Starting phenix.real_space_refine
on Thu Jun 12 17:24:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zr0_14875/06_2025/7zr0_14875.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zr0_14875/06_2025/7zr0_14875.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zr0_14875/06_2025/7zr0_14875.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zr0_14875/06_2025/7zr0_14875.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zr0_14875/06_2025/7zr0_14875.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zr0_14875/06_2025/7zr0_14875.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.026
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       7      5.49       5
     S      73      5.16       5
     C    8870      2.51       5
     N    2388      2.21       5
     O    2714      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 42 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 14052
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 5132
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 633, 5132
          Classifications: {'peptide': 633}
          Link IDs: {'PTRANS': 17, 'TRANS': 615}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 5112
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 631, 5112
          Classifications: {'peptide': 631}
          Link IDs: {'PTRANS': 17, 'TRANS': 613}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2243
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 266, 2243
          Classifications: {'peptide': 266}
          Link IDs: {'PTRANS': 4, 'TRANS': 261}
    Chain: "K"
      Number of atoms: 1503
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 186, 1503
          Classifications: {'peptide': 186}
          Link IDs: {'PTRANS': 9, 'TRANS': 176}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 8.29, per 1000 atoms: 0.59
  Number of scatterers: 14052
  At special positions: 0
  Unit cell: (118.68, 126.42, 139.32, 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      73     16.00
     P       7     15.00
     O    2714      8.00
     N    2388      7.00
     C    8870      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.17
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3284

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 14 sheets defined
      44.8% alpha, 8.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.58
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 31
    Processing helix  chain 'A' and resid 37 through 61
      removed outlier: 4.049A  pdb=" N   ARG A  41 " --> pdb=" O   GLU A  37 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   ASP A  49 " --> pdb=" O   SER A  45 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ILE A  54 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   SER A  58 " --> pdb=" O   ILE A  54 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   LEU A  59 " --> pdb=" O   ARG A  55 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   THR A  60 " --> pdb=" O   TYR A  56 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   ASP A  61 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 117
      removed outlier: 3.822A  pdb=" N   LEU A 117 " --> pdb=" O   PHE A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 138
    Processing helix  chain 'A' and resid 195 through 206
    Processing helix  chain 'A' and resid 292 through 296
      removed outlier: 3.944A  pdb=" N   ILE A 296 " --> pdb=" O   PRO A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 307
      removed outlier: 3.552A  pdb=" N   TYR A 301 " --> pdb=" O   THR A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 420
      removed outlier: 4.231A  pdb=" N   VAL A 403 " --> pdb=" O   LYS A 399 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ALA A 420 " --> pdb=" O   PHE A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 433
      removed outlier: 4.059A  pdb=" N   LYS A 428 " --> pdb=" O   GLU A 424 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ALA A 432 " --> pdb=" O   LYS A 428 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 441
      removed outlier: 3.847A  pdb=" N   GLY A 440 " --> pdb=" O   ASN A 436 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ILE A 441 " --> pdb=" O   LEU A 437 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 436 through 441'
    Processing helix  chain 'A' and resid 447 through 452
    Processing helix  chain 'A' and resid 469 through 474
    Processing helix  chain 'A' and resid 491 through 496
      removed outlier: 3.991A  pdb=" N   ASN A 496 " --> pdb=" O   GLU A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 507
      removed outlier: 3.826A  pdb=" N   GLY A 507 " --> pdb=" O   VAL A 503 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 523
      removed outlier: 3.845A  pdb=" N   GLU A 519 " --> pdb=" O   GLU A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 546 through 557
      removed outlier: 3.590A  pdb=" N   LYS A 550 " --> pdb=" O   ASP A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 572
      removed outlier: 3.691A  pdb=" N   LYS A 565 " --> pdb=" O   GLU A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 599 through 609
