Starting phenix.real_space_refine
on Thu Jul  2 09:12:00 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7l1k_23110/07_2026/7l1k_23110.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7l1k_23110/07_2026/7l1k_23110.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7l1k_23110/07_2026/7l1k_23110.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7l1k_23110/07_2026/7l1k_23110.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7l1k_23110/07_2026/7l1k_23110.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7l1k_23110/07_2026/7l1k_23110.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7l1k_23110/07_2026/7l1k_23110.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7l1k_23110/07_2026/7l1k_23110.cif"
  }
  resolution = 3.16
  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
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.112
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1216 atoms to isotropic.
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       9      5.49       5
     S      36      5.16       5
     C    4621      2.51       5
     N    1202      2.21       5
     O    1349      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7217
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1233
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 149, 1233
          Classifications: {'peptide': 149}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 4, 'TRANS': 144}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 5315
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 660, 5309
          Classifications: {'peptide': 660}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 628}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
      Conformer: "B"
        Number of residues, atoms: 660, 5309
          Classifications: {'peptide': 660}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 628}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
          bond proxies already assigned to first conformer: 5420
    Chain: "C"
      Number of atoms: 555
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 70, 555
          Classifications: {'peptide': 70}
          Link IDs: {'PTRANS': 1, 'TRANS': 68}
    Chain: "D"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 27
          Classifications: {'peptide': 4}
          Link IDs: {'PTRANS': 1, 'TRANS': 2}
    Chain: "A"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 36
          Unusual residues: {'IHP': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 51
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 51
          Unusual residues: {'CMC': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'CMC:plan-5': 1}
          Unresolved non-hydrogen planarities: 1
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ASER B 190 " occ=0.50
      ... (10 atoms not shown)
      pdb=" OG BSER B 190 " occ=0.50
  Time building chain proxies: 2.42, per 1000 atoms: 0.34
  Number of scatterers: 7217
  At special positions: 0
  Unit cell: (86.52, 97.44, 108.36, 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      36     16.00
     P       9     15.00
     O    1349      8.00
     N    1202      7.00
     C    4621      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.60
  Conformation dependent library (CDL) restraints added in 564.0 milliseconds
  

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1704

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 4 sheets defined
      51.8% alpha, 7.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 10
      No H-bonds generated for 'chain 'A' and resid 8 through 10'
    Processing helix  chain 'A' and resid 11 through 20
      removed outlier: 3.788A  pdb=" N   GLN A  17 " --> pdb=" O   LYS A  13 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 28 through 37
      removed outlier: 4.247A  pdb=" N   TYR A  32 " --> pdb=" O   SER A  28 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ARG A  33 " --> pdb=" O   LYS A  29 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   TYR A  34 " --> pdb=" O   TYR A  30 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   PHE A  35 " --> pdb=" O   VAL A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 82
      removed outlier: 3.928A  pdb=" N   ARG A  82 " --> pdb=" O   LYS A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 101
      removed outlier: 3.905A  pdb=" N   VAL A  97 " --> pdb=" O   ALA A  93 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   MET A  98 " --> pdb=" O   SER A  94 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LYS A  99 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 125
    Processing helix  chain 'B' and resid 65 through 69
      removed outlier: 3.815A  pdb=" N   ILE B  68 " --> pdb=" O   LEU B  65 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   SER B  69 " --> pdb=" O   ASP B  66 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 65 through 69'
    Processing helix  chain 'B' and resid 100 through 112
      removed outlier: 3.533A  pdb=" N   VAL B 108 " --> pdb=" O   MET B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 124 through 128
      removed outlier: 3.542A  pdb=" N   SER B 127 " --> pdb=" O   LEU B 124 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   ALA B 128 " --> pdb=" O   LEU B 125 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 124 through 128'
    Processing helix  chain 'B' and resid 129 through 134
      removed outlier: 3.528A  pdb=" N   ILE B 133 " --> pdb=" O   HIS B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 173
      removed outlier: 3.803A  pdb=" N   PHE B 162 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ILE B 172 " --> pdb=" O   LYS B 168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 173 through 178
    Processing helix  chain 'B' and resid 202 through 218
      removed outlier: 3.797A  pdb=" N   ILE B 214 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 250
      removed outlier: 3.729A  pdb=" N   ASN B 237 " --> pdb=" O   GLU B 233 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ARG B 238 " --> pdb=" O   GLY B 234 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLY B 244 " --> pdb=" O   GLN B 240 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ARG B 247 " --> pdb=" O   ILE B 243 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   VAL B 248 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 272
      removed outlier: 3.695A  pdb=" N   LYS B 265 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ASN B 266 " --> pdb=" O   HIS B 262 " (cutoff:3.500A)
      Proline residue:  B 269  - end of helix
    Processing helix  chain 'B' and resid 274 through 278
      removed outlier: 4.022A  pdb=" N   VAL B 277 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   VAL B 278 " --> pdb=" O   VAL B 275 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 274 through 278'
    Processing helix  chain 'B' and resid 281 through 286
      removed outlier: 3.573A  pdb=" N   SER B 285 " --> pdb=" O   SER B 281 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 299
    Processing helix  chain 'B' and resid 312 through 331
      removed outlier: 3.601A  pdb=" N   GLN B 318 " --> pdb=" O   GLU B 314 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ILE B 320 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ASP B 326 " --> pdb=" O   TYR B 322 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   LEU B 328 " --> pdb=" O   ALA B 324 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   LEU B 329 " --> pdb=" O   ASP B 325 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 335
    Processing helix  chain 'B' and resid 339 through 349
      removed outlier: 3.648A  pdb=" N   TYR B 343 " --> pdb=" O   SER B 339 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   CYS B 346 " --> pdb=" O   VAL B 342 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   LEU B 347 " --> pdb=" O   TYR B 343 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 350 through 352
