681 (t-170)
REVERT: A  698 MET cc_start: 0.9019 (mmm) cc_final: 0.8653 (mmm)
REVERT: A  702 TRP cc_start: 0.9189 (t60) cc_final: 0.8962 (t60)
REVERT: A  735 ASP cc_start: 0.9407 (m-30) cc_final: 0.9145 (m-30)
REVERT: A  773 ASN cc_start: 0.9038 (t0) cc_final: 0.8167 (m110)
REVERT: A  799 MET cc_start: 0.9518 (mtt) cc_final: 0.9161 (tpt)
REVERT: A  980 TRP cc_start: 0.6198 (m-10) cc_final: 0.5630 (t-100)
REVERT: A 1001 MET cc_start: 0.8753 (ppp) cc_final: 0.8454 (ppp)
REVERT: A 1011 THR cc_start: 0.8940 (m) cc_final: 0.8626 (p)
REVERT: A 1046 ARG cc_start: 0.9342 (ttm110) cc_final: 0.8884 (ttm110)
REVERT: A 1081 ASP cc_start: 0.8873 (t0) cc_final: 0.8434 (p0)
REVERT: A 1090 MET cc_start: 0.8942 (mmt) cc_final: 0.8591 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 205
  average time/residue: 0.0920
  time to fit residues: 24.6519
Evaluate side-chains
  166 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 10 optimal weight:    0.3980
   chunk 4 optimal weight:    6.9990
   chunk 32 optimal weight:   10.0000
   chunk 68 optimal weight:    8.9990
   chunk 94 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0670
   chunk 47 optimal weight:    4.9990
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
A 674 GLN
** A 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 773 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.090368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.070689 restraints weight = 34553.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.072629 restraints weight = 25947.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.074165 restraints weight = 20699.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.075333 restraints weight = 17231.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.076249 restraints weight = 14836.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.5515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7654  Z= 0.141
  Angle     :  0.695   7.129  10325  Z= 0.361
  Chirality :  0.042   0.146   1215
  Planarity :  0.004   0.044   1358
  Dihedral  :  4.750  20.143   1060
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 16.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  1.48 %
    Favored  : 98.40 %
  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: -0.12 (0.27), residues: 991
  helix:  0.31 (0.18), residues: 817
  sheet:  None (None), residues: 0
  loop : -1.43 (0.49), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 547 
 TYR   0.018   0.002   TYR A 107 
 PHE   0.046   0.003   PHE A 212 
 TRP   0.039   0.003   TRP A 980 
 HIS   0.009   0.001   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 7654)
  covalent geometry    : angle       0.69538 (10325)
  hydrogen bonds       : bond        0.03557 (  551)
  hydrogen bonds       : angle       4.28901 ( 1653)

*********************** 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
  203 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 202
  time to evaluate  : 0.264 
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: 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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 MET cc_start: 0.9000 (mmm) cc_final: 0.8725 (mmm)
REVERT: A  227 LEU cc_start: 0.9692 (tp) cc_final: 0.9374 (pp)
REVERT: A  237 MET cc_start: 0.9385 (mtm) cc_final: 0.9069 (mmm)
REVERT: A  247 VAL cc_start: 0.9050 (t) cc_final: 0.8566 (t)
REVERT: A  350 MET cc_start: -0.2441 (tpt) cc_final: -0.2787 (tpt)
REVERT: A  525 GLU cc_start: 0.9359 (mm-30) cc_final: 0.9033 (mm-30)
REVERT: A  533 MET cc_start: 0.9394 (mtm) cc_final: 0.8962 (mtm)
REVERT: A  618 ASP cc_start: 0.8839 (t0) cc_final: 0.8509 (m-30)
REVERT: A  633 PHE cc_start: 0.9238 (t80) cc_final: 0.8963 (t80)
REVERT: A  635 ASN cc_start: 0.9138 (m110) cc_final: 0.8897 (m110)
REVERT: A  662 GLN cc_start: 0.9397 (mt0) cc_final: 0.9117 (mp10)
REVERT: A  701 GLN cc_start: 0.9311 (tp40) cc_final: 0.9072 (tp-100)
REVERT: A  702 TRP cc_start: 0.9252 (t60) cc_final: 0.8991 (t60)
REVERT: A  799 MET cc_start: 0.9561 (mtt) cc_final: 0.9172 (tpt)
REVERT: A  980 TRP cc_start: 0.6200 (m-10) cc_final: 0.5664 (t60)
REVERT: A 1001 MET cc_start: 0.8849 (ppp) cc_final: 0.8586 (ppp)
REVERT: A 1011 THR cc_start: 0.8993 (m) cc_final: 0.8716 (p)
REVERT: A 1046 ARG cc_start: 0.9328 (ttm110) cc_final: 0.8856 (ttm110)
REVERT: A 1073 MET cc_start: 0.9193 (mmp) cc_final: 0.8946 (mmm)
REVERT: A 1081 ASP cc_start: 0.8971 (t0) cc_final: 0.8548 (p0)
REVERT: A 1090 MET cc_start: 0.8920 (mmt) cc_final: 0.8573 (mmm)
  outliers start: 1
  outliers final: 1
  residues processed: 202
  average time/residue: 0.1039