    Processing helix  chain 'A' and resid 613 through 618
      removed outlier: 4.680A  pdb=" N   MET A 617 " --> pdb=" O   ASP A 613 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   GLY A 618 " --> pdb=" O   ASN A 614 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 613 through 618'
    Processing helix  chain 'A' and resid 632 through 645
      removed outlier: 4.106A  pdb=" N   ALA A 644 " --> pdb=" O   GLN A 640 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ASP A 645 " --> pdb=" O   LYS A 641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 649 through 665
    Processing helix  chain 'A' and resid 673 through 687
      removed outlier: 3.578A  pdb=" N   SER A 677 " --> pdb=" O   PRO A 673 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 21 through 32
    Processing helix  chain 'B' and resid 38 through 59
      removed outlier: 3.733A  pdb=" N   LEU B  59 " --> pdb=" O   ARG B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 65
      removed outlier: 3.782A  pdb=" N   LYS B  64 " --> pdb=" O   ASP B  61 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   LEU B  65 " --> pdb=" O   PRO B  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 61 through 65'
    Processing helix  chain 'B' and resid 94 through 103
    Processing helix  chain 'B' and resid 108 through 117
      removed outlier: 4.225A  pdb=" N   ALA B 112 " --> pdb=" O   SER B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 140
      removed outlier: 3.676A  pdb=" N   SER B 135 " --> pdb=" O   GLY B 132 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   ALA B 140 " --> pdb=" O   TYR B 137 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 206
    Processing helix  chain 'B' and resid 298 through 307
    Processing helix  chain 'B' and resid 342 through 346
      removed outlier: 4.307A  pdb=" N   ASN B 346 " --> pdb=" O   LEU B 343 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 398 through 420
      removed outlier: 3.888A  pdb=" N   LYS B 402 " --> pdb=" O   SER B 398 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   LYS B 406 " --> pdb=" O   LYS B 402 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ASN B 407 " --> pdb=" O   VAL B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 425 through 431
    Processing helix  chain 'B' and resid 433 through 443
      removed outlier: 4.311A  pdb=" N   LEU B 437 " --> pdb=" O   PHE B 433 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   LYS B 438 " --> pdb=" O   SER B 434 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   GLU B 443 " --> pdb=" O   LEU B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 469 through 475
      removed outlier: 3.530A  pdb=" N   VAL B 473 " --> pdb=" O   LEU B 469 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   SER B 474 " --> pdb=" O   SER B 470 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ARG B 475 " --> pdb=" O   GLU B 471 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 469 through 475'
    Processing helix  chain 'B' and resid 516 through 525
      removed outlier: 4.412A  pdb=" N   TYR B 520 " --> pdb=" O   PRO B 516 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   GLN B 524 " --> pdb=" O   TYR B 520 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 546 through 560
    Processing helix  chain 'B' and resid 562 through 571
      removed outlier: 3.538A  pdb=" N   LYS B 568 " --> pdb=" O   CYS B 564 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 599 through 607
    Processing helix  chain 'B' and resid 616 through 621
      removed outlier: 3.912A  pdb=" N   MET B 620 " --> pdb=" O   THR B 616 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 632 through 645
      removed outlier: 3.570A  pdb=" N   ALA B 644 " --> pdb=" O   GLN B 640 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 648 through 666
    Processing helix  chain 'B' and resid 672 through 687
      removed outlier: 4.095A  pdb=" N   HIS B 676 " --> pdb=" O   ASP B 672 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   MET B 683 " --> pdb=" O   ARG B 679 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 72
      removed outlier: 3.953A  pdb=" N   ARG C  30 " --> pdb=" O   ALA C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 78 through 112
      removed outlier: 3.642A  pdb=" N   LYS C 107 " --> pdb=" O   GLU C 103 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 115 through 119
      removed outlier: 3.840A  pdb=" N   LEU C 119 " --> pdb=" O   ASN C 115 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 115 through 119'
    Processing helix  chain 'C' and resid 139 through 164
      removed outlier: 4.101A  pdb=" N   MET C 164 " --> pdb=" O   LYS C 160 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 168 through 182
    Processing helix  chain 'C' and resid 183 through 201
      removed outlier: 3.521A  pdb=" N   ALA C 187 " --> pdb=" O   CYS C 183 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 202 through 227
    Processing helix  chain 'C' and resid 234 through 243
      removed outlier: 3.580A  pdb=" N   THR C 243 " --> pdb=" O   THR C 239 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 245 through 266