      No H-bonds generated for 'chain 'B' and resid 350 through 352'
    Processing helix  chain 'B' and resid 357 through 363
    Processing helix  chain 'B' and resid 363 through 370
      removed outlier: 3.539A  pdb=" N   LEU B 367 " --> pdb=" O   SER B 363 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   THR B 369 " --> pdb=" O   GLN B 365 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   ALA B 370 " --> pdb=" O   ALA B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 392
      removed outlier: 3.996A  pdb=" N   MET B 384 " --> pdb=" O   PRO B 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 416
    Processing helix  chain 'B' and resid 416 through 437
      removed outlier: 3.637A  pdb=" N   VAL B 420 " --> pdb=" O   TYR B 416 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   SER B 422 " --> pdb=" O   PRO B 418 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ALA B 425 " --> pdb=" O   GLU B 421 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ASN B 429 " --> pdb=" O   ALA B 425 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   ILE B 430 " --> pdb=" O   HIS B 426 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   ASP B 433 " --> pdb=" O   ASN B 429 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 441 through 451
      removed outlier: 3.522A  pdb=" N   ARG B 446 " --> pdb=" O   PRO B 442 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   ARG B 447 " --> pdb=" O   CYS B 443 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ASN B 451 " --> pdb=" O   ARG B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 462
      removed outlier: 3.843A  pdb=" N   VAL B 458 " --> pdb=" O   PRO B 454 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 466 through 470
      removed outlier: 3.790A  pdb=" N   PHE B 470 " --> pdb=" O   ASP B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 481 through 503
      removed outlier: 3.787A  pdb=" N   HIS B 487 " --> pdb=" O   SER B 483 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 507 through 509
      No H-bonds generated for 'chain 'B' and resid 507 through 509'
    Processing helix  chain 'B' and resid 510 through 533
      removed outlier: 3.623A  pdb=" N   PHE B 514 " --> pdb=" O   GLN B 510 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ALA B 516 " --> pdb=" O   PRO B 512 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ASP B 519 " --> pdb=" O   PHE B 515 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   HIS B 520 " --> pdb=" O   ALA B 516 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   LEU B 531 " --> pdb=" O   THR B 527 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 542 through 561
      removed outlier: 3.654A  pdb=" N   THR B 547 " --> pdb=" O   LYS B 543 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   TYR B 548 " --> pdb=" O   THR B 544 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ARG B 551 " --> pdb=" O   THR B 547 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 563 through 573
      removed outlier: 3.507A  pdb=" N   LEU B 569 " --> pdb=" O   LEU B 565 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ARG B 572 " --> pdb=" O   VAL B 568 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 579 through 583
      removed outlier: 3.581A  pdb=" N   THR B 582 " --> pdb=" O   PRO B 579 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   LEU B 583 " --> pdb=" O   SER B 580 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 579 through 583'
    Processing helix  chain 'B' and resid 584 through 596
      removed outlier: 4.031A  pdb=" N   SER B 590 " --> pdb=" O   LYS B 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 597 through 602
      removed outlier: 3.913A  pdb=" N   ASN B 601 " --> pdb=" O   ARG B 597 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   LEU B 602 " --> pdb=" O   PRO B 598 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 597 through 602'
    Processing helix  chain 'B' and resid 609 through 622
      removed outlier: 4.162A  pdb=" N   CYS B 615 " --> pdb=" O   SER B 611 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ILE B 616 " --> pdb=" O   GLU B 612 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ILE B 617 " --> pdb=" O   ALA B 613 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ASN B 622 " --> pdb=" O   LYS B 618 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 624 through 648
      removed outlier: 3.536A  pdb=" N   ILE B 629 " --> pdb=" O   THR B 625 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   ILE B 630 " --> pdb=" O   ASP B 626 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   GLU B 634 " --> pdb=" O   ILE B 630 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   LYS B 635 " --> pdb=" O   LYS B 631 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   PHE B 636 " --> pdb=" O   SER B 632 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   THR B 637 " --> pdb=" O   ASN B 633 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ASN B 645 " --> pdb=" O   ASN B 641 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   VAL B 646 " --> pdb=" O   SER B 642 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 668 through 673
    Processing helix  chain 'B' and resid 680 through 687
      removed outlier: 3.537A  pdb=" N   ASP B 687 " --> pdb=" O   ILE B 683 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 48 through 55
      removed outlier: 3.650A  pdb=" N   TRP C  55 " --> pdb=" O   LEU C  51 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 105 through 109
      removed outlier: 4.040A  pdb=" N   ILE C 109 " --> pdb=" O   GLY C 106 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5
      removed outlier: 7.135A  pdb=" N   ALA A  55 " --> pdb=" O   LEU A  75 " (cutoff:3.500A)
      removed outlier: 4.673A  pdb=" N   LEU A  75 " --> pdb=" O   ALA A  55 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   ILE A  57 " --> pdb=" O   ALA A  73 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   LEU A  68 " --> pdb=" O   GLU A 105 " (cutoff:3.500A)
      removed outlier: 7.928A  pdb=" N   VAL A 107 " --> pdb=" O   LEU A  68 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   GLY A  70 " --> pdb=" O   VAL A 107 " (cutoff:3.500A)
      removed outlier: 8.601A  pdb=" N   GLU A 109 " --> pdb=" O   GLY A  70 " (cutoff:3.500A)
      removed outlier: 8.166A  pdb=" N   ILE A  72 " --> pdb=" O   GLU A 109 " (cutoff:3.500A)
      removed outlier: 10.300A  pdb=" N   GLU A 111 " --> pdb=" O   ILE A  72 " (cutoff:3.500A)
      removed outlier: 13.582A  pdb=" N   MET A  74 " --> pdb=" O   GLU A 111 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   ILE A 146 " --> pdb=" O   ARG A 128 " (cutoff:3.500A)
      removed outlier: 5.698A  pdb=" N   ARG A 128 " --> pdb=" O   ILE A 146 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 57 through 58
      removed outlier: 3.535A  pdb=" N   THR C  77 " --> pdb=" O   VAL B  57 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   ILE C  71 " --> pdb=" O   THR C  88 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   THR C  88 " --> pdb=" O   ILE C  71 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   ILE C  84 " --> pdb=" O   LEU C  75 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 57 through 58
      removed outlier: 3.535A  pdb=" N   THR C  77 " --> pdb=" O   VAL B  57 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLY C  72 " --> pdb=" O   VAL C  60 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   SER C 113 " --> pdb=" O   HIS C  61 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLU C  63 " --> pdb=" O   SER C 111 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 694 through 695
      removed outlier: 3.605A  pdb=" N   SER B 704 " --> pdb=" O   VAL B 695 " (cutoff:3.500A)

    243 hydrogen bonds defined for protein.
