Starting phenix.real_space_refine
on Thu Mar  5 01:20:04 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zr6_14884/03_2026/7zr6_14884.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zr6_14884/03_2026/7zr6_14884.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zr6_14884/03_2026/7zr6_14884.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zr6_14884/03_2026/7zr6_14884.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zr6_14884/03_2026/7zr6_14884.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zr6_14884/03_2026/7zr6_14884.cif"
  }
  resolution = 4.2
  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=   0.002 sd=   0.029
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       7      5.49       5
     S      91      5.16       5
     C   11196      2.51       5
     N    3012      2.21       5
     O    3394      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 55 residue(s): 0.02s

  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: 17700
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 5132
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 633, 5132
          Classifications: {'peptide': 633}
          Link IDs: {'PTRANS': 17, 'TRANS': 615}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 5112
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 631, 5112
          Classifications: {'peptide': 631}
          Link IDs: {'PTRANS': 17, 'TRANS': 613}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2337
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 277, 2337
          Classifications: {'peptide': 277}
          Link IDs: {'PTRANS': 4, 'TRANS': 272}
    Chain: "K"
      Number of atoms: 1503
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 186, 1503
          Classifications: {'peptide': 186}
          Link IDs: {'PTRANS': 9, 'TRANS': 176}
          Chain breaks: 1
    Chain: "P"
      Number of atoms: 3554
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 441, 3554
          Classifications: {'peptide': 441}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 422}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 3
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.67, per 1000 atoms: 0.21
  Number of scatterers: 17700
  At special positions: 0
  Unit cell: (127.28, 140.18, 195.22, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      91     16.00
     P       7     15.00
     O    3394      8.00
     N    3012      7.00
     C   11196      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=3, symmetry=0
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.66
  Conformation dependent library (CDL) restraints added in 659.4 milliseconds
  

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4128

  Finding SS restraints...
    Secondary structure from input PDB file:
      83 helices and 16 sheets defined
      49.4% alpha, 8.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 31
    Processing helix  chain 'A' and resid 37 through 46
      removed outlier: 4.026A  pdb=" N   ARG A  41 " --> pdb=" O   GLU A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 61
      removed outlier: 3.654A  pdb=" N   LEU A  51 " --> pdb=" O   ALA A  47 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LYS A  53 " --> pdb=" O   ASP A  49 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   LEU A  59 " --> pdb=" O   ARG A  55 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   THR A  60 " --> pdb=" O   TYR A  56 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   ASP A  61 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 102
      removed outlier: 4.198A  pdb=" N   ILE A  99 " --> pdb=" O   LYS A  95 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   ASN A 100 " --> pdb=" O   ALA A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 117
      removed outlier: 4.218A  pdb=" N   ALA A 112 " --> pdb=" O   SER A 108 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   LEU A 117 " --> pdb=" O   PHE A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 138
      removed outlier: 3.587A  pdb=" N   SER A 135 " --> pdb=" O   GLY A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 205
      removed outlier: 3.680A  pdb=" N   VAL A 198 " --> pdb=" O   GLU A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 296
      removed outlier: 3.695A  pdb=" N   ILE A 296 " --> pdb=" O   PRO A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 307
      removed outlier: 4.179A  pdb=" N   TYR A 301 " --> pdb=" O   THR A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 420
    Processing helix  chain 'A' and resid 424 through 444
      removed outlier: 4.422A  pdb=" N   LYS A 428 " --> pdb=" O   GLU A 424 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   ALA A 432 " --> pdb=" O   LYS A 428 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   SER A 434 " --> pdb=" O   TYR A 430 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   LYS A 435 " --> pdb=" O   GLU A 431 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   ASN A 436 " --> pdb=" O   ALA A 432 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LEU A 437 " --> pdb=" O   PHE A 433 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LYS A 438 " --> pdb=" O   SER A 434 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   LEU A 439 " --> pdb=" O   LYS A 435 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   GLY A 440 " --> pdb=" O   ASN A 436 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   ILE A 441 " --> pdb=" O   LEU A 437 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   HIS A 442 " --> pdb=" O   LYS A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 452
    Processing helix  chain 'A' and resid 453 through 455
      No H-bonds generated for 'chain 'A' and resid 453 through 455'
    Processing helix  chain 'A' and resid 468 through 474
      removed outlier: 3.740A  pdb=" N   TYR A 472 " --> pdb=" O   SER A 468 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 490 through 496
      removed outlier: 3.891A  pdb=" N   VAL A 494 " --> pdb=" O   SER A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 507
      removed outlier: 3.544A  pdb=" N   GLY A 507 " --> pdb=" O   VAL A 503 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 523
      removed outlier: 4.416A  pdb=" N   GLN A 523 " --> pdb=" O   GLU A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 546 through 559
      removed outlier: 3.855A  pdb=" N   LYS A 550 " --> pdb=" O   ASP A 546 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   ALA A 558 " --> pdb=" O   GLU A 554 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   LYS A 559 " --> pdb=" O   GLU A 555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 571
      removed outlier: 4.266A  pdb=" N   LYS A 565 " --> pdb=" O   GLU A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 599 through 608
    Processing helix  chain 'A' and resid 616 through 621
      removed outlier: 4.202A  pdb=" N   MET A 621 " --> pdb=" O   GLY A 618 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 632 through 643
      removed outlier: 3.777A  pdb=" N   GLU A 636 " --> pdb=" O   HIS A 632 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 649 through 665
      removed outlier: 4.000A  pdb=" N   ASP A 653 " --> pdb=" O   LYS A 649 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 689
      removed outlier: 3.589A  pdb=" N   HIS A 676 " --> pdb=" O   ASP A 672 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 21 through 31
    Processing helix  chain 'B' and resid 38 through 59
      removed outlier: 3.584A  pdb=" N   LEU B  59 " --> pdb=" O   ARG B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 65
      removed outlier: 3.804A  pdb=" N   LEU B  65 " --> pdb=" O   PRO B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 94 through 102
    Processing helix  chain 'B' and resid 108 through 117
      removed outlier: 4.092A  pdb=" N   ALA B 112 " --> pdb=" O   SER B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 136
    Processing helix  chain 'B' and resid 194 through 205
      removed outlier: 3.689A  pdb=" N   VAL B 198 " --> pdb=" O   GLU B 194 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 297
      removed outlier: 3.723A  pdb=" N   ILE B 296 " --> pdb=" O   PRO B 293 " (cutoff:3.500A)
      removed outlier: 5.509A  pdb=" N   THR B 297 " --> pdb=" O   ASP B 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 309
      removed outlier: 3.758A  pdb=" N   TYR B 305 " --> pdb=" O   TYR B 301 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   LYS B 306 " --> pdb=" O   GLY B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 375
    Processing helix  chain 'B' and resid 399 through 419
      removed outlier: 4.194A  pdb=" N   ARG B 405 " --> pdb=" O   LEU B 401 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   LYS B 406 " --> pdb=" O   LYS B 402 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ASN B 407 " --> pdb=" O   VAL B 403 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLU B 414 " --> pdb=" O   LYS B 410 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   LEU B 415 " --> pdb=" O   LYS B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 441
      removed outlier: 3.740A  pdb=" N   LYS B 427 " --> pdb=" O   LYS B 423 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   LYS B 428 " --> pdb=" O   GLU B 424 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ALA B 432 " --> pdb=" O   LYS B 428 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   SER B 434 " --> pdb=" O   TYR B 430 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   LYS B 435 " --> pdb=" O   GLU B 431 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   ASN B 436 " --> pdb=" O   ALA B 432 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   LEU B 437 " --> pdb=" O   PHE B 433 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 469 through 473
    Processing helix  chain 'B' and resid 490 through 496
      removed outlier: 3.656A  pdb=" N   ASN B 496 " --> pdb=" O   GLU B 492 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 499 through 504
      removed outlier: 4.438A  pdb=" N   VAL B 503 " --> pdb=" O   PHE B 499 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 515 through 525
      removed outlier: 3.728A  pdb=" N   GLU B 519 " --> pdb=" O   GLU B 515 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   TYR B 520 " --> pdb=" O   PRO B 516 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLN B 524 " --> pdb=" O   TYR B 520 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 547 through 560
      removed outlier: 4.167A  pdb=" N   LYS B 551 " --> pdb=" O   GLU B 547 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   LYS B 552 " --> pdb=" O   GLU B 548 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 560 through 571
      removed outlier: 3.532A  pdb=" N   CYS B 564 " --> pdb=" O   PHE B 560 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   LYS B 568 " --> pdb=" O   CYS B 564 " (cutoff:3.500A)
      removed outlier: 4.465A  pdb=" N   GLU B 569 " --> pdb=" O   LYS B 565 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   ILE B 570 " --> pdb=" O   LEU B 566 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 599 through 608
      removed outlier: 3.500A  pdb=" N   ARG B 604 " --> pdb=" O   ALA B 600 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LYS B 607 " --> pdb=" O   GLU B 603 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 616 through 621
      removed outlier: 3.906A  pdb=" N   MET B 620 " --> pdb=" O   THR B 616 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   MET B 621 " --> pdb=" O   MET B 617 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 616 through 621'
    Processing helix  chain 'B' and resid 632 through 645
      removed outlier: 4.051A  pdb=" N   GLU B 636 " --> pdb=" O   HIS B 632 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ARG B 639 " --> pdb=" O   VAL B 635 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   GLN B 640 " --> pdb=" O   GLU B 636 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   LYS B 641 " --> pdb=" O   THR B 637 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 648 through 666
      removed outlier: 3.662A  pdb=" N   LYS B 652 " --> pdb=" O   ASP B 648 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   SER B 666 " --> pdb=" O   ALA B 662 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 672 through 689
      removed outlier: 3.940A  pdb=" N   HIS B 676 " --> pdb=" O   ASP B 672 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   MET B 683 " --> pdb=" O   ARG B 679 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ILE B 684 " --> pdb=" O   ILE B 680 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   LYS B 685 " --> pdb=" O   TYR B 681 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   LEU B 686 " --> pdb=" O   ARG B 682 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LEU B 688 " --> pdb=" O   ILE B 684 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 24 through 74
    Processing helix  chain 'C' and resid 77 through 111
      removed outlier: 3.957A  pdb=" N   LYS C 110 " --> pdb=" O   ARG C 106 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   SER C 111 " --> pdb=" O   LYS C 107 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 115 through 119
    Processing helix  chain 'C' and resid 142 through 163
      removed outlier: 3.603A  pdb=" N   GLN C 146 " --> pdb=" O   GLU C 142 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   LYS C 147 " --> pdb=" O   VAL C 143 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   HIS C 148 " --> pdb=" O   ARG C 144 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   THR C 150 " --> pdb=" O   GLN C 146 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   TYR C 155 " --> pdb=" O   PHE C 151 " (cutoff:3.500A)
      removed outlier: 4.834A  pdb=" N   LYS C 157 " --> pdb=" O   GLU C 153 " (cutoff:3.500A)
      removed outlier: 5.428A  pdb=" N   GLN C 158 " --> pdb=" O   LYS C 154 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 167 through 182
    Processing helix  chain 'C' and resid 184 through 198
    Processing helix  chain 'C' and resid 199 through 201
      No H-bonds generated for 'chain 'C' and resid 199 through 201'
    Processing helix  chain 'C' and resid 202 through 227
    Processing helix  chain 'C' and resid 229 through 233
    Processing helix  chain 'C' and resid 234 through 243
      removed outlier: 3.734A  pdb=" N   THR C 243 " --> pdb=" O   THR C 239 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 245 through 278
    Processing helix  chain 'K' and resid 537 through 543
      removed outlier: 3.683A  pdb=" N   LEU K 541 " --> pdb=" O   LEU K 537 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   HIS K 542 " --> pdb=" O   TYR K 538 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 549 through 569
      removed outlier: 4.201A  pdb=" N   LEU K 553 " --> pdb=" O   GLU K 549 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 578 through 580
      No H-bonds generated for 'chain 'K' and resid 578 through 580'
    Processing helix  chain 'K' and resid 634 through 652
      removed outlier: 3.979A  pdb=" N   ASP K 638 " --> pdb=" O   SER K 634 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 661 through 671
    Processing helix  chain 'K' and resid 686 through 697
      removed outlier: 4.189A  pdb=" N   LEU K 697 " --> pdb=" O   MET K 693 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 706 through 719
      removed outlier: 4.071A  pdb=" N   ILE K 710 " --> pdb=" O   LEU K 706 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 21 through 41
      removed outlier: 3.863A  pdb=" N   LEU P  25 " --> pdb=" O   ALA P  21 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 43 through 58
    Processing helix  chain 'P' and resid 61 through 75
      removed outlier: 3.882A  pdb=" N   TYR P  65 " --> pdb=" O   ASN P  61 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 77 through 92
      removed outlier: 3.616A  pdb=" N   ALA P  81 " --> pdb=" O   CYS P  77 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 95 through 110
    Processing helix  chain 'P' and resid 111 through 126
      removed outlier: 4.344A  pdb=" N   ALA P 115 " --> pdb=" O   LYS P 111 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 129 through 149
    Processing helix  chain 'P' and resid 187 through 200
    Processing helix  chain 'P' and resid 205 through 222
      removed outlier: 3.737A  pdb=" N   ALA P 209 " --> pdb=" O   HIS P 205 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   LYS P 222 " --> pdb=" O   GLU P 218 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 246 through 257
    Processing helix  chain 'P' and resid 278 through 293
      removed outlier: 3.606A  pdb=" N   VAL P 282 " --> pdb=" O   PHE P 278 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 306 through 313
      removed outlier: 3.965A  pdb=" N   ILE P 312 " --> pdb=" O   ASN P 308 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 314 through 323
    Processing helix  chain 'P' and resid 324 through 336
    Processing helix  chain 'P' and resid 362 through 368
      removed outlier: 4.378A  pdb=" N   ILE P 366 " --> pdb=" O   THR P 362 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 379 through 387
      removed outlier: 4.147A  pdb=" N   LEU P 385 " --> pdb=" O   MET P 381 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 407 through 418
      removed outlier: 3.642A  pdb=" N   THR P 411 " --> pdb=" O   GLY P 407 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 450 through 454
    Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 16
      removed outlier: 3.729A  pdb=" N   GLU A  13 " --> pdb=" O   VAL B 167 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   SER B 159 " --> pdb=" O   VAL B 143 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   VAL B 143 " --> pdb=" O   SER B 159 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   LYS B 142 " --> pdb=" O   HIS B 184 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 155 through 159
      removed outlier: 3.749A  pdb=" N   THR A  83 " --> pdb=" O   ASN A  78 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 105
    Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 324
      removed outlier: 3.760A  pdb=" N   ALA A 317 " --> pdb=" O   ILE A 335 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   PHE A 321 " --> pdb=" O   ALA A 331 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ALA A 331 " --> pdb=" O   PHE A 321 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   VAL A 323 " --> pdb=" O   PHE A 329 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   PHE A 329 " --> pdb=" O   VAL A 323 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ARG A 378 " --> pdb=" O   PHE A 334 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   LYS A 354 " --> pdb=" O   VAL A 381 " (cutoff:3.500A)
      removed outlier: 7.352A  pdb=" N   SER A 383 " --> pdb=" O   LYS A 354 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   TYR A 356 " --> pdb=" O   SER A 383 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   LEU A 355 " --> pdb=" O   MET A 363 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   MET A 363 " --> pdb=" O   LEU A 355 " (cutoff:3.500A)
      removed outlier: 6.196A  pdb=" N   VAL A 357 " --> pdb=" O   PHE A 361 " (cutoff:3.500A)
      removed outlier: 5.662A  pdb=" N   PHE A 361 " --> pdb=" O   VAL A 357 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 511 through 513
      removed outlier: 7.113A  pdb=" N   TYR A 484 " --> pdb=" O   VAL A 511 " (cutoff:3.500A)
      removed outlier: 8.221A  pdb=" N   MET A 513 " --> pdb=" O   TYR A 484 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   ILE A 486 " --> pdb=" O   MET A 513 " (cutoff:3.500A)
      removed outlier: 5.695A  pdb=" N   ILE A 483 " --> pdb=" O   VAL A 534 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 578 through 579
      removed outlier: 3.511A  pdb=" N   ILE A 628 " --> pdb=" O   THR A 579 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   VAL A 592 " --> pdb=" O   HIS A 625 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 83 through 85
      removed outlier: 6.806A  pdb=" N   ILE B  73 " --> pdb=" O   THR B 214 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 333 through 336
      removed outlier: 7.021A  pdb=" N   LEU B 333 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
      removed outlier: 4.634A  pdb=" N   VAL B 318 " --> pdb=" O   LEU B 333 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   ILE B 335 " --> pdb=" O   LEU B 316 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   VAL B 318 " --> pdb=" O   MET C 128 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   MET C 128 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 329 through 330
      removed outlier: 6.826A  pdb=" N   SER B 322 " --> pdb=" O   GLY C 123 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   GLY C 123 " --> pdb=" O   SER B 322 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   GLU B 324 " --> pdb=" O   LYS C 121 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 467 through 468
      removed outlier: 4.707A  pdb=" N   HIS B 458 " --> pdb=" O   TYR B 512 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   VAL B 511 " --> pdb=" O   TYR B 484 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 575 through 580
      removed outlier: 7.365A  pdb=" N   LEU B 626 " --> pdb=" O   GLU B 576 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   VAL B 578 " --> pdb=" O   LEU B 626 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   ILE B 628 " --> pdb=" O   VAL B 578 " (cutoff:3.500A)
      removed outlier: 4.974A  pdb=" N   ILE B 580 " --> pdb=" O   ILE B 628 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'K' and resid 582 through 584
    Processing sheet with id=AB4, first strand: chain 'P' and resid 266 through 268
      removed outlier: 5.976A  pdb=" N   GLN P 465 " --> pdb=" O   ARG P 470 " (cutoff:3.500A)
      removed outlier: 5.967A  pdb=" N   ARG P 470 " --> pdb=" O   GLN P 465 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'P' and resid 342 through 344
    Processing sheet with id=AB6, first strand: chain 'P' and resid 396 through 397
      removed outlier: 3.839A  pdb=" N   SER P 396 " --> pdb=" O   GLN P 405 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'P' and resid 424 through 425
      removed outlier: 6.110A  pdb=" N   ARG P 425 " --> pdb=" O   VAL P 445 " (cutoff:3.500A)