    Processing helix  chain 'K' and resid 536 through 543
      removed outlier: 3.572A  pdb=" N   HIS K 540 " --> pdb=" O   SER K 536 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU K 541 " --> pdb=" O   LEU K 537 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 549 through 568
      removed outlier: 3.514A  pdb=" N   LEU K 553 " --> pdb=" O   GLU K 549 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 634 through 652
      removed outlier: 3.741A  pdb=" N   ASP K 638 " --> pdb=" O   SER K 634 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 661 through 671
    Processing helix  chain 'K' and resid 687 through 697
      removed outlier: 3.786A  pdb=" N   LEU K 697 " --> pdb=" O   MET K 693 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 706 through 719
      removed outlier: 3.639A  pdb=" N   ILE K 710 " --> pdb=" O   LEU K 706 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 16
      removed outlier: 3.669A  pdb=" N   GLU A  13 " --> pdb=" O   VAL B 167 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   PHE B 165 " --> pdb=" O   PHE A  15 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   SER B 159 " --> pdb=" O   VAL B 143 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   VAL B 143 " --> pdb=" O   SER B 159 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   LYS B 142 " --> pdb=" O   HIS B 184 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 19
      removed outlier: 6.878A  pdb=" N   GLN A  18 " --> pdb=" O   ILE B 105 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 155 through 159
      removed outlier: 3.833A  pdb=" N   LYS A 142 " --> pdb=" O   HIS A 184 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   GLY A 178 " --> pdb=" O   LYS A 148 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   THR A  83 " --> pdb=" O   ASN A  78 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   ILE A  73 " --> pdb=" O   THR A 214 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 105
      removed outlier: 3.714A  pdb=" N   ILE A 105 " --> pdb=" O   GLN B  18 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 318 through 324
      removed outlier: 3.859A  pdb=" N   PHE A 321 " --> pdb=" O   ALA A 331 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   PHE A 329 " --> pdb=" O   VAL A 323 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ARG A 378 " --> pdb=" O   PHE A 334 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   LYS A 354 " --> pdb=" O   VAL A 381 " (cutoff:3.500A)
      removed outlier: 7.751A  pdb=" N   SER A 383 " --> pdb=" O   LYS A 354 " (cutoff:3.500A)
      removed outlier: 6.876A  pdb=" N   TYR A 356 " --> pdb=" O   SER A 383 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 456 through 457
    Processing sheet with id=AA7, first strand: chain 'A' and resid 510 through 513
      removed outlier: 6.935A  pdb=" N   TYR A 484 " --> pdb=" O   VAL A 511 " (cutoff:3.500A)
      removed outlier: 8.121A  pdb=" N   MET A 513 " --> pdb=" O   TYR A 484 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   ILE A 486 " --> pdb=" O   MET A 513 " (cutoff:3.500A)
      removed outlier: 5.752A  pdb=" N   ILE A 483 " --> pdb=" O   VAL A 534 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 579 through 580
      removed outlier: 7.410A  pdb=" N   THR A 579 " --> pdb=" O   ILE A 628 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 83 through 85
      removed outlier: 6.707A  pdb=" N   ILE B  73 " --> pdb=" O   THR B 214 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 334 through 335
      removed outlier: 3.532A  pdb=" N   ILE B 335 " --> pdb=" O   ALA B 317 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   ALA B 317 " --> pdb=" O   ILE B 335 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 329 through 330
      removed outlier: 3.691A  pdb=" N   PHE B 329 " --> pdb=" O   VAL B 323 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 361 through 364
      removed outlier: 7.324A  pdb=" N   LEU B 355 " --> pdb=" O   ILE B 362 " (cutoff:3.500A)
      removed outlier: 5.334A  pdb=" N   ASP B 364 " --> pdb=" O   ILE B 353 " (cutoff:3.500A)
      removed outlier: 7.691A  pdb=" N   ILE B 353 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   LYS B 354 " --> pdb=" O   GLY B 379 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 462 through 468
      removed outlier: 6.969A  pdb=" N   GLU B 465 " --> pdb=" O   THR B 459 " (cutoff:3.500A)
      removed outlier: 5.315A  pdb=" N   THR B 459 " --> pdb=" O   GLU B 465 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   HIS B 458 " --> pdb=" O   TYR B 512 " (cutoff:3.500A)
      removed outlier: 7.415A  pdb=" N   TYR B 484 " --> pdb=" O   VAL B 511 " (cutoff:3.500A)
      removed outlier: 7.909A  pdb=" N   MET B 513 " --> pdb=" O   TYR B 484 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   ILE B 486 " --> pdb=" O   MET B 513 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 575 through 580
      removed outlier: 6.388A  pdb=" N   LYS B 624 " --> pdb=" O   VAL B 575 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   LYS B 577 " --> pdb=" O   LYS B 624 " (cutoff:3.500A)

    550 hydrogen bonds defined for protein.