    684 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.05

  Time building geometry restraints manager: 0.80 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1150
        1.29 -     1.42: 1952
        1.42 -     1.55: 4205
        1.55 -     1.68: 18
        1.68 -     1.81: 53
  Bond restraints: 7378
  Sorted by residual:
  bond pdb=" C   GLY D 403 "
       pdb=" N   PRO D 404 "
    ideal  model  delta    sigma   weight residual
    1.341  1.496 -0.155 1.60e-02 3.91e+03 9.40e+01
  bond pdb=" O3B CMC D 501 "
       pdb=" P3B CMC D 501 "
    ideal  model  delta    sigma   weight residual
    1.728  1.588  0.140 2.00e-02 2.50e+03 4.90e+01
  bond pdb=" C   GLN B 507 "
       pdb=" N   PRO B 508 "
    ideal  model  delta    sigma   weight residual
    1.334  1.489 -0.155 2.34e-02 1.83e+03 4.41e+01
  bond pdb=" O23 IHP A 301 "
       pdb=" P3  IHP A 301 "
    ideal  model  delta    sigma   weight residual
    1.530  1.404  0.126 2.00e-02 2.50e+03 3.97e+01
  bond pdb=" O43 IHP A 301 "
       pdb=" P3  IHP A 301 "
    ideal  model  delta    sigma   weight residual
    1.532  1.416  0.116 2.00e-02 2.50e+03 3.37e+01
  ... (remaining 7373 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.08: 9864
        4.08 -     8.17: 110
        8.17 -    12.25: 36
       12.25 -    16.34: 2
       16.34 -    20.42: 3
  Bond angle restraints: 10015
  Sorted by residual:
  angle pdb=" CA  GLY D 403 "
        pdb=" C   GLY D 403 "
        pdb=" N   PRO D 404 "
      ideal   model   delta    sigma   weight residual
     115.52  127.47  -11.95 1.13e+00 7.83e-01 1.12e+02
  angle pdb=" CA  GLN B 507 "
        pdb=" C   GLN B 507 "
        pdb=" N   PRO B 508 "
      ideal   model   delta    sigma   weight residual
     118.45  127.91   -9.46 9.60e-01 1.09e+00 9.71e+01
  angle pdb=" C   GLN B 507 "
        pdb=" N   PRO B 508 "
        pdb=" CA  PRO B 508 "
      ideal   model   delta    sigma   weight residual
     119.84  131.34  -11.50 1.25e+00 6.40e-01 8.47e+01
  angle pdb=" O   GLY D 403 "
        pdb=" C   GLY D 403 "
        pdb=" N   PRO D 404 "
      ideal   model   delta    sigma   weight residual
     122.03  114.12    7.91 1.14e+00 7.69e-01 4.82e+01
  angle pdb=" C   GLU B 227 "
        pdb=" CA  GLU B 227 "
        pdb=" CB  GLU B 227 "
      ideal   model   delta    sigma   weight residual
     109.75  121.64  -11.89 1.72e+00 3.38e-01 4.78e+01
  ... (remaining 10010 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.02: 3980
       18.02 -    36.04: 380
       36.04 -    54.06: 80
       54.06 -    72.09: 20
       72.09 -    90.11: 10
  Dihedral angle restraints: 4470
    sinusoidal: 1842
      harmonic: 2628
  Sorted by residual:
  dihedral pdb=" C   GLU B 227 "
           pdb=" N   GLU B 227 "
           pdb=" CA  GLU B 227 "
           pdb=" CB  GLU B 227 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -138.29   15.69     0      2.50e+00 1.60e-01 3.94e+01
  dihedral pdb=" N   LEU D 402 "
           pdb=" C   LEU D 402 "
           pdb=" CA  LEU D 402 "
           pdb=" CB  LEU D 402 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  107.46   15.34     0      2.50e+00 1.60e-01 3.76e+01
  dihedral pdb=" CA  PRO B  86 "
           pdb=" C   PRO B  86 "
           pdb=" N   LEU B  87 "
           pdb=" CA  LEU B  87 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.59   28.41     0      5.00e+00 4.00e-02 3.23e+01
  ... (remaining 4467 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.913: 1130
       0.913 -    1.827: 0
       1.827 -    2.740: 0
       2.740 -    3.654: 0
       3.654 -    4.567: 4
  Chirality restraints: 1134
  Sorted by residual:
  chirality pdb=" C1  IHP A 301 "
            pdb=" C2  IHP A 301 "
            pdb=" C6  IHP A 301 "
            pdb=" O11 IHP A 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.32   -2.25    4.57 2.00e-01 2.50e+01 5.21e+02
  chirality pdb=" C2  IHP A 301 "
            pdb=" C1  IHP A 301 "
            pdb=" C3  IHP A 301 "
            pdb=" O12 IHP A 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.52    1.77   -4.29 2.00e-01 2.50e+01 4.60e+02
  chirality pdb=" C5  IHP A 301 "
            pdb=" C4  IHP A 301 "
            pdb=" C6  IHP A 301 "
            pdb=" O15 IHP A 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.42    1.84   -4.25 2.00e-01 2.50e+01 4.52e+02
  ... (remaining 1131 not shown)

  Planarity restraints: 1254
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C3P CMC D 501 "    0.212 2.00e-02 2.50e+03   1.76e-01 3.85e+02
        pdb=" C5P CMC D 501 "   -0.045 2.00e-02 2.50e+03
        pdb=" C6P CMC D 501 "    0.147 2.00e-02 2.50e+03
        pdb=" N4P CMC D 501 "   -0.292 2.00e-02 2.50e+03
        pdb=" O5P CMC D 501 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C7P CMC D 501 "    0.191 2.00e-02 2.50e+03   1.54e-01 2.98e+02
        pdb=" C9P CMC D 501 "   -0.087 2.00e-02 2.50e+03
        pdb=" CAP CMC D 501 "    0.152 2.00e-02 2.50e+03
        pdb=" N8P CMC D 501 "   -0.226 2.00e-02 2.50e+03
        pdb=" O9P CMC D 501 "   -0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 224 "   -0.017 2.00e-02 2.50e+03   3.42e-02 1.17e+01
        pdb=" C   PHE B 224 "    0.059 2.00e-02 2.50e+03
        pdb=" O   PHE B 224 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   SER B 225 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 1251 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 2386
        2.83 -     3.35: 6166
        3.35 -     3.87: 11209
        3.87 -     4.38: 14179
        4.38 -     4.90: 23998
  Nonbonded interactions: 57938
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU B 386 "
            pdb=" OH  TYR B 399 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" O   HIS B 506 "
            pdb=" CZ3 TRP B 511 "
     model   vdw
     2.322 3.340
  nonbonded pdb=" NH2 ARG A  69 "
            pdb=" O43 IHP A 301 "
     model   vdw
     2.328 3.120
  nonbonded pdb=" O   SER B 477 "
            pdb=" OG  SER B 477 "
     model   vdw
     2.330 3.040
  nonbonded pdb=" OD1 ASP B 105 "
            pdb=" OH  TYR B 317 "
     model   vdw
     2.343 3.040
  ... (remaining 57933 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             0.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.240
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8781
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      :  0.010   0.282   7379  Z= 0.600
  Angle     :  1.239  20.421  10015  Z= 0.650
  Chirality :  0.266   4.567   1134
  Planarity :  0.009   0.176   1254
  Dihedral  : 15.717  90.107   2766
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  9.76 %