    736 hydrogen bonds defined for protein.
    2118 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: 2.83

  Time building geometry restraints manager: 2.11 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: 5625
        1.34 -     1.46: 2741
        1.46 -     1.58: 9493
        1.58 -     1.70: 14
        1.70 -     1.82: 151
  Bond restraints: 18024
  Sorted by residual:
  bond pdb=" O1P SEP C  13 "
       pdb=" P   SEP C  13 "
    ideal  model  delta    sigma   weight residual
    1.610  1.656 -0.046 2.00e-02 2.50e+03 5.33e+00
  bond pdb=" CA  ARG C  36 "
       pdb=" CB  ARG C  36 "
    ideal  model  delta    sigma   weight residual
    1.528  1.555 -0.027 1.59e-02 3.96e+03 2.83e+00
  bond pdb=" CB  VAL A 144 "
       pdb=" CG2 VAL A 144 "
    ideal  model  delta    sigma   weight residual
    1.521  1.469  0.052 3.30e-02 9.18e+02 2.51e+00
  bond pdb=" CA  LEU B 401 "
       pdb=" C   LEU B 401 "
    ideal  model  delta    sigma   weight residual
    1.522  1.501  0.022 1.38e-02 5.25e+03 2.46e+00
  bond pdb=" C   GLU A 368 "
       pdb=" N   LEU A 369 "
    ideal  model  delta    sigma   weight residual
    1.332  1.313  0.019 1.40e-02 5.10e+03 1.90e+00
  ... (remaining 18019 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 23525
        2.01 -     4.02: 604
        4.02 -     6.03: 88
        6.03 -     8.04: 19
        8.04 -    10.05: 9
  Bond angle restraints: 24245
  Sorted by residual:
  angle pdb=" C   ASP K 587 "
        pdb=" CA  ASP K 587 "
        pdb=" CB  ASP K 587 "
      ideal   model   delta    sigma   weight residual
     117.23  109.21    8.02 1.36e+00 5.41e-01 3.48e+01
  angle pdb=" C   GLN B 118 "
        pdb=" CA  GLN B 118 "
        pdb=" CB  GLN B 118 "
      ideal   model   delta    sigma   weight residual
     115.79  108.77    7.02 1.19e+00 7.06e-01 3.48e+01
  angle pdb=" CG  ARG C  36 "
        pdb=" CD  ARG C  36 "
        pdb=" NE  ARG C  36 "
      ideal   model   delta    sigma   weight residual
     112.00  122.05  -10.05 2.20e+00 2.07e-01 2.09e+01
  angle pdb=" C   PHE P 190 "
        pdb=" N   MET P 191 "
        pdb=" CA  MET P 191 "
      ideal   model   delta    sigma   weight residual
     121.14  113.39    7.75 1.75e+00 3.27e-01 1.96e+01
  angle pdb=" CA  ASP K 587 "
        pdb=" C   ASP K 587 "
        pdb=" N   LEU K 588 "
      ideal   model   delta    sigma   weight residual
     119.98  116.26    3.72 8.50e-01 1.38e+00 1.92e+01
  ... (remaining 24240 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 9936
       17.93 -    35.87: 990
       35.87 -    53.80: 156
       53.80 -    71.74: 21
       71.74 -    89.67: 25
  Dihedral angle restraints: 11128
    sinusoidal: 4754
      harmonic: 6374
  Sorted by residual:
  dihedral pdb=" CA  ARG C 167 "
           pdb=" C   ARG C 167 "
           pdb=" N   TRP C 168 "
           pdb=" CA  TRP C 168 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.61  -27.39     0      5.00e+00 4.00e-02 3.00e+01
  dihedral pdb=" CA  LYS K 522 "
           pdb=" C   LYS K 522 "
           pdb=" N   PRO K 523 "
           pdb=" CA  PRO K 523 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.19  -26.81     0      5.00e+00 4.00e-02 2.87e+01
  dihedral pdb=" CA  THR B 309 "
           pdb=" C   THR B 309 "
           pdb=" N   ASN B 310 "
           pdb=" CA  ASN B 310 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.94   26.06     0      5.00e+00 4.00e-02 2.72e+01
  ... (remaining 11125 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 2020
       0.051 -    0.101: 509
       0.101 -    0.152: 99
       0.152 -    0.202: 4
       0.202 -    0.253: 4
  Chirality restraints: 2636
  Sorted by residual:
  chirality pdb=" CA  PRO K 523 "
            pdb=" N   PRO K 523 "
            pdb=" C   PRO K 523 "
            pdb=" CB  PRO K 523 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.47    0.25 2.00e-01 2.50e+01 1.60e+00
  chirality pdb=" CB  ILE B 605 "
            pdb=" CA  ILE B 605 "
            pdb=" CG1 ILE B 605 "
            pdb=" CG2 ILE B 605 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.86   -0.21 2.00e-01 2.50e+01 1.14e+00
  chirality pdb=" CG  LEU K 588 "
            pdb=" CB  LEU K 588 "
            pdb=" CD1 LEU K 588 "
            pdb=" CD2 LEU K 588 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.38   -0.21 2.00e-01 2.50e+01 1.06e+00
  ... (remaining 2633 not shown)