    1614 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: 4.14

  Time building geometry restraints manager: 3.73 seconds

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

  Histogram of bond lengths:
        0.86 -     1.05: 1
        1.05 -     1.24: 1742
        1.24 -     1.43: 4127
        1.43 -     1.62: 8299
        1.62 -     1.81: 124
  Bond restraints: 14293
  Sorted by residual:
  bond pdb=" CB  PRO A  79 "
       pdb=" CG  PRO A  79 "
    ideal  model  delta    sigma   weight residual
    1.492  0.858  0.634 5.00e-02 4.00e+02 1.61e+02
  bond pdb=" CG  PRO A  79 "
       pdb=" CD  PRO A  79 "
    ideal  model  delta    sigma   weight residual
    1.503  1.257  0.246 3.40e-02 8.65e+02 5.25e+01
  bond pdb=" N   PRO A  77 "
       pdb=" CD  PRO A  77 "
    ideal  model  delta    sigma   weight residual
    1.473  1.399  0.074 1.40e-02 5.10e+03 2.80e+01
  bond pdb=" N   PRO B  79 "
       pdb=" CD  PRO B  79 "
    ideal  model  delta    sigma   weight residual
    1.473  1.540 -0.067 1.40e-02 5.10e+03 2.26e+01
  bond pdb=" C   MET C 112 "
       pdb=" N   PRO C 113 "
    ideal  model  delta    sigma   weight residual
    1.330  1.292  0.038 1.25e-02 6.40e+03 9.40e+00
  ... (remaining 14288 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    14.77: 19213
       14.77 -    29.54: 2
       29.54 -    44.31: 0
       44.31 -    59.08: 0
       59.08 -    73.85: 1
  Bond angle restraints: 19216
  Sorted by residual:
  angle pdb=" CB  PRO A  79 "
        pdb=" CG  PRO A  79 "
        pdb=" CD  PRO A  79 "
      ideal   model   delta    sigma   weight residual
     106.10  179.95  -73.85 3.20e+00 9.77e-02 5.33e+02
  angle pdb=" N   PRO A  79 "
        pdb=" CD  PRO A  79 "
        pdb=" CG  PRO A  79 "
      ideal   model   delta    sigma   weight residual
     103.20   78.91   24.29 1.50e+00 4.44e-01 2.62e+02
  angle pdb=" CA  PRO A  79 "
        pdb=" CB  PRO A  79 "
        pdb=" CG  PRO A  79 "
      ideal   model   delta    sigma   weight residual
     104.50   77.07   27.43 1.90e+00 2.77e-01 2.08e+02
  angle pdb=" N   ILE A 690 "
        pdb=" CA  ILE A 690 "
        pdb=" C   ILE A 690 "
      ideal   model   delta    sigma   weight residual
     112.96  107.29    5.67 1.00e+00 1.00e+00 3.21e+01
  angle pdb=" CA  PRO A  79 "
        pdb=" N   PRO A  79 "
        pdb=" CD  PRO A  79 "
      ideal   model   delta    sigma   weight residual
     112.00  104.27    7.73 1.40e+00 5.10e-01 3.05e+01
  ... (remaining 19211 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 7155
       17.95 -    35.90: 1276
       35.90 -    53.85: 353
       53.85 -    71.80: 65
       71.80 -    89.74: 30
  Dihedral angle restraints: 8879
    sinusoidal: 3826
      harmonic: 5053
  Sorted by residual:
  dihedral pdb=" CA  THR B 309 "
           pdb=" C   THR B 309 "
           pdb=" N   ASN B 310 "
           pdb=" CA  ASN B 310 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.78   31.22     0      5.00e+00 4.00e-02 3.90e+01
  dihedral pdb=" CA  MET C 112 "
           pdb=" C   MET C 112 "
           pdb=" N   PRO C 113 "
           pdb=" CA  PRO C 113 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -148.99  -31.01     0      5.00e+00 4.00e-02 3.85e+01
  dihedral pdb=" N   PRO A  79 "
           pdb=" CG  PRO A  79 "
           pdb=" CD  PRO A  79 "
           pdb=" CB  PRO A  79 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00 -112.14   82.14     1      1.50e+01 4.44e-03 3.68e+01
  ... (remaining 8876 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 1476
       0.043 -    0.086: 483
       0.086 -    0.130: 126
       0.130 -    0.173: 18
       0.173 -    0.216: 5
  Chirality restraints: 2108
  Sorted by residual:
  chirality pdb=" CA  PRO K 523 "
            pdb=" N   PRO K 523 "
            pdb=" C   PRO K 523 "
            pdb=" CB  PRO K 523 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.50    0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CA  GLU B 539 "
            pdb=" N   GLU B 539 "
            pdb=" C   GLU B 539 "
            pdb=" CB  GLU B 539 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CB  THR B 190 "
            pdb=" CA  THR B 190 "
            pdb=" OG1 THR B 190 "
            pdb=" CG2 THR B 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 2105 not shown)

  Planarity restraints: 2455