  time to fit residues: 26.8569
Evaluate side-chains
  163 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 162
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 72 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   chunk 82 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 89 optimal weight:   10.0000
   chunk 43 optimal weight:    0.6980
   chunk 65 optimal weight:    0.1980
   chunk 50 optimal weight:    8.9990
   chunk 94 optimal weight:    1.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A  22 HIS
A 184 HIS
** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.090323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.070887 restraints weight = 34442.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.072772 restraints weight = 26026.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.074269 restraints weight = 20920.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.075408 restraints weight = 17485.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.076360 restraints weight = 15138.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.5727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7654  Z= 0.144
  Angle     :  0.714   9.916  10325  Z= 0.371
  Chirality :  0.042   0.153   1215
  Planarity :  0.004   0.044   1358
  Dihedral  :  4.725  19.905   1060
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 17.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  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: -0.01 (0.27), residues: 991
  helix:  0.37 (0.18), residues: 815
  sheet:  None (None), residues: 0
  loop : -1.32 (0.49), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 759 
 TYR   0.016   0.001   TYR A 107 
 PHE   0.044   0.003   PHE A 212 
 TRP   0.030   0.003   TRP A 980 
 HIS   0.010   0.001   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 7654)
  covalent geometry    : angle       0.71381 (10325)
  hydrogen bonds       : bond        0.03511 (  551)
  hydrogen bonds       : angle       4.36198 ( 1653)

*********************** 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
  202 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 0.300 
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: 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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 HIS cc_start: 0.8346 (t70) cc_final: 0.8088 (t70)
REVERT: A  174 MET cc_start: 0.8978 (mmm) cc_final: 0.8735 (mmm)
REVERT: A  227 LEU cc_start: 0.9687 (tp) cc_final: 0.9333 (pp)
REVERT: A  237 MET cc_start: 0.9383 (mtm) cc_final: 0.9085 (mmm)
REVERT: A  245 ILE cc_start: 0.9476 (mt) cc_final: 0.9230 (mt)
REVERT: A  533 MET cc_start: 0.9388 (mtm) cc_final: 0.8792 (mtm)
REVERT: A  618 ASP cc_start: 0.8840 (t0) cc_final: 0.8528 (m-30)
REVERT: A  633 PHE cc_start: 0.9181 (t80) cc_final: 0.8874 (t80)
REVERT: A  635 ASN cc_start: 0.9132 (m110) cc_final: 0.8873 (m110)
REVERT: A  646 LYS cc_start: 0.9300 (mttt) cc_final: 0.8984 (mttt)
REVERT: A  694 HIS cc_start: 0.9147 (t70) cc_final: 0.8936 (t-90)
REVERT: A  701 GLN cc_start: 0.9226 (tp40) cc_final: 0.9009 (tp-100)
REVERT: A  702 TRP cc_start: 0.9197 (t60) cc_final: 0.8924 (t60)
REVERT: A  735 ASP cc_start: 0.9341 (m-30) cc_final: 0.9122 (m-30)
REVERT: A  759 ARG cc_start: 0.9118 (mpt90) cc_final: 0.8811 (mmt90)
REVERT: A  799 MET cc_start: 0.9546 (mtt) cc_final: 0.9174 (tpt)
REVERT: A 1001 MET cc_start: 0.8846 (ppp) cc_final: 0.8558 (ppp)
REVERT: A 1011 THR cc_start: 0.9000 (m) cc_final: 0.8725 (p)
REVERT: A 1046 ARG cc_start: 0.9298 (ttm110) cc_final: 0.8823 (ttm110)
REVERT: A 1073 MET cc_start: 0.9195 (mmp) cc_final: 0.8984 (mmm)
REVERT: A 1083 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7569 (mm-30)
REVERT: A 1090 MET cc_start: 0.8889 (mmt) cc_final: 0.8559 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 202
  average time/residue: 0.0995
  time to fit residues: 26.0544
Evaluate side-chains
  165 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 66 optimal weight:    0.9980
   chunk 41 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   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 516 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.090135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.070797 restraints weight = 34755.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.072727 restraints weight = 26041.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.074222 restraints weight = 20787.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.075355 restraints weight = 17339.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.076272 restraints weight = 14989.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.5939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7654  Z= 0.146