  Planarity restraints: 3109
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C  36 "   -0.232 9.50e-02 1.11e+02   1.06e-01 1.11e+01
        pdb=" NE  ARG C  36 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  ARG C  36 "    0.039 2.00e-02 2.50e+03
        pdb=" NH1 ARG C  36 "   -0.010 2.00e-02 2.50e+03
        pdb=" NH2 ARG C  36 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 587 "    0.039 5.00e-02 4.00e+02   5.97e-02 5.70e+00
        pdb=" N   PRO A 588 "   -0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO A 588 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 588 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE K 707 "    0.035 5.00e-02 4.00e+02   5.22e-02 4.36e+00
        pdb=" N   PRO K 708 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO K 708 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO K 708 "    0.030 5.00e-02 4.00e+02
  ... (remaining 3106 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.66: 407
        2.66 -     3.22: 18207
        3.22 -     3.78: 26979
        3.78 -     4.34: 35014
        4.34 -     4.90: 53635
  Nonbonded interactions: 134242
  Sorted by model distance:
  nonbonded pdb=" O   LEU A  27 "
            pdb=" OG1 THR A  31 "
     model   vdw
     2.106 3.040
  nonbonded pdb=" O   LEU B 102 "
            pdb=" OH  TYR B 134 "
     model   vdw
     2.151 3.040
  nonbonded pdb=" OD1 ASN A 101 "
            pdb=" O3' ATP A 801 "
     model   vdw
     2.162 3.040
  nonbonded pdb=" OD1 ASN B 425 "
            pdb=" OG1 THR C 131 "
     model   vdw
     2.173 3.040
  nonbonded pdb=" OG  SER B 434 "
            pdb=" NZ  LYS B 438 "
     model   vdw
     2.181 3.120
  ... (remaining 134237 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 10 through 220 or resid 273 through 801))
  selection = chain 'B'
}

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:             2.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.770
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6117
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      :  0.003   0.052  18027  Z= 0.162
  Angle     :  0.792  10.050  24245  Z= 0.435
  Chirality :  0.046   0.253   2636
  Planarity :  0.005   0.106   3109
  Dihedral  : 14.743  89.672   7000
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 16.38
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  7.69 %
    Favored  : 92.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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: -1.90 (0.17), residues: 2147
  helix: -0.34 (0.16), residues: 942
  sheet: -0.16 (0.39), residues: 200
  loop : -2.45 (0.18), residues: 1005

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.037   0.001   ARG C  36 
 TYR   0.016   0.002   TYR P  51 
 PHE   0.026   0.002   PHE P 287 
 TRP   0.025   0.003   TRP B 598 
 HIS   0.005   0.001   HIS P 205 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (18024)
  covalent geometry    : angle       0.79228 (24245)
  hydrogen bonds       : bond        0.14884 (  736)
  hydrogen bonds       : angle       6.34323 ( 2118)
  Misc. bond           : bond        0.00377 (    3)

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

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

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  430 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 430
  time to evaluate  : 0.499 
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: A   75 ILE cc_start: 0.8208 (tp) cc_final: 0.7945 (tp)
REVERT: A   76 ILE cc_start: 0.7722 (mt) cc_final: 0.7435 (mm)
REVERT: A   95 LYS cc_start: 0.7825 (ttmm) cc_final: 0.7508 (mmmt)
REVERT: A  286 LYS cc_start: 0.8407 (ttmt) cc_final: 0.8181 (ttmt)
REVERT: A  288 ILE cc_start: 0.8033 (tt) cc_final: 0.7704 (tt)
REVERT: A  289 TRP cc_start: 0.6593 (p90) cc_final: 0.6237 (p90)
REVERT: A  337 ARG cc_start: 0.7054 (mtt-85) cc_final: 0.6511 (mtt-85)
REVERT: A  392 ARG cc_start: 0.7512 (mmt90) cc_final: 0.7125 (mmt-90)
REVERT: A  394 MET cc_start: 0.6674 (ppp) cc_final: 0.6346 (ppp)
REVERT: A  421 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7777 (mm-30)
REVERT: A  431 GLU cc_start: 0.7358 (tp30) cc_final: 0.7143 (tm-30)
REVERT: A  550 LYS cc_start: 0.8118 (pttp) cc_final: 0.7889 (ptmm)
REVERT: A  557 LYS cc_start: 0.7989 (pttp) cc_final: 0.7676 (pttp)
REVERT: A  621 MET cc_start: 0.5867 (mmp) cc_final: 0.5346 (mmm)
REVERT: A  639 ARG cc_start: 0.7319 (ttp80) cc_final: 0.7067 (ttp80)
REVERT: A  640 GLN cc_start: 0.8267 (pp30) cc_final: 0.7985 (pp30)
REVERT: A  645 ASP cc_start: 0.7105 (t0) cc_final: 0.6549 (t0)
REVERT: A  672 ASP cc_start: 0.7719 (p0) cc_final: 0.7420 (p0)
REVERT: A  680 ILE cc_start: 0.8688 (mp) cc_final: 0.8277 (mp)
REVERT: A  684 ILE cc_start: 0.8226 (pt) cc_final: 0.7931 (pt)
REVERT: B   18 GLN cc_start: 0.7194 (mp10) cc_final: 0.6939 (mp10)
REVERT: B   58 SER cc_start: 0.5676 (t) cc_final: 0.5281 (p)
REVERT: B  153 GLU cc_start: 0.8094 (mp0) cc_final: 0.7738 (mp0)
REVERT: B  200 GLU cc_start: 0.7086 (tm-30) cc_final: 0.6857 (tm-30)
REVERT: B  361 PHE cc_start: 0.8130 (t80) cc_final: 0.7652 (t80)
REVERT: B  364 ASP cc_start: 0.7164 (p0) cc_final: 0.6795 (p0)
REVERT: B  423 LYS cc_start: 0.8286 (mppt) cc_final: 0.8017 (mmtm)
REVERT: B  428 LYS cc_start: 0.7135 (mmmt) cc_final: 0.6919 (mmmt)
REVERT: B  450 ARG cc_start: 0.6802 (ttt-90) cc_final: 0.6585 (ttt180)
REVERT: B  471 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7120 (tm-30)
REVERT: B  475 ARG cc_start: 0.7329 (pmt170) cc_final: 0.6219 (pmt170)
REVERT: B  553 MET cc_start: 0.5409 (tmm) cc_final: 0.5170 (tmm)
REVERT: B  613 ASP cc_start: 0.5747 (p0) cc_final: 0.5451 (p0)
REVERT: B  648 ASP cc_start: 0.7698 (p0) cc_final: 0.7441 (p0)
REVERT: B  652 LYS cc_start: 0.8915 (mtmm) cc_final: 0.8650 (mttp)
REVERT: C   39 ARG cc_start: 0.7881 (ttp80) cc_final: 0.7620 (ttp80)
REVERT: C   49 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8451 (tm-30)
REVERT: C  217 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8498 (mm-40)
REVERT: C  253 ASN cc_start: 0.6550 (m110) cc_final: 0.6345 (m110)
REVERT: K  646 LEU cc_start: 0.5116 (tp) cc_final: 0.4844 (tt)
REVERT: P   39 PHE cc_start: 0.5000 (t80) cc_final: 0.4730 (t80)
REVERT: P   80 TYR cc_start: 0.7791 (m-80) cc_final: 0.7506 (m-80)
REVERT: P  293 TYR cc_start: 0.5344 (m-80) cc_final: 0.5132 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 430
  average time/residue: 0.1610
  time to fit residues: 97.8768
Evaluate side-chains
  382 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 382
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 215
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 194 optimal weight:    9.9990
   chunk 107 optimal weight:    0.6980
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    5.9990
   chunk 200 optimal weight:    2.9990
   chunk 212 optimal weight:    0.0020
   chunk 77 optimal weight:    2.9990
   overall best weight:    0.9192

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

Flipped N/Q/H residues before XYZ refinement:
A 375 ASN
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 609 GLN
C  34 GLN
C 188 ASN
K 585 HIS
P 342 GLN
** P 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4506 r_free = 0.4506 target = 0.200053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.171630 restraints weight = 35268.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.167718 restraints weight = 59061.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.169649 restraints weight = 54726.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.169701 restraints weight = 35979.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.170387 restraints weight = 31373.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.4070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6276
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  18027  Z= 0.154
  Angle     :  0.668   8.751  24245  Z= 0.354
  Chirality :  0.046   0.234   2636
  Planarity :  0.005   0.121   3109
  Dihedral  :  8.436 168.817   2430
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  7.92 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  6.07 %
    Favored  : 93.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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: -1.74 (0.18), residues: 2147
  helix: -0.05 (0.16), residues: 972
  sheet: -0.73 (0.35), residues: 231
  loop : -2.49 (0.19), residues: 944

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG C  36 
 TYR   0.022   0.002   TYR A 373 
 PHE   0.027   0.002   PHE A  32 
 TRP   0.020   0.002   TRP B 312 
 HIS   0.005   0.001   HIS P 128 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (18024)
  covalent geometry    : angle       0.66830 (24245)
  hydrogen bonds       : bond        0.04479 (  736)
  hydrogen bonds       : angle       4.98438 ( 2118)
  Misc. bond           : bond        0.00316 (    3)