    Favored  : 89.90 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  5.50 %
    Favored  : 93.75 %
  Cbeta Deviations :  0.59 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -6.55 (0.18), residues: 874
  helix: -4.83 (0.08), residues: 474
  sheet: -3.29 (0.54), residues: 60
  loop : -3.50 (0.28), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 144 
 TYR   0.014   0.002   TYR A 129 
 PHE   0.015   0.002   PHE B 656 
 TRP   0.013   0.002   TRP B 511 
 HIS   0.008   0.001   HIS B 506 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00997 /  0.50 ( 7378)
  covalent geometry    : angle       1.23936 /  0.65 (10015)
  hydrogen bonds       : bond        0.32332 / 20.81 (  242)
  hydrogen bonds       : angle      10.25813 /  7.06 (  684)
  Misc. bond           : bond        0.28215 / 14.85 (    1)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 89
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A   41 GLU cc_start: 0.8061 (pm20) cc_final: 0.7748 (pm20)
REVERT: A  123 ARG cc_start: 0.8234 (ttp80) cc_final: 0.7933 (ttp80)
REVERT: B   93 ARG cc_start: 0.8006 (ttt90) cc_final: 0.7731 (ttp80)
REVERT: B  184 ASP cc_start: 0.8120 (t0) cc_final: 0.7863 (t0)
REVERT: B  571 MET cc_start: 0.9038 (mtm) cc_final: 0.8808 (mtp)
REVERT: B  660 TYR cc_start: 0.8511 (m-80) cc_final: 0.7879 (m-80)
REVERT: C   78 ASP cc_start: 0.8963 (p0) cc_final: 0.8721 (p0)
REVERT: C   80 GLU cc_start: 0.8557 (mp0) cc_final: 0.7986 (mp0)
  outliers start: 6
  outliers final: 3
  residues processed: 93
  average time/residue: 0.1094
  time to fit residues: 13.1623
Evaluate side-chains
  71 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   73 ILE
Chi-restraints excluded: chain B residue  227 GLU
Chi-restraints excluded: chain C residue  114 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0970
   chunk 74 optimal weight:    9.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 115 HIS
B 296 GLN
B 332 ASN
B 365 GLN
B 487 HIS
B 507 GLN
B 532 HIS
** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.098025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.081175 restraints weight = 25552.303|
|-----------------------------------------------------------------------------|
r_work (start): 0.2874 rms_B_bonded: 3.50
r_work: 0.2713 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2713
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2725
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2725 r_free = 0.2725    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2725 r_free = 0.2725    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2725
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9001
moved from start:          0.1495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7379  Z= 0.128
  Angle     :  0.710  12.845  10015  Z= 0.356
  Chirality :  0.050   0.693   1134
  Planarity :  0.005   0.052   1254
  Dihedral  : 10.633  73.163   1043
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.53 %
    Favored  : 90.47 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  8.00 %
    Favored  : 91.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.73 (0.23), residues: 874
  helix: -3.20 (0.18), residues: 447
  sheet: -2.51 (0.57), residues: 76
  loop : -2.98 (0.31), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 707 
 TYR   0.013   0.001   TYR B 509 
 PHE   0.014   0.001   PHE B 177 
 TRP   0.023   0.001   TRP B 511 
 HIS   0.010   0.001   HIS B 334 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.13 ( 7378)
  covalent geometry    : angle       0.71024 /  0.36 (10015)
  hydrogen bonds       : bond        0.05083 /  3.28 (  242)
  hydrogen bonds       : angle       5.00829 /  3.39 (  684)
  Misc. bond           : bond        0.00100 /  0.05 (    1)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.295 
Fit side-chains
REVERT: A   29 LYS cc_start: 0.9075 (ttpt) cc_final: 0.8867 (ttpt)
REVERT: A  123 ARG cc_start: 0.8724 (ttp80) cc_final: 0.8444 (ttp80)
REVERT: A  137 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.7715 (pp)
REVERT: B   93 ARG cc_start: 0.7980 (ttt90) cc_final: 0.7671 (ttp80)
REVERT: B  188 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7533 (tp)
REVERT: B  227 GLU cc_start: 0.8027 (pt0) cc_final: 0.7347 (tm-30)
REVERT: B  378 ASP cc_start: 0.8239 (p0) cc_final: 0.7811 (p0)
REVERT: B  571 MET cc_start: 0.9282 (mtm) cc_final: 0.9069 (mtp)
REVERT: B  660 TYR cc_start: 0.8639 (m-80) cc_final: 0.8180 (m-80)
REVERT: C   80 GLU cc_start: 0.8849 (mp0) cc_final: 0.8372 (mp0)
  outliers start: 8
  outliers final: 2
  residues processed: 88
  average time/residue: 0.1083
  time to fit residues: 12.4732
Evaluate side-chains
  79 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 75
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain C residue  114 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 73 optimal weight:    1.9990
   chunk 86 optimal weight:    8.9990
   chunk 83 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9980
   chunk 62 optimal weight:    6.9990
   chunk 61 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 54 optimal weight:    0.7980
   overall best weight:    1.5584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  55 GLN
B 402 ASN
** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.097654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.081915 restraints weight = 17963.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.2882 rms_B_bonded: 2.88
r_work: 0.2736 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2745
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2745 r_free = 0.2745    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2745 r_free = 0.2745    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2745
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8990
moved from start:          0.1849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7379  Z= 0.145
  Angle     :  0.658   9.956  10015  Z= 0.333
  Chirality :  0.047   0.401   1134
  Planarity :  0.004   0.052   1254
  Dihedral  :  9.865  73.260   1038
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.64 %
    Favored  : 90.36 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  :  9.62 %
    Favored  : 88.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.72 (0.26), residues: 874
  helix: -2.16 (0.21), residues: 453
  sheet: -2.12 (0.61), residues: 74
  loop : -2.80 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 707 
 TYR   0.010   0.001   TYR B 383 
 PHE   0.015   0.001   PHE B 656 
 TRP   0.012   0.001   TRP B 511 