  Angle     :  0.719  10.070  10325  Z= 0.373
  Chirality :  0.042   0.146   1215
  Planarity :  0.004   0.045   1358
  Dihedral  :  4.717  20.851   1060
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 18.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  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: -0.04 (0.27), residues: 991
  helix:  0.37 (0.18), residues: 816
  sheet:  None (None), residues: 0
  loop : -1.46 (0.48), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 759 
 TYR   0.017   0.001   TYR A 107 
 PHE   0.018   0.002   PHE A 212 
 TRP   0.043   0.003   TRP A 980 
 HIS   0.009   0.001   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 7654)
  covalent geometry    : angle       0.71859 (10325)
  hydrogen bonds       : bond        0.03596 (  551)
  hydrogen bonds       : angle       4.42150 ( 1653)

********************** 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
  204 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  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: 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: 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   10 GLU cc_start: 0.9297 (tm-30) cc_final: 0.9047 (tp30)
REVERT: A  174 MET cc_start: 0.8986 (mmm) cc_final: 0.8714 (mmm)
REVERT: A  227 LEU cc_start: 0.9706 (tp) cc_final: 0.9366 (pp)
REVERT: A  237 MET cc_start: 0.9375 (mtm) cc_final: 0.9084 (mmm)
REVERT: A  533 MET cc_start: 0.9423 (mtm) cc_final: 0.8811 (mtm)
REVERT: A  633 PHE cc_start: 0.9190 (t80) cc_final: 0.8908 (t80)
REVERT: A  635 ASN cc_start: 0.9149 (m110) cc_final: 0.8887 (m110)
REVERT: A  643 THR cc_start: 0.9365 (p) cc_final: 0.8742 (p)
REVERT: A  701 GLN cc_start: 0.9250 (tp40) cc_final: 0.9041 (tp-100)
REVERT: A  702 TRP cc_start: 0.9172 (t60) cc_final: 0.8923 (t60)
REVERT: A  735 ASP cc_start: 0.9373 (m-30) cc_final: 0.9151 (m-30)
REVERT: A  759 ARG cc_start: 0.9106 (mpt90) cc_final: 0.8746 (mmt90)
REVERT: A  799 MET cc_start: 0.9550 (mtt) cc_final: 0.9185 (tpt)
REVERT: A  980 TRP cc_start: 0.5982 (m-10) cc_final: 0.5712 (t60)
REVERT: A 1011 THR cc_start: 0.9014 (m) cc_final: 0.8758 (p)
REVERT: A 1046 ARG cc_start: 0.9302 (ttm110) cc_final: 0.8797 (ttm110)
REVERT: A 1081 ASP cc_start: 0.8771 (t70) cc_final: 0.8503 (t0)
REVERT: A 1083 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7541 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 204
  average time/residue: 0.1015
  time to fit residues: 26.7807
Evaluate side-chains
  161 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 48 optimal weight:    6.9990
   chunk 98 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9980
   chunk 92 optimal weight:    7.9990
   chunk 94 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 97 optimal weight:    3.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 184 HIS
A 694 HIS
** A 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.088371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.069325 restraints weight = 35120.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.071231 restraints weight = 26275.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.072717 restraints weight = 20969.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.073845 restraints weight = 17449.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.074724 restraints weight = 15064.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.5895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   7654  Z= 0.175
  Angle     :  0.749   7.696  10325  Z= 0.393
  Chirality :  0.043   0.185   1215
  Planarity :  0.004   0.045   1358
  Dihedral  :  4.740  21.491   1060
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 19.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  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:  0.07 (0.27), residues: 991
  helix:  0.47 (0.18), residues: 813
  sheet:  None (None), residues: 0
  loop : -1.53 (0.48), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 759 
 TYR   0.016   0.001   TYR A 107 
 PHE   0.044   0.003   PHE A 212 
 TRP   0.036   0.003   TRP A 980 
 HIS   0.008   0.001   HIS A 187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 7654)
  covalent geometry    : angle       0.74858 (10325)
  hydrogen bonds       : bond        0.03873 (  551)
  hydrogen bonds       : angle       4.56075 ( 1653)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1421.82 seconds
wall clock time: 25 minutes 16.22 seconds (1516.22 seconds total)