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

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

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  412 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 407
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 LYS cc_start: 0.6629 (ptmm) cc_final: 0.6270 (ptmt)
REVERT: A   74 ASP cc_start: 0.6728 (m-30) cc_final: 0.6434 (m-30)
REVERT: A  170 ASP cc_start: 0.7507 (p0) cc_final: 0.7283 (p0)
REVERT: A  177 ARG cc_start: 0.7271 (ptt-90) cc_final: 0.6986 (ptt90)
REVERT: A  274 GLU cc_start: 0.6930 (mp0) cc_final: 0.6613 (mp0)
REVERT: A  288 ILE cc_start: 0.8434 (tt) cc_final: 0.8120 (tt)
REVERT: A  289 TRP cc_start: 0.7035 (p90) cc_final: 0.6513 (p90)
REVERT: A  380 VAL cc_start: 0.8475 (t) cc_final: 0.8057 (m)
REVERT: A  392 ARG cc_start: 0.7039 (mmt90) cc_final: 0.6773 (mmt-90)
REVERT: A  428 LYS cc_start: 0.8139 (ptmm) cc_final: 0.7551 (ttpp)
REVERT: A  431 GLU cc_start: 0.6528 (tp30) cc_final: 0.6181 (tp30)
REVERT: A  435 LYS cc_start: 0.8262 (mttt) cc_final: 0.8020 (mttm)
REVERT: A  519 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7147 (mm-30)
REVERT: A  550 LYS cc_start: 0.8057 (pttp) cc_final: 0.7852 (ptmm)
REVERT: A  557 LYS cc_start: 0.7758 (pttp) cc_final: 0.7427 (pttp)
REVERT: A  577 LYS cc_start: 0.7577 (mtmm) cc_final: 0.7330 (mtmm)
REVERT: A  639 ARG cc_start: 0.6904 (ttp80) cc_final: 0.6466 (ttp80)
REVERT: A  640 GLN cc_start: 0.7953 (pp30) cc_final: 0.7329 (pp30)
REVERT: A  680 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8051 (tt)
REVERT: A  684 ILE cc_start: 0.8414 (pt) cc_final: 0.7801 (pt)
REVERT: B   69 LYS cc_start: 0.8155 (mptt) cc_final: 0.7912 (mptt)
REVERT: B   72 LYS cc_start: 0.7698 (pttt) cc_final: 0.7479 (pttt)
REVERT: B  125 MET cc_start: 0.6934 (tpp) cc_final: 0.6683 (ttm)
REVERT: B  133 PHE cc_start: 0.7081 (t80) cc_final: 0.6820 (t80)
REVERT: B  139 VAL cc_start: 0.8482 (t) cc_final: 0.8250 (m)
REVERT: B  145 VAL cc_start: 0.7675 (t) cc_final: 0.7333 (p)
REVERT: B  157 TRP cc_start: 0.7995 (t60) cc_final: 0.7232 (t60)
REVERT: B  204 LYS cc_start: 0.8502 (tmtt) cc_final: 0.8071 (tmtt)
REVERT: B  297 THR cc_start: 0.7115 (p) cc_final: 0.6758 (p)
REVERT: B  342 ASP cc_start: 0.6904 (p0) cc_final: 0.6382 (p0)
REVERT: B  385 ASP cc_start: 0.7240 (p0) cc_final: 0.7009 (p0)
REVERT: B  395 LEU cc_start: 0.8115 (tt) cc_final: 0.7833 (tt)
REVERT: B  428 LYS cc_start: 0.7541 (mmmt) cc_final: 0.7292 (mmmt)
REVERT: B  471 GLU cc_start: 0.7138 (tm-30) cc_final: 0.6727 (tm-30)
REVERT: B  475 ARG cc_start: 0.7523 (pmt170) cc_final: 0.6300 (pmt170)
REVERT: B  553 MET cc_start: 0.5486 (tmm) cc_final: 0.5156 (tmm)
REVERT: B  567 MET cc_start: 0.7247 (ppp) cc_final: 0.6808 (ppp)
REVERT: B  613 ASP cc_start: 0.6549 (p0) cc_final: 0.6329 (p0)
REVERT: B  637 THR cc_start: 0.8244 (p) cc_final: 0.7951 (p)
REVERT: C   48 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7328 (pm20)
REVERT: C  106 ARG cc_start: 0.7878 (tmt-80) cc_final: 0.7595 (tpt90)
REVERT: C  107 LYS cc_start: 0.7711 (mtmm) cc_final: 0.7174 (mtmm)
REVERT: C  231 ARG cc_start: 0.4129 (ttp80) cc_final: 0.3907 (mmm160)
REVERT: C  253 ASN cc_start: 0.6736 (m110) cc_final: 0.6478 (m110)
REVERT: K  584 LEU cc_start: 0.4774 (mp) cc_final: 0.4392 (tt)
REVERT: K  689 MET cc_start: 0.6847 (mmp) cc_final: 0.6609 (mmp)
REVERT: P   46 ASN cc_start: 0.6553 (t0) cc_final: 0.6111 (m-40)
REVERT: P  134 MET cc_start: 0.6040 (ppp) cc_final: 0.5592 (ppp)
REVERT: P  320 LYS cc_start: 0.8302 (tppt) cc_final: 0.8084 (tppt)
REVERT: P  331 PHE cc_start: 0.7364 (m-80) cc_final: 0.7107 (m-80)
  outliers start: 5
  outliers final: 0
  residues processed: 408
  average time/residue: 0.1617
  time to fit residues: 93.6836
Evaluate side-chains
  365 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 363
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 215
   random chunks:
   chunk 32 optimal weight:    8.9990
   chunk 140 optimal weight:   10.0000
   chunk 194 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 193 optimal weight:    1.9990
   chunk 125 optimal weight:    5.9990
   chunk 55 optimal weight:    0.6980
   chunk 169 optimal weight:    0.9990
   chunk 93 optimal weight:    0.2980
   chunk 73 optimal weight:    0.7980
   chunk 2 optimal weight:    0.2980
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
A 205 HIS
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 524 GLN
A 609 GLN
** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  34 GLN
P 246 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4523 r_free = 0.4523 target = 0.201713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.174294 restraints weight = 35419.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.171511 restraints weight = 56757.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.173193 restraints weight = 48246.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.173300 restraints weight = 31210.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.173479 restraints weight = 27863.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.4090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6202
moved from start:          0.2505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  18027  Z= 0.128
  Angle     :  0.630   8.229  24245  Z= 0.332
  Chirality :  0.043   0.238   2636
  Planarity :  0.005   0.107   3109
  Dihedral  :  7.466  83.479   2430
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  7.31 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  3.91 %
    Favored  : 95.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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: -1.64 (0.18), residues: 2147
  helix:  0.06 (0.17), residues: 969
  sheet: -0.70 (0.34), residues: 234
  loop : -2.46 (0.18), residues: 944

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C  36 
 TYR   0.025   0.001   TYR C 189 
 PHE   0.020   0.002   PHE C 237 
 TRP   0.041   0.002   TRP C  98 
 HIS   0.003   0.001   HIS B 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (18024)
  covalent geometry    : angle       0.62996 (24245)
  hydrogen bonds       : bond        0.04117 (  736)
  hydrogen bonds       : angle       4.72903 ( 2118)
  Misc. bond           : bond        0.00217 (    3)

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

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

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  404 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 401
  time to evaluate  : 0.661 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  289 TRP cc_start: 0.6888 (p90) cc_final: 0.6364 (p90)
REVERT: A  380 VAL cc_start: 0.8432 (t) cc_final: 0.7980 (m)
REVERT: A  519 GLU cc_start: 0.7338 (mm-30) cc_final: 0.6894 (mm-30)
REVERT: A  557 LYS cc_start: 0.7777 (pttp) cc_final: 0.7534 (pttp)
REVERT: A  606 MET cc_start: 0.7657 (tpt) cc_final: 0.7352 (tpp)
REVERT: A  611 LEU cc_start: 0.7435 (mp) cc_final: 0.7201 (mp)
REVERT: A  636 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7526 (mm-30)
REVERT: A  639 ARG cc_start: 0.6915 (ttp80) cc_final: 0.6615 (ttp80)
REVERT: A  640 GLN cc_start: 0.7976 (pp30) cc_final: 0.7694 (pp30)
REVERT: A  648 ASP cc_start: 0.7424 (t0) cc_final: 0.6914 (t70)
REVERT: A  680 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8450 (mt)
REVERT: A  684 ILE cc_start: 0.8414 (pt) cc_final: 0.7879 (pt)
REVERT: B   69 LYS cc_start: 0.8120 (mptt) cc_final: 0.7878 (mptt)
REVERT: B   71 LEU cc_start: 0.8255 (tt) cc_final: 0.7948 (mp)
REVERT: B   72 LYS cc_start: 0.7653 (pttt) cc_final: 0.7360 (pttt)
REVERT: B  125 MET cc_start: 0.6669 (tpp) cc_final: 0.6415 (ttm)
REVERT: B  145 VAL cc_start: 0.7833 (t) cc_final: 0.7485 (p)
REVERT: B  204 LYS cc_start: 0.8490 (tmtt) cc_final: 0.8147 (tmtt)
REVERT: B  342 ASP cc_start: 0.6996 (p0) cc_final: 0.6364 (p0)
REVERT: B  385 ASP cc_start: 0.7259 (p0) cc_final: 0.7031 (p0)
REVERT: B  448 ARG cc_start: 0.6791 (ttm-80) cc_final: 0.6487 (ttm170)
REVERT: B  496 ASN cc_start: 0.7824 (p0) cc_final: 0.7516 (p0)
REVERT: B  567 MET cc_start: 0.7215 (ppp) cc_final: 0.6801 (ppp)
REVERT: B  674 GLN cc_start: 0.7710 (tm-30) cc_final: 0.7437 (tm-30)
REVERT: B  684 ILE cc_start: 0.8748 (mt) cc_final: 0.8510 (mm)
REVERT: C   42 GLN cc_start: 0.7773 (tm-30) cc_final: 0.7527 (tm-30)
REVERT: C   48 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7198 (pm20)
REVERT: C  106 ARG cc_start: 0.7820 (tmt-80) cc_final: 0.7529 (tmt-80)
REVERT: C  107 LYS cc_start: 0.7769 (mtmm) cc_final: 0.6895 (mtmm)
REVERT: C  108 LYS cc_start: 0.6870 (pttp) cc_final: 0.6303 (ttpp)
REVERT: C  217 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8580 (mm-40)
REVERT: C  249 MET cc_start: 0.3409 (tpp) cc_final: 0.3155 (tmm)
REVERT: C  253 ASN cc_start: 0.6808 (m110) cc_final: 0.5415 (m110)
REVERT: P  134 MET cc_start: 0.5794 (ppp) cc_final: 0.5396 (ppp)
REVERT: P  320 LYS cc_start: 0.8368 (tppt) cc_final: 0.8116 (tppt)
REVERT: P  331 PHE cc_start: 0.7338 (m-80) cc_final: 0.7092 (m-80)
REVERT: P  381 MET cc_start: 0.4587 (ttp) cc_final: 0.4099 (ttp)
  outliers start: 3
  outliers final: 0
  residues processed: 401
  average time/residue: 0.1553
  time to fit residues: 88.9340
Evaluate side-chains
  368 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 366
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 215
   random chunks:
   chunk 153 optimal weight:    0.7980
   chunk 139 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 50 optimal weight:    0.7980
   chunk 106 optimal weight:    0.0270
   chunk 7 optimal weight:    0.2980
   chunk 73 optimal weight:    2.9990
   chunk 127 optimal weight:    0.5980
   chunk 54 optimal weight:    2.9990
   chunk 173 optimal weight:    3.9990
   chunk 132 optimal weight:    8.9990
   overall best weight:    0.5038

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

Flipped N/Q/H residues before XYZ refinement:
A 461 GLN
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  34 GLN
P 246 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4569 r_free = 0.4569 target = 0.205522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.182907 restraints weight = 37071.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.180770 restraints weight = 67606.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.181189 restraints weight = 58852.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.179870 restraints weight = 45418.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.180547 restraints weight = 42484.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.4127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6149
moved from start:          0.2918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  18027  Z= 0.121
  Angle     :  0.623   8.687  24245  Z= 0.327
  Chirality :  0.043   0.170   2636
  Planarity :  0.005   0.125   3109
  Dihedral  :  7.303  83.558   2430
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.22 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  3.14 %
    Favored  : 96.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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: -1.57 (0.17), residues: 2147
  helix:  0.13 (0.17), residues: 970
  sheet: -0.77 (0.35), residues: 227
  loop : -2.40 (0.18), residues: 950

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG C  36 
 TYR   0.022   0.001   TYR C 189 
 PHE   0.029   0.002   PHE P  39 
 TRP   0.020   0.002   TRP C  98 
 HIS   0.004   0.001   HIS A 184 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (18024)
  covalent geometry    : angle       0.62258 (24245)
  hydrogen bonds       : bond        0.03885 (  736)
  hydrogen bonds       : angle       4.64209 ( 2118)
  Misc. bond           : bond        0.00373 (    3)