 HIS   0.008   0.001   HIS B 334 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00340 /  0.14 ( 7378)
  covalent geometry    : angle       0.65782 /  0.33 (10015)
  hydrogen bonds       : bond        0.04216 /  2.74 (  242)
  hydrogen bonds       : angle       4.33172 /  2.93 (  684)
  Misc. bond           : bond        0.00005 /  0.00 (    1)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.304 
Fit side-chains
REVERT: A   29 LYS cc_start: 0.9078 (ttpt) cc_final: 0.8730 (ttpt)
REVERT: A  123 ARG cc_start: 0.8680 (ttp80) cc_final: 0.8364 (ttp80)
REVERT: A  137 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.7765 (pp)
REVERT: B   93 ARG cc_start: 0.7854 (ttt90) cc_final: 0.7625 (ttp80)
REVERT: B  188 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7620 (tp)
REVERT: B  227 GLU cc_start: 0.7879 (pt0) cc_final: 0.7381 (tm-30)
REVERT: B  378 ASP cc_start: 0.8203 (p0) cc_final: 0.7758 (p0)
REVERT: B  660 TYR cc_start: 0.8587 (m-80) cc_final: 0.8162 (m-80)
REVERT: C   80 GLU cc_start: 0.8658 (mp0) cc_final: 0.7970 (mp0)
  outliers start: 17
  outliers final: 5
  residues processed: 88
  average time/residue: 0.1008
  time to fit residues: 11.6631
Evaluate side-chains
  84 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain B residue  186 GLU
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  583 LEU
Chi-restraints excluded: chain C residue  114 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 13 optimal weight:    6.9990
   chunk 19 optimal weight:    7.9990
   chunk 51 optimal weight:    5.9990
   chunk 14 optimal weight:    8.9990
   chunk 44 optimal weight:    0.0040
   chunk 75 optimal weight:    6.9990
   chunk 28 optimal weight:    3.9990
   chunk 1 optimal weight:    7.9990
   chunk 47 optimal weight:   10.0000
   chunk 3 optimal weight:    4.9990
   chunk 64 optimal weight:    5.9990
   overall best weight:    4.2000

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  60 GLN
B  55 GLN
** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.092559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.075762 restraints weight = 21667.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.2791 rms_B_bonded: 3.25
r_work: 0.2631 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2631
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2632
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2632 r_free = 0.2632    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2632 r_free = 0.2632    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2632
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9075
moved from start:          0.1878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.059   7379  Z= 0.299
  Angle     :  0.770  11.549  10015  Z= 0.389
  Chirality :  0.053   0.477   1134
  Planarity :  0.005   0.058   1254
  Dihedral  :  9.873  70.523   1038
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  9.99 %
    Favored  : 89.90 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 11.75 %
    Favored  : 86.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.62 (0.26), residues: 874
  helix: -2.03 (0.22), residues: 474
  sheet: -2.09 (0.60), residues: 75
  loop : -2.84 (0.32), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 707 
 TYR   0.016   0.002   TYR A   7 
 PHE   0.027   0.002   PHE B 656 
 TRP   0.008   0.002   TRP B 511 
 HIS   0.009   0.001   HIS B 334 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00731 /  0.30 ( 7378)
  covalent geometry    : angle       0.76997 /  0.39 (10015)
  hydrogen bonds       : bond        0.04985 /  3.27 (  242)
  hydrogen bonds       : angle       4.42296 /  3.01 (  684)
  Misc. bond           : bond        0.00027 /  0.01 (    1)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A   29 LYS cc_start: 0.9066 (ttpt) cc_final: 0.8751 (ttpt)
REVERT: A  123 ARG cc_start: 0.8838 (ttp80) cc_final: 0.8602 (ttp80)
REVERT: A  137 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.7848 (pp)
REVERT: B   93 ARG cc_start: 0.7939 (ttt90) cc_final: 0.7728 (ttp80)
REVERT: B  188 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.7775 (tp)
REVERT: B  227 GLU cc_start: 0.7982 (pt0) cc_final: 0.7553 (tm-30)
REVERT: B  378 ASP cc_start: 0.8238 (p0) cc_final: 0.7806 (p0)
REVERT: B  660 TYR cc_start: 0.8723 (m-80) cc_final: 0.8220 (m-80)
REVERT: C   80 GLU cc_start: 0.8697 (mp0) cc_final: 0.8075 (mp0)
  outliers start: 14
  outliers final: 11
  residues processed: 86
  average time/residue: 0.1026
  time to fit residues: 11.6661
Evaluate side-chains
  86 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain B residue   55 GLN
Chi-restraints excluded: chain B residue  186 GLU
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  243 ILE
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  407 ILE
Chi-restraints excluded: chain B residue  583 LEU
Chi-restraints excluded: chain B residue  620 LEU
Chi-restraints excluded: chain B residue  648 LYS
Chi-restraints excluded: chain C residue  114 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 67 optimal weight:    6.9990
   chunk 1 optimal weight:    5.9990
   chunk 75 optimal weight:    0.5980
   chunk 37 optimal weight:   10.0000
   chunk 82 optimal weight:    4.9990
   chunk 72 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 79 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 18 optimal weight:    0.4980
   chunk 66 optimal weight:    0.0970
   overall best weight:    1.6382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 448 ASN
** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.096391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.078546 restraints weight = 29048.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.2836 rms_B_bonded: 3.77
r_work: 0.2663 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2663
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2665
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2665 r_free = 0.2665    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2665 r_free = 0.2665    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (4 function evaluations)
r_final: 0.2665
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9028
moved from start:          0.2051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7379  Z= 0.149
  Angle     :  0.650   8.911  10015  Z= 0.333
  Chirality :  0.047   0.334   1134
  Planarity :  0.004   0.054   1254
  Dihedral  :  9.356  68.811   1038
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  8.73 %
    Favored  : 91.16 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 12.50 %
    Favored  : 85.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.08 (0.27), residues: 874