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 173 "   -0.080 5.00e-02 4.00e+02   1.18e-01 2.25e+01
        pdb=" N   PRO B 174 "    0.205 5.00e-02 4.00e+02
        pdb=" CA  PRO B 174 "   -0.063 5.00e-02 4.00e+02
        pdb=" CD  PRO B 174 "   -0.062 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS C  20 "   -0.051 5.00e-02 4.00e+02   7.84e-02 9.84e+00
        pdb=" N   PRO C  21 "    0.136 5.00e-02 4.00e+02
        pdb=" CA  PRO C  21 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO C  21 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS C   9 "   -0.014 2.00e-02 2.50e+03   2.77e-02 7.68e+00
        pdb=" C   HIS C   9 "    0.048 2.00e-02 2.50e+03
        pdb=" O   HIS C   9 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   ILE C  10 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 2452 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 137
        2.59 -     3.17: 11270
        3.17 -     3.74: 19896
        3.74 -     4.32: 25260
        4.32 -     4.90: 43624
  Nonbonded interactions: 100187
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B  94 "
            pdb=" OD2 ASP B 152 "
     model   vdw
     2.011 3.040
  nonbonded pdb=" O   ILE A 690 "
            pdb=" OE1 GLU A 692 "
     model   vdw
     2.119 3.040
  nonbonded pdb=" O   LEU A  27 "
            pdb=" OG1 THR A  31 "
     model   vdw
     2.129 3.040
  nonbonded pdb=" O   SER B 160 "
            pdb=" OG  SER B 160 "
     model   vdw
     2.182 3.040
  nonbonded pdb=" N   GLU A 542 "
            pdb=" OE1 GLU A 542 "
     model   vdw
     2.197 3.120
  ... (remaining 100182 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 10 through 220 or resid 273 through 692 or resid 801))
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             2.200
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.560
  Check model and map are aligned:         0.110
  Set scattering table:                    0.120
  Process input model:                     32.120
  Find NCS groups from input model:        0.470
  Set up NCS constraints:                  0.060
  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:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.634  14293  Z= 0.245
  Angle     :  0.995  73.851  19216  Z= 0.497
  Chirality :  0.046   0.216   2108
  Planarity :  0.006   0.118   2455
  Dihedral  : 19.990  89.744   5595
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.59 %
    Allowed  : 10.06 %
    Favored  : 89.35 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  : 35.74 %
    Favored  : 64.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.13 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.37 (0.19), residues: 1699
  helix:  0.39 (0.20), residues: 719
  sheet: -2.11 (0.36), residues: 199
  loop : -3.47 (0.18), residues: 781

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C 114 
 HIS   0.009   0.002   HIS A 632 
 PHE   0.023   0.002   PHE B 165 
 TYR   0.026   0.002   TYR A 137 
 ARG   0.010   0.000   ARG C 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19768 (  550)
  hydrogen bonds       : angle       6.32932 ( 1614)
  covalent geometry    : bond        0.00733 (14293)
  covalent geometry    : angle       0.99511 (19216)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 299
  time to evaluate  : 1.658 
Fit side-chains
REVERT: B   52 ASP cc_start: 0.8359 (t0) cc_final: 0.8020 (m-30)
  outliers start: 3
  outliers final: 2
  residues processed: 299
  average time/residue: 0.3022
  time to fit residues: 125.7449
Evaluate side-chains
  298 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 296
  time to evaluate  : 1.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 ASP
Chi-restraints excluded: chain A residue  395 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 143 optimal weight:    7.9990
   chunk 128 optimal weight:    0.0040
   chunk 71 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 86 optimal weight:    0.2980
   chunk 68 optimal weight:    0.0020
   chunk 133 optimal weight:   40.0000
   chunk 51 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9980
   chunk 99 optimal weight:    0.9980
   chunk 154 optimal weight:    2.9990
   overall best weight:    0.4600

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

Flipped N/Q/H residues before XYZ refinement:
A 100 ASN
** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 523 GLN
B 101 ASN
B 320 HIS
B 609 GLN
** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 585 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.153471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.122857 restraints weight = 20214.667|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 2.20
r_work: 0.3363 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3201 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.1061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  14293  Z= 0.135
  Angle     :  0.647  12.900  19216  Z= 0.342
  Chirality :  0.043   0.208   2108
  Planarity :  0.005   0.077   2455
  Dihedral  :  7.189  81.353   1936
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  :  8.83 %
    Favored  : 90.70 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 32.65 %
    Favored  : 64.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.13 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.82 (0.20), residues: 1699
  helix:  0.84 (0.20), residues: 727
  sheet: -1.71 (0.39), residues: 185
  loop : -3.24 (0.18), residues: 787

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP C 114 
 HIS   0.004   0.001   HIS B 676 
 PHE   0.012   0.001   PHE B 165 
 TYR   0.013   0.001   TYR A 134 
 ARG   0.004   0.000   ARG K 575 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05169 (  550)
  hydrogen bonds       : angle       4.87530 ( 1614)
  covalent geometry    : bond        0.00300 (14293)
  covalent geometry    : angle       0.64658 (19216)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  352 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 303
  time to evaluate  : 1.472 
Fit side-chains
REVERT: A  137 TYR cc_start: 0.6778 (OUTLIER) cc_final: 0.5992 (t80)
REVERT: A  303 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7205 (mp0)
REVERT: A  311 ASP cc_start: 0.7539 (t0) cc_final: 0.7274 (t0)
REVERT: A  380 VAL cc_start: 0.8576 (m) cc_final: 0.8375 (t)
REVERT: A  491 LYS cc_start: 0.8329 (tmtt) cc_final: 0.8090 (tttm)
REVERT: A  523 GLN cc_start: 0.8150 (tt0) cc_final: 0.7946 (tt0)
REVERT: B  277 ILE cc_start: 0.7759 (OUTLIER) cc_final: 0.7544 (pt)
REVERT: B  454 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8277 (mt)
REVERT: B  522 VAL cc_start: 0.8741 (OUTLIER) cc_final: 0.8534 (p)
  outliers start: 49
  outliers final: 16
  residues processed: 330
  average time/residue: 0.2838
  time to fit residues: 132.0232
Evaluate side-chains
  314 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 293
  time to evaluate  : 1.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 TYR
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  303 GLU
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  562 ASN
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  454 LEU
Chi-restraints excluded: chain B residue  468 SER
Chi-restraints excluded: chain B residue  522 VAL
Chi-restraints excluded: chain B residue  579 THR
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain B residue  632 HIS
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain K residue  577 LEU
Chi-restraints excluded: chain K residue  592 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 169 optimal weight:    1.9990
   chunk 90 optimal weight:    0.2980
   chunk 113 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 81 optimal weight:    0.4980
   chunk 130 optimal weight:    4.9990
   chunk 159 optimal weight:    3.9990
   chunk 110 optimal weight:    0.0570
   chunk 61 optimal weight:    2.9990
   chunk 109 optimal weight:    0.6980
   chunk 89 optimal weight:    0.8980
   overall best weight:    0.4698

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

Flipped N/Q/H residues before XYZ refinement:
A 100 ASN
** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 609 GLN
** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 211 HIS
** K 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 585 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.153843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.123191 restraints weight = 20307.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3507 rms_B_bonded: 2.22
r_work: 0.3376 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3210 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.1392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068  14293  Z= 0.129
  Angle     :  0.610  11.999  19216  Z= 0.320
  Chirality :  0.042   0.204   2108
  Planarity :  0.004   0.062   2455