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

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

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  392 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 391
  time to evaluate  : 0.656 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 LYS cc_start: 0.6554 (ptmt) cc_final: 0.6338 (ptmt)
REVERT: A  126 ILE cc_start: 0.7910 (mm) cc_final: 0.7647 (mt)
REVERT: A  168 ARG cc_start: 0.8091 (ttp80) cc_final: 0.7682 (tmm-80)
REVERT: A  170 ASP cc_start: 0.7655 (p0) cc_final: 0.7351 (p0)
REVERT: A  289 TRP cc_start: 0.6816 (p90) cc_final: 0.6196 (p90)
REVERT: A  380 VAL cc_start: 0.8378 (t) cc_final: 0.7928 (m)
REVERT: A  394 MET cc_start: 0.6968 (ppp) cc_final: 0.6684 (ppp)
REVERT: A  489 GLU cc_start: 0.6148 (mp0) cc_final: 0.5647 (mp0)
REVERT: A  519 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6894 (mm-30)
REVERT: A  547 GLU cc_start: 0.8196 (mp0) cc_final: 0.7983 (mp0)
REVERT: A  557 LYS cc_start: 0.7824 (pttp) cc_final: 0.7492 (pttp)
REVERT: A  577 LYS cc_start: 0.7510 (mtmm) cc_final: 0.7191 (mtmm)
REVERT: A  617 MET cc_start: 0.6211 (ppp) cc_final: 0.5978 (ppp)
REVERT: A  636 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7501 (mm-30)
REVERT: A  639 ARG cc_start: 0.6932 (ttp80) cc_final: 0.6585 (ttp80)
REVERT: A  640 GLN cc_start: 0.8014 (pp30) cc_final: 0.7694 (pp30)
REVERT: A  684 ILE cc_start: 0.8439 (pt) cc_final: 0.8068 (pt)
REVERT: B   69 LYS cc_start: 0.8315 (mptt) cc_final: 0.7809 (mptt)
REVERT: B   71 LEU cc_start: 0.8307 (tt) cc_final: 0.7282 (mp)
REVERT: B   72 LYS cc_start: 0.7749 (pttt) cc_final: 0.7476 (pttt)
REVERT: B  102 LEU cc_start: 0.7212 (tt) cc_final: 0.6794 (tt)
REVERT: B  125 MET cc_start: 0.6639 (tpp) cc_final: 0.6425 (ttm)
REVERT: B  145 VAL cc_start: 0.7832 (t) cc_final: 0.7460 (p)
REVERT: B  157 TRP cc_start: 0.8090 (t60) cc_final: 0.7122 (t60)
REVERT: B  203 LYS cc_start: 0.7787 (mmtt) cc_final: 0.7349 (ttmm)
REVERT: B  204 LYS cc_start: 0.8447 (tmtt) cc_final: 0.8050 (tmtt)
REVERT: B  277 ILE cc_start: 0.6437 (mp) cc_final: 0.6191 (mt)
REVERT: B  342 ASP cc_start: 0.7092 (p0) cc_final: 0.6485 (p0)
REVERT: B  359 ARG cc_start: 0.6814 (ttp-170) cc_final: 0.6535 (ttp-170)
REVERT: B  385 ASP cc_start: 0.7218 (p0) cc_final: 0.6970 (p0)
REVERT: B  489 GLU cc_start: 0.6231 (mm-30) cc_final: 0.5929 (mm-30)
REVERT: B  552 LYS cc_start: 0.7695 (pttm) cc_final: 0.7478 (pttm)
REVERT: B  567 MET cc_start: 0.7242 (ppp) cc_final: 0.6777 (ppp)
REVERT: C   42 GLN cc_start: 0.7359 (tm-30) cc_final: 0.7148 (tm-30)
REVERT: C  107 LYS cc_start: 0.7890 (mtmm) cc_final: 0.7274 (mtmm)
REVERT: C  249 MET cc_start: 0.3667 (tpp) cc_final: 0.3401 (tmm)
REVERT: C  253 ASN cc_start: 0.6815 (m110) cc_final: 0.5404 (m110)
REVERT: P   46 ASN cc_start: 0.6454 (t0) cc_final: 0.5959 (m110)
REVERT: P  134 MET cc_start: 0.5689 (ppp) cc_final: 0.5364 (ppp)
REVERT: P  320 LYS cc_start: 0.8367 (tppt) cc_final: 0.8093 (tppt)
REVERT: P  331 PHE cc_start: 0.7327 (m-80) cc_final: 0.7078 (m-80)
REVERT: P  381 MET cc_start: 0.4765 (ttp) cc_final: 0.4305 (ttp)
  outliers start: 1
  outliers final: 0
  residues processed: 392
  average time/residue: 0.1580
  time to fit residues: 88.8038
Evaluate side-chains
  360 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 360
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 215
   random chunks:
   chunk 95 optimal weight:    0.7980
   chunk 175 optimal weight:    9.9990
   chunk 3 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0970
   chunk 150 optimal weight:   10.0000
   chunk 147 optimal weight:    2.9990
   chunk 131 optimal weight:   30.0000
   chunk 192 optimal weight:    0.8980
   chunk 47 optimal weight:    0.7980
   chunk 139 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
A 461 GLN
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  34 GLN
P 342 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4563 r_free = 0.4563 target = 0.204880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.181753 restraints weight = 36842.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.180018 restraints weight = 65206.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.181320 restraints weight = 57240.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.181065 restraints weight = 35729.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.181548 restraints weight = 34455.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.4142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6118
moved from start:          0.3254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  18027  Z= 0.130
  Angle     :  0.629   9.218  24245  Z= 0.328
  Chirality :  0.043   0.166   2636
  Planarity :  0.005   0.107   3109
  Dihedral  :  7.343  81.362   2430
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.55 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.04 %
    Favored  : 96.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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: -1.51 (0.18), residues: 2147
  helix:  0.18 (0.16), residues: 975
  sheet: -0.74 (0.34), residues: 231
  loop : -2.39 (0.18), residues: 941

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG C  36 
 TYR   0.018   0.001   TYR B 134 
 PHE   0.023   0.002   PHE B 560 
 TRP   0.019   0.002   TRP C   7 
 HIS   0.005   0.001   HIS K 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (18024)
  covalent geometry    : angle       0.62925 (24245)
  hydrogen bonds       : bond        0.03963 (  736)
  hydrogen bonds       : angle       4.54864 ( 2118)
  Misc. bond           : bond        0.00258 (    3)

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

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

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  386 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 384
  time to evaluate  : 0.711 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 MET cc_start: 0.6550 (tmm) cc_final: 0.6132 (tmm)
REVERT: A   72 LYS cc_start: 0.6555 (ptmt) cc_final: 0.6349 (ptmt)
REVERT: A  168 ARG cc_start: 0.8165 (ttp80) cc_final: 0.7794 (tmm-80)
REVERT: A  170 ASP cc_start: 0.7666 (p0) cc_final: 0.7323 (p0)
REVERT: A  289 TRP cc_start: 0.6775 (p90) cc_final: 0.6185 (p90)
REVERT: A  380 VAL cc_start: 0.8359 (t) cc_final: 0.7875 (m)
REVERT: A  394 MET cc_start: 0.6938 (ppp) cc_final: 0.6689 (ppp)
REVERT: A  395 LEU cc_start: 0.7227 (mt) cc_final: 0.6109 (mt)
REVERT: A  489 GLU cc_start: 0.6231 (mp0) cc_final: 0.5611 (mp0)
REVERT: A  505 LYS cc_start: 0.7231 (pptt) cc_final: 0.7030 (pptt)
REVERT: A  519 GLU cc_start: 0.7342 (mm-30) cc_final: 0.7078 (mm-30)
REVERT: A  557 LYS cc_start: 0.7827 (pttp) cc_final: 0.7444 (pttp)
REVERT: A  577 LYS cc_start: 0.7531 (mtmm) cc_final: 0.7220 (mtmm)
REVERT: A  611 LEU cc_start: 0.7303 (mp) cc_final: 0.7092 (mt)
REVERT: A  620 MET cc_start: 0.7161 (tpt) cc_final: 0.6715 (tpp)
REVERT: A  636 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7414 (mm-30)
REVERT: A  639 ARG cc_start: 0.6920 (ttp80) cc_final: 0.6655 (ttp80)
REVERT: A  640 GLN cc_start: 0.7830 (pp30) cc_final: 0.7509 (pp30)
REVERT: A  680 ILE cc_start: 0.8730 (mt) cc_final: 0.8495 (mt)
REVERT: A  684 ILE cc_start: 0.8416 (pt) cc_final: 0.7869 (pt)
REVERT: B   69 LYS cc_start: 0.8213 (mptt) cc_final: 0.7853 (mptt)
REVERT: B   71 LEU cc_start: 0.8039 (tt) cc_final: 0.7408 (tt)
REVERT: B  102 LEU cc_start: 0.7377 (tt) cc_final: 0.6999 (tt)
REVERT: B  125 MET cc_start: 0.6821 (tpp) cc_final: 0.5996 (ttm)
REVERT: B  145 VAL cc_start: 0.7880 (t) cc_final: 0.7491 (p)
REVERT: B  157 TRP cc_start: 0.8178 (t60) cc_final: 0.7251 (t60)
REVERT: B  203 LYS cc_start: 0.7793 (mmtt) cc_final: 0.7496 (ttmm)
REVERT: B  204 LYS cc_start: 0.8401 (tmtt) cc_final: 0.8018 (tmtt)
REVERT: B  342 ASP cc_start: 0.7150 (p0) cc_final: 0.6730 (p0)
REVERT: B  359 ARG cc_start: 0.6815 (ttp-170) cc_final: 0.6607 (ttp-170)
REVERT: B  385 ASP cc_start: 0.7105 (p0) cc_final: 0.6882 (p0)
REVERT: B  428 LYS cc_start: 0.7359 (pttp) cc_final: 0.7137 (ttpp)
REVERT: B  489 GLU cc_start: 0.6242 (mm-30) cc_final: 0.6006 (mm-30)
REVERT: B  550 LYS cc_start: 0.7998 (mmtp) cc_final: 0.7597 (mmtp)
REVERT: B  567 MET cc_start: 0.7249 (ppp) cc_final: 0.6750 (ppp)
REVERT: B  639 ARG cc_start: 0.7325 (tmm160) cc_final: 0.6790 (tmm160)
REVERT: C   29 PHE cc_start: 0.7482 (m-10) cc_final: 0.7261 (m-80)
REVERT: C  105 MET cc_start: 0.6015 (ppp) cc_final: 0.5729 (ppp)
REVERT: C  106 ARG cc_start: 0.7765 (tmt-80) cc_final: 0.7151 (tmt-80)
REVERT: C  107 LYS cc_start: 0.7975 (mtmm) cc_final: 0.6805 (mtmm)
REVERT: C  249 MET cc_start: 0.3916 (tpp) cc_final: 0.3579 (tmm)
REVERT: C  253 ASN cc_start: 0.6819 (m110) cc_final: 0.5430 (m110)
REVERT: P   46 ASN cc_start: 0.6326 (t0) cc_final: 0.5953 (m-40)
REVERT: P  134 MET cc_start: 0.5498 (ppp) cc_final: 0.5230 (ppp)
REVERT: P  320 LYS cc_start: 0.8421 (tppt) cc_final: 0.8135 (tppt)
REVERT: P  381 MET cc_start: 0.4784 (ttp) cc_final: 0.4339 (ttp)
  outliers start: 2
  outliers final: 0
  residues processed: 386
  average time/residue: 0.1558
  time to fit residues: 86.6498
Evaluate side-chains
  355 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 355
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 215
   random chunks:
   chunk 31 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 119 optimal weight:    0.2980
   chunk 186 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 2 optimal weight:    0.1980
   chunk 133 optimal weight:   30.0000
   chunk 132 optimal weight:    7.9990
   chunk 192 optimal weight:    0.0980
   chunk 79 optimal weight:    4.9990
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
A 461 GLN
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  34 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4574 r_free = 0.4574 target = 0.206021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.184622 restraints weight = 36750.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.182411 restraints weight = 58971.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.182752 restraints weight = 51798.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.181636 restraints weight = 38273.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.182081 restraints weight = 39466.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.4149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6110
moved from start:          0.3461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  18027  Z= 0.116
  Angle     :  0.623   9.668  24245  Z= 0.325
  Chirality :  0.043   0.169   2636
  Planarity :  0.004   0.092   3109
  Dihedral  :  7.191  83.552   2430
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.17 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  1.96 %
    Favored  : 97.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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: -1.47 (0.18), residues: 2147
  helix:  0.20 (0.17), residues: 975
  sheet: -0.74 (0.34), residues: 240
  loop : -2.35 (0.18), residues: 932