  helix: -1.55 (0.23), residues: 465
  sheet: -1.96 (0.61), residues: 74
  loop : -2.62 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 707 
 TYR   0.011   0.001   TYR B 596 
 PHE   0.016   0.001   PHE B 656 
 TRP   0.010   0.001   TRP B 511 
 HIS   0.008   0.001   HIS B 334 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00356 /  0.15 ( 7378)
  covalent geometry    : angle       0.65003 /  0.33 (10015)
  hydrogen bonds       : bond        0.03943 /  2.57 (  242)
  hydrogen bonds       : angle       4.10355 /  2.80 (  684)
  Misc. bond           : bond        0.00011 /  0.01 (    1)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A   29 LYS cc_start: 0.9060 (ttpt) cc_final: 0.8437 (tttt)
REVERT: A  137 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.7775 (pp)
REVERT: B   93 ARG cc_start: 0.7839 (ttt90) cc_final: 0.7586 (ttp80)
REVERT: B  188 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7729 (tp)
REVERT: B  227 GLU cc_start: 0.8034 (pt0) cc_final: 0.7546 (tm-30)
REVERT: B  378 ASP cc_start: 0.8193 (p0) cc_final: 0.7758 (p0)
REVERT: B  660 TYR cc_start: 0.8583 (m-80) cc_final: 0.8171 (m-80)
REVERT: C   80 GLU cc_start: 0.8641 (mp0) cc_final: 0.8162 (mp0)
  outliers start: 14
  outliers final: 9
  residues processed: 85
  average time/residue: 0.0949
  time to fit residues: 10.6681
Evaluate side-chains
  88 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain B residue  186 GLU
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  243 ILE
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  583 LEU
Chi-restraints excluded: chain B residue  620 LEU
Chi-restraints excluded: chain B residue  648 LYS
Chi-restraints excluded: chain C residue  114 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 55 optimal weight:    6.9990
   chunk 43 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 13 optimal weight:    6.9990
   chunk 76 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   overall best weight:    1.9588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 440 HIS
B 448 ASN
** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.095994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.078074 restraints weight = 35069.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.2821 rms_B_bonded: 4.04
r_work: 0.2641 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.2641
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2648
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2648 r_free = 0.2648    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2648 r_free = 0.2648    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (4 function evaluations)
r_final: 0.2648
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9031
moved from start:          0.2141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7379  Z= 0.162
  Angle     :  0.661  10.033  10015  Z= 0.335
  Chirality :  0.047   0.313   1134
  Planarity :  0.004   0.053   1254
  Dihedral  :  9.059  65.995   1038
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.84 %
    Favored  : 91.16 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 13.12 %
    Favored  : 85.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.83 (0.28), residues: 874
  helix: -1.33 (0.23), residues: 465
  sheet: -1.92 (0.62), residues: 74
  loop : -2.53 (0.34), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 707 
 TYR   0.012   0.001   TYR B 383 
 PHE   0.018   0.001   PHE B 656 
 TRP   0.008   0.001   TRP B 511 
 HIS   0.008   0.001   HIS B 334 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00390 /  0.16 ( 7378)
  covalent geometry    : angle       0.66111 /  0.34 (10015)
  hydrogen bonds       : bond        0.03952 /  2.58 (  242)
  hydrogen bonds       : angle       4.04535 /  2.76 (  684)
  Misc. bond           : bond        0.00016 /  0.01 (    1)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A   29 LYS cc_start: 0.9090 (ttpt) cc_final: 0.8415 (tttt)
REVERT: A  137 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.7762 (pp)
REVERT: B   93 ARG cc_start: 0.7864 (ttt90) cc_final: 0.7597 (ttp80)
REVERT: B  188 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7763 (tp)
REVERT: B  227 GLU cc_start: 0.8093 (pt0) cc_final: 0.7612 (tm-30)
REVERT: B  378 ASP cc_start: 0.8184 (p0) cc_final: 0.7751 (p0)
REVERT: B  660 TYR cc_start: 0.8563 (m-80) cc_final: 0.8166 (m-80)
REVERT: C   80 GLU cc_start: 0.8622 (mp0) cc_final: 0.8102 (mp0)
  outliers start: 15
  outliers final: 10
  residues processed: 86
  average time/residue: 0.0911
  time to fit residues: 10.5735
Evaluate side-chains
  86 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain B residue  186 GLU
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  243 ILE
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  583 LEU
Chi-restraints excluded: chain B residue  620 LEU
Chi-restraints excluded: chain B residue  648 LYS
Chi-restraints excluded: chain C residue  114 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 74 optimal weight:    7.9990
   chunk 36 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 1 optimal weight:    7.9990
   chunk 78 optimal weight:    0.0020
   chunk 62 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.9794

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.099712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.082244 restraints weight = 23637.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.2897 rms_B_bonded: 3.45
r_work: 0.2733 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2733
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2744
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2744 r_free = 0.2744    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2744 r_free = 0.2744    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (4 function evaluations)
r_final: 0.2744
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8963
moved from start:          0.2406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7379  Z= 0.113
  Angle     :  0.606   8.994  10015  Z= 0.309
  Chirality :  0.044   0.232   1134
  Planarity :  0.004   0.051   1254
  Dihedral  :  8.506  62.648   1038
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.04 %
    Favored  : 91.96 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 13.62 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.58 (0.28), residues: 874
  helix: -1.04 (0.24), residues: 466
  sheet: -2.04 (0.62), residues: 73
  loop : -2.48 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 707 
 TYR   0.010   0.001   TYR B 383 
 PHE   0.013   0.001   PHE B 177 
 TRP   0.015   0.001   TRP B 511 
 HIS   0.007   0.001   HIS B 334 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00260 /  0.11 ( 7378)
  covalent geometry    : angle       0.60605 /  0.31 (10015)
  hydrogen bonds       : bond        0.03348 /  2.17 (  242)
  hydrogen bonds       : angle       3.88835 /  2.67 (  684)
  Misc. bond           : bond        0.00010 /  0.01 (    1)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.306 
Fit side-chains
REVERT: A   29 LYS cc_start: 0.9039 (ttpt) cc_final: 0.8442 (tttt)
REVERT: A  137 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7640 (pp)
REVERT: B  156 ASP cc_start: 0.9077 (m-30) cc_final: 0.8814 (m-30)
REVERT: B  188 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7638 (tp)
REVERT: B  227 GLU cc_start: 0.7937 (pt0) cc_final: 0.7548 (tm-30)
REVERT: B  378 ASP cc_start: 0.8130 (p0) cc_final: 0.7698 (p0)
REVERT: B  505 LEU cc_start: 0.8835 (pp) cc_final: 0.8578 (pp)
REVERT: B  660 TYR cc_start: 0.8441 (m-80) cc_final: 0.8103 (m-80)
REVERT: C   80 GLU cc_start: 0.8569 (mp0) cc_final: 0.8096 (mp0)
  outliers start: 14
  outliers final: 9
  residues processed: 84
  average time/residue: 0.0942
  time to fit residues: 10.5767
Evaluate side-chains
  82 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain B residue  186 GLU
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  243 ILE
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  437 ILE
Chi-restraints excluded: chain B residue  583 LEU
Chi-restraints excluded: chain B residue  648 LYS
Chi-restraints excluded: chain C residue  114 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   chunk 76 optimal weight:    5.9990
   chunk 7 optimal weight:    6.9990
   chunk 81 optimal weight:    3.9990
   chunk 11 optimal weight:    9.9990
   chunk 47 optimal weight:    9.9990
   chunk 24 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.8784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.100537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.082938 restraints weight = 24072.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.2911 rms_B_bonded: 3.50
r_work: 0.2745 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2751
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2751 r_free = 0.2751    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2751 r_free = 0.2751    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (4 function evaluations)
r_final: 0.2751
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8948
moved from start:          0.2568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7379  Z= 0.109
  Angle     :  0.596   9.010  10015  Z= 0.303
  Chirality :  0.044   0.219   1134
  Planarity :  0.004   0.050   1254
  Dihedral  :  8.131  59.582   1038
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.38 %
    Favored  : 91.62 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 14.25 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.34 (0.28), residues: 874
  helix: -0.81 (0.24), residues: 466
  sheet: -2.04 (0.61), residues: 73
  loop : -2.41 (0.34), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 707 
 TYR   0.010   0.001   TYR B 596 
 PHE   0.012   0.001   PHE B 177 
 TRP   0.014   0.001   TRP B 511 
 HIS   0.007   0.001   HIS B 334 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00251 /  0.11 ( 7378)
  covalent geometry    : angle       0.59583 /  0.30 (10015)
  hydrogen bonds       : bond        0.03275 /  2.13 (  242)
  hydrogen bonds       : angle       3.82471 /  2.62 (  684)
  Misc. bond           : bond        0.00008 /  0.00 (    1)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A   29 LYS cc_start: 0.9048 (ttpt) cc_final: 0.8451 (tttt)
REVERT: A  137 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7662 (pp)
REVERT: B  156 ASP cc_start: 0.9065 (m-30) cc_final: 0.8810 (m-30)
REVERT: B  188 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7737 (tp)
REVERT: B  227 GLU cc_start: 0.7916 (pt0) cc_final: 0.7555 (tm-30)
REVERT: B  378 ASP cc_start: 0.8096 (p0) cc_final: 0.7667 (p0)
REVERT: B  436 ARG cc_start: 0.8511 (ttt-90) cc_final: 0.8251 (ttp80)
REVERT: B  505 LEU cc_start: 0.8793 (pp) cc_final: 0.8528 (pp)
REVERT: B  660 TYR cc_start: 0.8436 (m-80) cc_final: 0.8047 (m-80)
REVERT: C   80 GLU cc_start: 0.8491 (mp0) cc_final: 0.8091 (mp0)
  outliers start: 10
  outliers final: 8
  residues processed: 81
  average time/residue: 0.0780
  time to fit residues: 8.6016
Evaluate side-chains
  83 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain B residue  186 GLU
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  243 ILE
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  583 LEU
Chi-restraints excluded: chain B residue  648 LYS
Chi-restraints excluded: chain C residue  114 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 43 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9980
   chunk 6 optimal weight:    6.9990
   chunk 56 optimal weight:    9.9990
   chunk 64 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 9 optimal weight:    6.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    1.1784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.100024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.082691 restraints weight = 22014.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.2904 rms_B_bonded: 3.35
r_work: 0.2742 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2754
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2754 r_free = 0.2754    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2754 r_free = 0.2754    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2754
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8958
moved from start:          0.2601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7379  Z= 0.120
  Angle     :  0.602   9.092  10015  Z= 0.305
  Chirality :  0.045   0.233   1134
  Planarity :  0.004   0.050   1254
  Dihedral  :  7.876  58.277   1038
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.04 %
    Favored  : 91.96 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 14.00 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.22 (0.28), residues: 874
  helix: -0.68 (0.24), residues: 469
  sheet: -2.09 (0.61), residues: 74
  loop : -2.38 (0.34), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 707 
 TYR   0.010   0.001   TYR B 383 
 PHE   0.012   0.001   PHE B 656 
 TRP   0.010   0.001   TRP B 511 
 HIS   0.007   0.001   HIS B 334 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.12 ( 7378)
  covalent geometry    : angle       0.60205 /  0.31 (10015)
  hydrogen bonds       : bond        0.03388 /  2.20 (  242)