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C  36 
 TYR   0.025   0.001   TYR A 137 
 PHE   0.044   0.001   PHE P 331 
 TRP   0.061   0.002   TRP C  98 
 HIS   0.004   0.001   HIS A 184 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 (18024)
  covalent geometry    : angle       0.62256 (24245)
  hydrogen bonds       : bond        0.03746 (  736)
  hydrogen bonds       : angle       4.57623 ( 2118)
  Misc. bond           : bond        0.00232 (    3)

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

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

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  383 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 382
  time to evaluate  : 0.572 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 MET cc_start: 0.6581 (tmm) cc_final: 0.6120 (tmm)
REVERT: A   46 ASN cc_start: 0.7858 (m-40) cc_final: 0.7587 (m-40)
REVERT: A  168 ARG cc_start: 0.8177 (ttp80) cc_final: 0.7811 (tmm-80)
REVERT: A  170 ASP cc_start: 0.7543 (p0) cc_final: 0.7275 (p0)
REVERT: A  289 TRP cc_start: 0.6714 (p90) cc_final: 0.5997 (p90)
REVERT: A  380 VAL cc_start: 0.8287 (t) cc_final: 0.7838 (m)
REVERT: A  407 ASN cc_start: 0.8288 (m110) cc_final: 0.7888 (m-40)
REVERT: A  489 GLU cc_start: 0.6170 (mp0) cc_final: 0.5590 (mp0)
REVERT: A  519 GLU cc_start: 0.7398 (mm-30) cc_final: 0.6905 (mm-30)
REVERT: A  557 LYS cc_start: 0.7902 (pttp) cc_final: 0.7478 (pttp)
REVERT: A  577 LYS cc_start: 0.7566 (mtmm) cc_final: 0.7228 (mtmm)
REVERT: A  606 MET cc_start: 0.7668 (tpt) cc_final: 0.7446 (tpp)
REVERT: A  636 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7501 (mm-30)
REVERT: A  639 ARG cc_start: 0.7006 (ttp80) cc_final: 0.6726 (ttp80)
REVERT: A  640 GLN cc_start: 0.7965 (pp30) cc_final: 0.7604 (pp30)
REVERT: A  674 GLN cc_start: 0.6899 (pm20) cc_final: 0.6652 (pm20)
REVERT: A  680 ILE cc_start: 0.8651 (mt) cc_final: 0.8365 (mm)
REVERT: A  684 ILE cc_start: 0.8415 (pt) cc_final: 0.7998 (pt)
REVERT: B   69 LYS cc_start: 0.8201 (mptt) cc_final: 0.7801 (mptt)
REVERT: B   71 LEU cc_start: 0.7972 (tt) cc_final: 0.7302 (mp)
REVERT: B   95 LYS cc_start: 0.8093 (ptmm) cc_final: 0.7656 (ptmm)
REVERT: B  102 LEU cc_start: 0.7270 (tt) cc_final: 0.6977 (tt)
REVERT: B  125 MET cc_start: 0.6874 (tpp) cc_final: 0.6556 (ttm)
REVERT: B  154 GLN cc_start: 0.7271 (tp40) cc_final: 0.6886 (tp40)
REVERT: B  157 TRP cc_start: 0.8122 (t60) cc_final: 0.7205 (t60)
REVERT: B  203 LYS cc_start: 0.7766 (mmtt) cc_final: 0.7364 (ttmm)
REVERT: B  204 LYS cc_start: 0.8432 (tmtt) cc_final: 0.7971 (tmtt)
REVERT: B  342 ASP cc_start: 0.7096 (p0) cc_final: 0.6671 (p0)
REVERT: B  441 ILE cc_start: 0.8745 (tp) cc_final: 0.8204 (tt)
REVERT: B  550 LYS cc_start: 0.8134 (mmtp) cc_final: 0.7835 (mmtp)
REVERT: B  567 MET cc_start: 0.7227 (ppp) cc_final: 0.6733 (ppp)
REVERT: C   42 GLN cc_start: 0.7742 (tm-30) cc_final: 0.7025 (tm-30)
REVERT: C  249 MET cc_start: 0.3844 (tpp) cc_final: 0.3472 (tmm)
REVERT: C  253 ASN cc_start: 0.6799 (m110) cc_final: 0.5417 (m110)
REVERT: K  668 MET cc_start: 0.3186 (tmm) cc_final: 0.1163 (ptm)
REVERT: P   46 ASN cc_start: 0.6281 (t0) cc_final: 0.5940 (m-40)
REVERT: P  134 MET cc_start: 0.5615 (ppp) cc_final: 0.5307 (ppp)
REVERT: P  320 LYS cc_start: 0.8400 (tppt) cc_final: 0.8102 (tppt)
REVERT: P  381 MET cc_start: 0.4870 (ttp) cc_final: 0.4389 (ttp)
  outliers start: 1
  outliers final: 0
  residues processed: 383
  average time/residue: 0.1568
  time to fit residues: 87.2005
Evaluate side-chains
  360 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 360
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 215
   random chunks:
   chunk 145 optimal weight:    5.9990
   chunk 74 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9980
   chunk 172 optimal weight:    9.9990
   chunk 107 optimal weight:    1.9990
   chunk 141 optimal weight:   10.0000
   chunk 89 optimal weight:    0.6980
   chunk 93 optimal weight:    0.8980
   chunk 83 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0370
   chunk 52 optimal weight:    3.9990
   overall best weight:    0.9260

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

Flipped N/Q/H residues before XYZ refinement:
A 447 ASN
A 461 GLN
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 609 GLN
** A 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  34 GLN
K 559 GLN
** K 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4549 r_free = 0.4549 target = 0.203657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.181612 restraints weight = 36836.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.177633 restraints weight = 60777.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.175190 restraints weight = 44847.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.174176 restraints weight = 41374.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.174956 restraints weight = 35652.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.4044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6346
moved from start:          0.3706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  18027  Z= 0.147
  Angle     :  0.652  10.847  24245  Z= 0.341
  Chirality :  0.044   0.193   2636
  Planarity :  0.007   0.255   3109
  Dihedral  :  7.283  85.735   2430
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.96 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.54 %
    Favored  : 98.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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: -1.45 (0.18), residues: 2147
  helix:  0.25 (0.17), residues: 963
  sheet: -0.74 (0.35), residues: 235
  loop : -2.35 (0.18), residues: 949

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.027   0.001   ARG C  36 
 TYR   0.021   0.002   TYR A 373 
 PHE   0.028   0.002   PHE A  32 
 TRP   0.039   0.002   TRP C  98 
 HIS   0.004   0.001   HIS B 320 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (18024)
  covalent geometry    : angle       0.65178 (24245)
  hydrogen bonds       : bond        0.04101 (  736)
  hydrogen bonds       : angle       4.58300 ( 2118)
  Misc. bond           : bond        0.00580 (    3)

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

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

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  383 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 381
  time to evaluate  : 0.618 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 MET cc_start: 0.6708 (tmm) cc_final: 0.6263 (tmm)
REVERT: A   46 ASN cc_start: 0.8062 (m-40) cc_final: 0.7856 (m-40)
REVERT: A  168 ARG cc_start: 0.8329 (ttp80) cc_final: 0.7927 (tmm-80)
REVERT: A  170 ASP cc_start: 0.7594 (p0) cc_final: 0.7260 (p0)
REVERT: A  292 ASN cc_start: 0.7698 (t0) cc_final: 0.7449 (t0)
REVERT: A  299 GLU cc_start: 0.7126 (pp20) cc_final: 0.6483 (pp20)
REVERT: A  309 THR cc_start: 0.7906 (p) cc_final: 0.7687 (p)
REVERT: A  380 VAL cc_start: 0.8123 (t) cc_final: 0.7617 (m)
REVERT: A  394 MET cc_start: 0.6919 (ppp) cc_final: 0.6705 (ppp)
REVERT: A  395 LEU cc_start: 0.7200 (mt) cc_final: 0.6178 (mt)
REVERT: A  407 ASN cc_start: 0.8373 (m110) cc_final: 0.8035 (m-40)
REVERT: A  466 MET cc_start: 0.7724 (tpt) cc_final: 0.7150 (tpt)
REVERT: A  489 GLU cc_start: 0.6121 (mp0) cc_final: 0.5554 (mp0)
REVERT: A  505 LYS cc_start: 0.7351 (pptt) cc_final: 0.7070 (pptt)
REVERT: A  519 GLU cc_start: 0.7417 (mm-30) cc_final: 0.7026 (mm-30)
REVERT: A  557 LYS cc_start: 0.8051 (pttp) cc_final: 0.7562 (pttp)
REVERT: A  577 LYS cc_start: 0.7562 (mtmm) cc_final: 0.7231 (mtmm)
REVERT: A  636 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7639 (mm-30)
REVERT: A  639 ARG cc_start: 0.7158 (ttp80) cc_final: 0.6893 (ttp80)
REVERT: A  640 GLN cc_start: 0.8049 (pp30) cc_final: 0.7661 (pp30)
REVERT: A  680 ILE cc_start: 0.8680 (mt) cc_final: 0.8266 (mm)
REVERT: A  684 ILE cc_start: 0.8402 (pt) cc_final: 0.7847 (pt)
REVERT: B   69 LYS cc_start: 0.8220 (mptt) cc_final: 0.8000 (mptt)
REVERT: B   95 LYS cc_start: 0.8168 (ptmm) cc_final: 0.7585 (ptmm)
REVERT: B  110 THR cc_start: 0.7278 (p) cc_final: 0.7037 (m)
REVERT: B  125 MET cc_start: 0.7102 (tpp) cc_final: 0.6263 (ttm)
REVERT: B  154 GLN cc_start: 0.7324 (tp40) cc_final: 0.6936 (tp40)
REVERT: B  203 LYS cc_start: 0.7828 (mmtt) cc_final: 0.7585 (ttmm)
REVERT: B  204 LYS cc_start: 0.8441 (tmtt) cc_final: 0.8088 (tmtt)
REVERT: B  428 LYS cc_start: 0.7503 (pttp) cc_final: 0.7275 (ttpp)
REVERT: B  441 ILE cc_start: 0.8606 (tp) cc_final: 0.8129 (tt)
REVERT: B  489 GLU cc_start: 0.6373 (mm-30) cc_final: 0.6067 (mm-30)
REVERT: B  550 LYS cc_start: 0.8121 (mmtp) cc_final: 0.7649 (mmtp)
REVERT: B  552 LYS cc_start: 0.7623 (pttm) cc_final: 0.7373 (pttm)
REVERT: B  567 MET cc_start: 0.7264 (ppp) cc_final: 0.6804 (ppp)
REVERT: C   29 PHE cc_start: 0.7336 (m-10) cc_final: 0.7127 (m-80)
REVERT: C  108 LYS cc_start: 0.7337 (ptmm) cc_final: 0.6672 (mtmm)
REVERT: C  249 MET cc_start: 0.3852 (tpp) cc_final: 0.3315 (tmm)
REVERT: C  253 ASN cc_start: 0.6866 (m110) cc_final: 0.5442 (m110)
REVERT: K  537 LEU cc_start: 0.6931 (tp) cc_final: 0.6526 (tp)
REVERT: K  668 MET cc_start: 0.3189 (tmm) cc_final: 0.1484 (ptm)
REVERT: P   46 ASN cc_start: 0.6287 (t0) cc_final: 0.6068 (m-40)
REVERT: P  320 LYS cc_start: 0.8304 (tppt) cc_final: 0.8010 (tppt)
  outliers start: 2
  outliers final: 0
  residues processed: 382
  average time/residue: 0.1586
  time to fit residues: 87.1698
Evaluate side-chains
  353 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 353
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 215
   random chunks:
   chunk 7 optimal weight:    6.9990
   chunk 204 optimal weight:   10.0000
   chunk 208 optimal weight:    3.9990
   chunk 132 optimal weight:   10.0000
   chunk 48 optimal weight:    0.0870
   chunk 79 optimal weight:    7.9990
   chunk 172 optimal weight:   10.0000
   chunk 47 optimal weight:    0.9990
   chunk 49 optimal weight:    5.9990
   chunk 133 optimal weight:   40.0000
   chunk 183 optimal weight:    0.8980
   overall best weight:    2.3964

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 461 GLN
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  30 ASN
B 458 HIS
** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 674 GLN
B 678 ASN
C  34 GLN
C 188 ASN
K 581 ASN
** K 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 137 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.197908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.174639 restraints weight = 36511.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.171888 restraints weight = 68018.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.173245 restraints weight = 60995.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.172889 restraints weight = 37285.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.173428 restraints weight = 36534.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.4053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6319
moved from start:          0.4328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.068  18027  Z= 0.295
  Angle     :  0.819  12.483  24245  Z= 0.434
  Chirality :  0.051   0.221   2636
  Planarity :  0.006   0.167   3109
  Dihedral  :  7.690  83.509   2430
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 13.86
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 10.01 %
    Favored  : 89.85 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.11 %
    Favored  : 97.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -1.94 (0.17), residues: 2147
  helix: -0.20 (0.16), residues: 951
  sheet: -0.93 (0.35), residues: 229
  loop : -2.54 (0.18), residues: 967

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.023   0.001   ARG C  36 
 TYR   0.036   0.003   TYR B 305 
 PHE   0.053   0.003   PHE A  32 
 TRP   0.032   0.003   TRP C  98 
 HIS   0.016   0.002   HIS A 676 

Details of bonding type rmsd
  covalent geometry    : bond        0.00667 (18024)
  covalent geometry    : angle       0.81851 (24245)
  hydrogen bonds       : bond        0.05787 (  736)
  hydrogen bonds       : angle       5.24185 ( 2118)
  Misc. bond           : bond        0.00641 (    3)

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

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

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  387 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 385
  time to evaluate  : 0.703 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 GLN cc_start: 0.7612 (mp10) cc_final: 0.7012 (mp10)
REVERT: A   25 MET cc_start: 0.6812 (tmm) cc_final: 0.6462 (tmm)
REVERT: A  152 ASP cc_start: 0.7996 (t0) cc_final: 0.7717 (t70)
REVERT: A  165 PHE cc_start: 0.7019 (p90) cc_final: 0.6617 (p90)
REVERT: A  168 ARG cc_start: 0.8491 (ttp80) cc_final: 0.7730 (tmm-80)
REVERT: A  170 ASP cc_start: 0.7509 (p0) cc_final: 0.7297 (p0)
REVERT: A  299 GLU cc_start: 0.7221 (pp20) cc_final: 0.6547 (pp20)
REVERT: A  309 THR cc_start: 0.7808 (p) cc_final: 0.7498 (p)
REVERT: A  364 ASP cc_start: 0.8425 (p0) cc_final: 0.8151 (p0)
REVERT: A  375 ASN cc_start: 0.7509 (t0) cc_final: 0.7213 (t0)
REVERT: A  378 ARG cc_start: 0.7199 (mmm-85) cc_final: 0.6941 (mmm-85)
REVERT: A  380 VAL cc_start: 0.8394 (t) cc_final: 0.7982 (m)
REVERT: A  395 LEU cc_start: 0.7355 (mt) cc_final: 0.6466 (mt)
REVERT: A  402 LYS cc_start: 0.8130 (pttm) cc_final: 0.7791 (mptt)
REVERT: A  453 GLU cc_start: 0.6907 (mp0) cc_final: 0.6618 (mp0)
REVERT: A  489 GLU cc_start: 0.6037 (mp0) cc_final: 0.5445 (mp0)
REVERT: A  505 LYS cc_start: 0.7454 (pptt) cc_final: 0.7081 (pptt)
REVERT: A  557 LYS cc_start: 0.8141 (pttp) cc_final: 0.7639 (pttp)
REVERT: A  577 LYS cc_start: 0.7657 (mtmm) cc_final: 0.7285 (mtmm)
REVERT: A  617 MET cc_start: 0.6337 (ppp) cc_final: 0.6054 (ppp)
REVERT: A  640 GLN cc_start: 0.8026 (pp30) cc_final: 0.7711 (pp30)
REVERT: A  648 ASP cc_start: 0.7011 (t0) cc_final: 0.6585 (t0)
REVERT: A  682 ARG cc_start: 0.7654 (ptm-80) cc_final: 0.7229 (ttp80)
REVERT: A  684 ILE cc_start: 0.8380 (pt) cc_final: 0.7760 (pt)
REVERT: B   69 LYS cc_start: 0.8475 (mptt) cc_final: 0.8099 (mptt)
REVERT: B   95 LYS cc_start: 0.8257 (ptmm) cc_final: 0.7862 (ptmm)
REVERT: B  102 LEU cc_start: 0.7385 (tt) cc_final: 0.7139 (tt)
REVERT: B  154 GLN cc_start: 0.7217 (tp40) cc_final: 0.6755 (tp40)
REVERT: B  157 TRP cc_start: 0.8293 (t60) cc_final: 0.7269 (t60)
REVERT: B  199 LYS cc_start: 0.8212 (mtpt) cc_final: 0.8009 (mtpt)
REVERT: B  428 LYS cc_start: 0.7582 (pttp) cc_final: 0.7371 (ttpp)
REVERT: B  489 GLU cc_start: 0.6241 (mm-30) cc_final: 0.5946 (mm-30)
REVERT: B  492 GLU cc_start: 0.5950 (tp30) cc_final: 0.5547 (tp30)
REVERT: B  522 VAL cc_start: 0.6018 (p) cc_final: 0.5779 (p)
REVERT: B  539 GLU cc_start: 0.7021 (tp30) cc_final: 0.6724 (tp30)
REVERT: B  567 MET cc_start: 0.7233 (ppp) cc_final: 0.6977 (ppp)
REVERT: B  569 GLU cc_start: 0.7720 (pm20) cc_final: 0.7323 (pm20)
REVERT: C  249 MET cc_start: 0.4053 (tpp) cc_final: 0.3520 (tmm)
REVERT: C  253 ASN cc_start: 0.7052 (m110) cc_final: 0.5853 (m110)
REVERT: K  668 MET cc_start: 0.3461 (tmm) cc_final: 0.1525 (ptm)
REVERT: P  320 LYS cc_start: 0.8483 (tppt) cc_final: 0.8156 (tppt)
REVERT: P  381 MET cc_start: 0.5337 (ttp) cc_final: 0.4620 (ttp)
  outliers start: 2
  outliers final: 1
  residues processed: 387
  average time/residue: 0.1584
  time to fit residues: 88.0248
Evaluate side-chains
  362 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 361
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 215
   random chunks:
   chunk 104 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 199 optimal weight:    1.9990
   chunk 197 optimal weight:   20.0000
   chunk 56 optimal weight:    4.9990
   chunk 132 optimal weight:   10.0000
   chunk 102 optimal weight:    0.5980
   chunk 112 optimal weight:    1.9990
   chunk 190 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9980
   chunk 87 optimal weight:    1.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 461 GLN
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 609 GLN
** A 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 524 GLN
C  34 GLN
C 130 ASN
** K 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4517 r_free = 0.4517 target = 0.200983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.178139 restraints weight = 36526.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.176367 restraints weight = 62467.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.177315 restraints weight = 56123.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.176967 restraints weight = 37082.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.177496 restraints weight = 33421.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.4104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6229
moved from start:          0.4448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  18027  Z= 0.181
  Angle     :  0.722  11.754  24245  Z= 0.377
  Chirality :  0.046   0.188   2636
  Planarity :  0.006   0.158   3109
  Dihedral  :  7.332  77.455   2430
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.38 %
    Favored  : 91.43 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.72 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    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: -1.81 (0.17), residues: 2147
  helix: -0.06 (0.16), residues: 963
  sheet: -1.05 (0.35), residues: 233
  loop : -2.48 (0.18), residues: 951

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG C  36 
 TYR   0.025   0.002   TYR B 301 
 PHE   0.033   0.002   PHE A  32 
 TRP   0.027   0.002   TRP C  98 
 HIS   0.006   0.001   HIS P 438 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 (18024)
  covalent geometry    : angle       0.72237 (24245)
  hydrogen bonds       : bond        0.04583 (  736)
  hydrogen bonds       : angle       4.91181 ( 2118)
  Misc. bond           : bond        0.00452 (    3)