  hydrogen bonds       : angle       3.81719 /  2.61 (  684)
  Misc. bond           : bond        0.00013 /  0.01 (    1)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A   29 LYS cc_start: 0.9077 (ttpt) cc_final: 0.8506 (tttt)
REVERT: A  137 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7658 (pp)
REVERT: B  156 ASP cc_start: 0.9065 (m-30) cc_final: 0.8821 (m-30)
REVERT: B  227 GLU cc_start: 0.7827 (pt0) cc_final: 0.7534 (tm-30)
REVERT: B  378 ASP cc_start: 0.8117 (p0) cc_final: 0.7684 (p0)
REVERT: B  436 ARG cc_start: 0.8528 (ttt-90) cc_final: 0.8181 (ttp80)
REVERT: B  660 TYR cc_start: 0.8459 (m-80) cc_final: 0.8120 (m-80)
REVERT: B  693 LYS cc_start: 0.8415 (mmmt) cc_final: 0.8078 (mmmt)
REVERT: C   80 GLU cc_start: 0.8459 (mp0) cc_final: 0.7972 (mp0)
  outliers start: 12
  outliers final: 7
  residues processed: 83
  average time/residue: 0.0928
  time to fit residues: 10.2903
Evaluate side-chains
  83 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain B residue  186 GLU
Chi-restraints excluded: chain B residue  243 ILE
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  648 LYS
Chi-restraints excluded: chain C residue  114 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 78 optimal weight:   10.0000
   chunk 4 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0980
   chunk 67 optimal weight:    0.0370
   chunk 38 optimal weight:    5.9990
   chunk 18 optimal weight:    7.9990
   overall best weight:    1.2062

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.100079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.082233 restraints weight = 24672.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.2897 rms_B_bonded: 3.56
r_work: 0.2730 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2741
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2741 r_free = 0.2741    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2741 r_free = 0.2741    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2741
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8956
moved from start:          0.2627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7379  Z= 0.120
  Angle     :  0.600   9.068  10015  Z= 0.305
  Chirality :  0.045   0.234   1134
  Planarity :  0.004   0.050   1254
  Dihedral  :  7.753  59.363   1038
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.50 %
    Favored  : 91.50 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 14.50 %
    Favored  : 84.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.07 (0.29), residues: 874
  helix: -0.53 (0.24), residues: 469
  sheet: -1.97 (0.62), residues: 72
  loop : -2.38 (0.34), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 707 
 TYR   0.011   0.001   TYR B 383 
 PHE   0.012   0.001   PHE B 656 
 TRP   0.010   0.001   TRP B 511 
 HIS   0.007   0.001   HIS B 334 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.12 ( 7378)
  covalent geometry    : angle       0.60026 /  0.30 (10015)
  hydrogen bonds       : bond        0.03395 /  2.21 (  242)
  hydrogen bonds       : angle       3.81128 /  2.61 (  684)
  Misc. bond           : bond        0.00009 /  0.00 (    1)

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

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

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1748 Ramachandran restraints generated.
    874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.324 
Fit side-chains
REVERT: A   29 LYS cc_start: 0.9079 (ttpt) cc_final: 0.8502 (tttt)
REVERT: A  137 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7649 (pp)
REVERT: B  156 ASP cc_start: 0.9056 (m-30) cc_final: 0.8804 (m-30)
REVERT: B  227 GLU cc_start: 0.7792 (pt0) cc_final: 0.7504 (tm-30)
REVERT: B  378 ASP cc_start: 0.8091 (p0) cc_final: 0.7659 (p0)
REVERT: B  436 ARG cc_start: 0.8508 (ttt-90) cc_final: 0.8184 (ttp80)
REVERT: B  660 TYR cc_start: 0.8458 (m-80) cc_final: 0.8114 (m-80)
REVERT: B  693 LYS cc_start: 0.8413 (mmmt) cc_final: 0.8081 (mmmt)
REVERT: C   80 GLU cc_start: 0.8462 (mp0) cc_final: 0.7956 (mp0)
  outliers start: 9
  outliers final: 7
  residues processed: 80
  average time/residue: 0.0923
  time to fit residues: 9.8393
Evaluate side-chains
  83 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain B residue  186 GLU
Chi-restraints excluded: chain B residue  243 ILE
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  648 LYS
Chi-restraints excluded: chain C residue  114 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 51 optimal weight:    6.9990
   chunk 74 optimal weight:    8.9990
   chunk 35 optimal weight:    0.7980
   chunk 78 optimal weight:    6.9990
   chunk 50 optimal weight:    0.0770
   chunk 63 optimal weight:    0.7980
   chunk 30 optimal weight:    3.9990
   chunk 7 optimal weight:    6.9990
   overall best weight:    0.6938

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  61 HIS
** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.102834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.085009 restraints weight = 23371.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.2940 rms_B_bonded: 3.49
r_work: 0.2778 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2789
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (6 function evaluations)
r_final: 0.2789
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8922
moved from start:          0.2829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7379  Z= 0.102
  Angle     :  0.571   8.606  10015  Z= 0.291
  Chirality :  0.043   0.212   1134
  Planarity :  0.004   0.049   1254
  Dihedral  :  7.442  58.218   1038
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.92 %
    Favored  : 92.08 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 14.12 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -1.87 (0.29), residues: 874
  helix: -0.32 (0.25), residues: 469
  sheet: -2.05 (0.61), residues: 74
  loop : -2.33 (0.34), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 707 
 TYR   0.011   0.001   TYR B 383 
 PHE   0.009   0.001   PHE B 656 
 TRP   0.015   0.001   TRP B 511 
 HIS   0.007   0.001   HIS B 334 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00230 /  0.10 ( 7378)
  covalent geometry    : angle       0.57054 /  0.29 (10015)
  hydrogen bonds       : bond        0.03123 /  2.02 (  242)
  hydrogen bonds       : angle       3.72921 /  2.55 (  684)
  Misc. bond           : bond        0.00007 /  0.00 (    1)

===============================================================================
Job complete
usr+sys time: 1584.31 seconds
wall clock time: 27 minutes 54.96 seconds (1674.96 seconds total)