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

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

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  384 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 381
  time to evaluate  : 0.621 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 GLN cc_start: 0.7508 (mp10) cc_final: 0.6903 (mp10)
REVERT: A   25 MET cc_start: 0.6776 (tmm) cc_final: 0.6420 (tmm)
REVERT: A  152 ASP cc_start: 0.7975 (t0) cc_final: 0.7722 (t0)
REVERT: A  168 ARG cc_start: 0.8350 (ttp80) cc_final: 0.7477 (tmm-80)
REVERT: A  299 GLU cc_start: 0.7282 (pp20) cc_final: 0.6966 (pp20)
REVERT: A  309 THR cc_start: 0.7896 (p) cc_final: 0.7511 (p)
REVERT: A  364 ASP cc_start: 0.8322 (p0) cc_final: 0.8062 (p0)
REVERT: A  375 ASN cc_start: 0.7388 (t0) cc_final: 0.7139 (t0)
REVERT: A  378 ARG cc_start: 0.7148 (mmm-85) cc_final: 0.6850 (mmm-85)
REVERT: A  380 VAL cc_start: 0.8246 (t) cc_final: 0.7815 (m)
REVERT: A  394 MET cc_start: 0.6988 (ppp) cc_final: 0.6724 (ppp)
REVERT: A  395 LEU cc_start: 0.7325 (mt) cc_final: 0.6434 (mt)
REVERT: A  453 GLU cc_start: 0.6849 (mp0) cc_final: 0.6526 (mp0)
REVERT: A  505 LYS cc_start: 0.7440 (pptt) cc_final: 0.7086 (pptt)
REVERT: A  557 LYS cc_start: 0.8143 (pttp) cc_final: 0.7587 (pttp)
REVERT: A  577 LYS cc_start: 0.7604 (mtmm) cc_final: 0.7256 (mtmm)
REVERT: A  606 MET cc_start: 0.7793 (tpp) cc_final: 0.7501 (tpt)
REVERT: A  620 MET cc_start: 0.7272 (tpp) cc_final: 0.7052 (tpp)
REVERT: A  636 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7340 (mm-30)
REVERT: A  640 GLN cc_start: 0.8004 (pp30) cc_final: 0.7650 (pp30)
REVERT: A  682 ARG cc_start: 0.7580 (ptm-80) cc_final: 0.7131 (ttp80)
REVERT: A  684 ILE cc_start: 0.8251 (pt) cc_final: 0.7669 (pt)
REVERT: B   21 ILE cc_start: 0.8253 (tp) cc_final: 0.8036 (tt)
REVERT: B   25 MET cc_start: 0.7075 (tpp) cc_final: 0.6796 (tpp)
REVERT: B   69 LYS cc_start: 0.8417 (mptt) cc_final: 0.7853 (mptt)
REVERT: B   71 LEU cc_start: 0.8551 (tt) cc_final: 0.8172 (tt)
REVERT: B   97 ASP cc_start: 0.7145 (t0) cc_final: 0.6523 (t0)
REVERT: B   98 LEU cc_start: 0.8892 (tt) cc_final: 0.8599 (tt)
REVERT: B  102 LEU cc_start: 0.7466 (tt) cc_final: 0.7188 (tt)
REVERT: B  154 GLN cc_start: 0.7205 (tp40) cc_final: 0.6730 (tp40)
REVERT: B  157 TRP cc_start: 0.8204 (t60) cc_final: 0.7152 (t60)
REVERT: B  203 LYS cc_start: 0.8059 (ttmm) cc_final: 0.7713 (ttmm)
REVERT: B  277 ILE cc_start: 0.6827 (mp) cc_final: 0.6582 (mt)
REVERT: B  428 LYS cc_start: 0.7557 (pttp) cc_final: 0.7333 (ttpp)
REVERT: B  441 ILE cc_start: 0.8720 (tp) cc_final: 0.8334 (tt)
REVERT: B  492 GLU cc_start: 0.5980 (tp30) cc_final: 0.5413 (tp30)
REVERT: B  493 GLN cc_start: 0.6092 (tm-30) cc_final: 0.5819 (tm-30)
REVERT: B  565 LYS cc_start: 0.8218 (tptp) cc_final: 0.8009 (tptp)
REVERT: B  567 MET cc_start: 0.7211 (ppp) cc_final: 0.6668 (ppp)
REVERT: B  571 LEU cc_start: 0.7957 (tp) cc_final: 0.7613 (tt)
REVERT: C   42 GLN cc_start: 0.7703 (tm-30) cc_final: 0.6962 (tm-30)
REVERT: C  249 MET cc_start: 0.3959 (tpp) cc_final: 0.3511 (tmm)
REVERT: C  253 ASN cc_start: 0.7000 (m110) cc_final: 0.5820 (m110)
REVERT: K  668 MET cc_start: 0.3543 (tmm) cc_final: 0.1697 (ptm)
REVERT: P  148 PHE cc_start: 0.6906 (t80) cc_final: 0.6701 (t80)
REVERT: P  320 LYS cc_start: 0.8437 (tppt) cc_final: 0.8112 (tppt)
REVERT: P  381 MET cc_start: 0.5193 (ttp) cc_final: 0.4586 (ttp)
  outliers start: 3
  outliers final: 1
  residues processed: 382
  average time/residue: 0.1564
  time to fit residues: 85.3398
Evaluate side-chains
  368 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 367
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 215
   random chunks:
   chunk 77 optimal weight:    0.8980
   chunk 124 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   chunk 141 optimal weight:    8.9990
   chunk 79 optimal weight:    2.9990
   chunk 155 optimal weight:    6.9990
   chunk 111 optimal weight:    0.0570
   chunk 120 optimal weight:    3.9990
   chunk 84 optimal weight:    0.0000
   chunk 202 optimal weight:    8.9990
   chunk 50 optimal weight:    3.9990
   overall best weight:    0.4702

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

Flipped N/Q/H residues before XYZ refinement:
A 461 GLN
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 436 ASN
** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  34 GLN
** K 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4554 r_free = 0.4554 target = 0.204349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.180651 restraints weight = 36479.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.178641 restraints weight = 60785.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.178865 restraints weight = 53139.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.178320 restraints weight = 37382.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.178958 restraints weight = 32807.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.4110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6224
moved from start:          0.4497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  18027  Z= 0.132
  Angle     :  0.697  11.897  24245  Z= 0.363
  Chirality :  0.045   0.258   2636
  Planarity :  0.005   0.138   3109
  Dihedral  :  6.921  83.969   2430
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.73 %
    Favored  : 92.08 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  0.41 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

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: -1.64 (0.18), residues: 2147
  helix:  0.09 (0.17), residues: 958
  sheet: -0.91 (0.35), residues: 229
  loop : -2.41 (0.18), residues: 960

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG C  36 
 TYR   0.016   0.001   TYR A 155 
 PHE   0.020   0.001   PHE P 331 
 TRP   0.027   0.002   TRP C  98 
 HIS   0.004   0.001   HIS A 184 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (18024)
  covalent geometry    : angle       0.69700 (24245)
  hydrogen bonds       : bond        0.04053 (  736)
  hydrogen bonds       : angle       4.76176 ( 2118)
  Misc. bond           : bond        0.00333 (    3)

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

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

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4294 Ramachandran restraints generated.
    2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  368 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 367
  time to evaluate  : 0.607 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 GLN cc_start: 0.7401 (mp10) cc_final: 0.6753 (mp10)
REVERT: A   25 MET cc_start: 0.6581 (tmm) cc_final: 0.6237 (tmm)
REVERT: A   76 ILE cc_start: 0.7129 (mm) cc_final: 0.6576 (mt)
REVERT: A  152 ASP cc_start: 0.7901 (t0) cc_final: 0.7585 (t70)
REVERT: A  168 ARG cc_start: 0.8300 (ttp80) cc_final: 0.7624 (tmm-80)
REVERT: A  170 ASP cc_start: 0.7417 (p0) cc_final: 0.7210 (p0)
REVERT: A  198 VAL cc_start: 0.7805 (t) cc_final: 0.7580 (m)
REVERT: A  289 TRP cc_start: 0.6857 (p90) cc_final: 0.6457 (p90)
REVERT: A  309 THR cc_start: 0.7913 (p) cc_final: 0.7652 (p)
REVERT: A  378 ARG cc_start: 0.7086 (mmm-85) cc_final: 0.6834 (mmm-85)
REVERT: A  380 VAL cc_start: 0.8057 (t) cc_final: 0.7722 (m)
REVERT: A  382 ASP cc_start: 0.7500 (t0) cc_final: 0.7123 (m-30)
REVERT: A  394 MET cc_start: 0.7073 (ppp) cc_final: 0.6669 (ppp)
REVERT: A  395 LEU cc_start: 0.7122 (mt) cc_final: 0.6121 (mt)
REVERT: A  453 GLU cc_start: 0.6719 (mp0) cc_final: 0.6431 (mp0)
REVERT: A  489 GLU cc_start: 0.6366 (mp0) cc_final: 0.6158 (mp0)
REVERT: A  557 LYS cc_start: 0.8137 (pttp) cc_final: 0.7577 (pttp)
REVERT: A  577 LYS cc_start: 0.7467 (mtmm) cc_final: 0.7140 (mtmm)
REVERT: A  606 MET cc_start: 0.7723 (tpp) cc_final: 0.7507 (tpp)
REVERT: A  639 ARG cc_start: 0.7083 (ptt-90) cc_final: 0.6811 (ttp80)
REVERT: A  640 GLN cc_start: 0.8044 (pp30) cc_final: 0.7372 (pp30)
REVERT: A  682 ARG cc_start: 0.7505 (ptm-80) cc_final: 0.7092 (ttp80)
REVERT: A  684 ILE cc_start: 0.8216 (pt) cc_final: 0.7665 (pt)
REVERT: B   21 ILE cc_start: 0.8125 (tp) cc_final: 0.7923 (tp)
REVERT: B   25 MET cc_start: 0.7039 (tpp) cc_final: 0.6728 (tpp)
REVERT: B   69 LYS cc_start: 0.8193 (mptt) cc_final: 0.7839 (mptt)
REVERT: B   95 LYS cc_start: 0.8224 (ptmm) cc_final: 0.7506 (ptmm)
REVERT: B  154 GLN cc_start: 0.7188 (tp40) cc_final: 0.6786 (tp40)
REVERT: B  157 TRP cc_start: 0.8092 (t60) cc_final: 0.7146 (t60)
REVERT: B  203 LYS cc_start: 0.8067 (ttmm) cc_final: 0.7732 (ttmm)
REVERT: B  277 ILE cc_start: 0.6793 (mp) cc_final: 0.6550 (mt)
REVERT: B  428 LYS cc_start: 0.7501 (pttp) cc_final: 0.7292 (ttpp)
REVERT: B  441 ILE cc_start: 0.8635 (tp) cc_final: 0.8008 (tt)
REVERT: B  489 GLU cc_start: 0.6150 (mm-30) cc_final: 0.5808 (mm-30)
REVERT: B  492 GLU cc_start: 0.5928 (tp30) cc_final: 0.5362 (tp30)
REVERT: B  493 GLN cc_start: 0.6025 (tm-30) cc_final: 0.5702 (tm-30)
REVERT: B  567 MET cc_start: 0.7244 (ppp) cc_final: 0.6722 (ppp)
REVERT: B  569 GLU cc_start: 0.7601 (pm20) cc_final: 0.7291 (pm20)
REVERT: B  571 LEU cc_start: 0.7866 (tp) cc_final: 0.7606 (tt)
REVERT: B  620 MET cc_start: 0.4422 (pmm) cc_final: 0.4162 (pmm)
REVERT: C  249 MET cc_start: 0.3966 (tpp) cc_final: 0.3486 (tmm)
REVERT: C  253 ASN cc_start: 0.6835 (m110) cc_final: 0.5733 (m110)
REVERT: K  537 LEU cc_start: 0.7005 (tp) cc_final: 0.6672 (tp)
REVERT: K  646 LEU cc_start: 0.6319 (mt) cc_final: 0.6065 (mt)
REVERT: K  668 MET cc_start: 0.3307 (tmm) cc_final: 0.1482 (ptm)
REVERT: P  320 LYS cc_start: 0.8392 (tppt) cc_final: 0.8078 (tppt)
REVERT: P  381 MET cc_start: 0.5271 (ttp) cc_final: 0.4636 (ttp)
  outliers start: 1
  outliers final: 1
  residues processed: 368
  average time/residue: 0.1605
  time to fit residues: 84.6040
Evaluate side-chains
  357 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 356
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 215
   random chunks:
   chunk 115 optimal weight:    0.0980
   chunk 40 optimal weight:    0.7980
   chunk 182 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 207 optimal weight:    3.9990
   chunk 151 optimal weight:    5.9990
   chunk 142 optimal weight:    8.9990
   chunk 210 optimal weight:    6.9990
   chunk 200 optimal weight:    0.8980
   chunk 56 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  46 ASN
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 609 GLN
** B 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  34 GLN
K 709 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4550 r_free = 0.4550 target = 0.203852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.180119 restraints weight = 36506.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.178533 restraints weight = 62004.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.179678 restraints weight = 52794.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.179038 restraints weight = 35637.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.179513 restraints weight = 34518.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.4121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6193
moved from start:          0.4617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  18027  Z= 0.139
  Angle     :  0.690  11.806  24245  Z= 0.359
  Chirality :  0.045   0.195   2636
  Planarity :  0.005   0.124   3109
  Dihedral  :  6.881  80.649   2430
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  7.73 %
    Favored  : 92.08 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.51 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.54 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

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: -1.56 (0.18), residues: 2147
  helix:  0.15 (0.17), residues: 959
  sheet: -0.84 (0.36), residues: 230
  loop : -2.37 (0.18), residues: 958

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG C  36 
 TYR   0.021   0.002   TYR A 137 
 PHE   0.024   0.002   PHE A  32 
 TRP   0.026   0.002   TRP C  98 
 HIS   0.004   0.001   HIS P 438 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (18024)
  covalent geometry    : angle       0.69034 (24245)
  hydrogen bonds       : bond        0.04117 (  736)
  hydrogen bonds       : angle       4.73501 ( 2118)
  Misc. bond           : bond        0.00341 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3133.58 seconds
wall clock time: 55 minutes 5.69 seconds (3305.69 seconds total)