  Dihedral  :  6.963  89.448   1934
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  9.01 %
    Favored  : 90.46 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 32.20 %
    Favored  : 64.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.13 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.20), residues: 1699
  helix:  1.01 (0.20), residues: 730
  sheet: -1.03 (0.41), residues: 173
  loop : -3.18 (0.18), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP C 114 
 HIS   0.004   0.001   HIS B 676 
 PHE   0.017   0.001   PHE C 238 
 TYR   0.011   0.001   TYR C 155 
 ARG   0.003   0.000   ARG B  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04940 (  550)
  hydrogen bonds       : angle       4.68787 ( 1614)
  covalent geometry    : bond        0.00286 (14293)
  covalent geometry    : angle       0.61003 (19216)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  361 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 304
  time to evaluate  : 1.665 
Fit side-chains
REVERT: A   79 PRO cc_start: 0.8672 (Cg_endo) cc_final: 0.8464 (Cg_exo)
REVERT: A  137 TYR cc_start: 0.6790 (OUTLIER) cc_final: 0.5941 (t80)
REVERT: A  303 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7276 (mp0)
REVERT: A  380 VAL cc_start: 0.8607 (m) cc_final: 0.8403 (t)
REVERT: A  491 LYS cc_start: 0.8269 (tmtt) cc_final: 0.8008 (tttm)
REVERT: B   80 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7367 (tm-30)
REVERT: B   81 GLU cc_start: 0.6960 (mp0) cc_final: 0.6676 (mp0)
REVERT: B  277 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7490 (pt)
REVERT: B  324 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7600 (mt-10)
REVERT: B  368 GLU cc_start: 0.7147 (pm20) cc_final: 0.6463 (pm20)
REVERT: B  424 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7655 (mm-30)
REVERT: B  454 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8272 (mt)
REVERT: B  522 VAL cc_start: 0.8757 (OUTLIER) cc_final: 0.8543 (p)
REVERT: B  613 ASP cc_start: 0.7432 (p0) cc_final: 0.7169 (p0)
REVERT: K  618 LEU cc_start: 0.6649 (OUTLIER) cc_final: 0.6434 (mt)
  outliers start: 57
  outliers final: 27
  residues processed: 337
  average time/residue: 0.2854
  time to fit residues: 135.2208
Evaluate side-chains
  324 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 289
  time to evaluate  : 1.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue  137 TYR
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  303 GLU
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain A residue  562 ASN
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  612 ARG
Chi-restraints excluded: chain A residue  632 HIS
Chi-restraints excluded: chain A residue  672 ASP
Chi-restraints excluded: chain B residue   32 PHE
Chi-restraints excluded: chain B residue   80 GLN
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  424 GLU
Chi-restraints excluded: chain B residue  454 LEU
Chi-restraints excluded: chain B residue  468 SER
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain B residue  522 VAL
Chi-restraints excluded: chain B residue  576 GLU
Chi-restraints excluded: chain B residue  579 THR
Chi-restraints excluded: chain B residue  591 ILE
Chi-restraints excluded: chain B residue  617 MET
Chi-restraints excluded: chain B residue  632 HIS
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain K residue  577 LEU
Chi-restraints excluded: chain K residue  592 ILE
Chi-restraints excluded: chain K residue  618 LEU
Chi-restraints excluded: chain K residue  689 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 156 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 63 optimal weight:    0.5980
   chunk 86 optimal weight:    0.4980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 100 ASN
A 154 GLN
** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 609 GLN
** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 130 ASN
K 585 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.152447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.121009 restraints weight = 20234.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 2.37
r_work: 0.3319 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3149 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
moved from start:          0.1521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  14293  Z= 0.152
  Angle     :  0.632  12.391  19216  Z= 0.331
  Chirality :  0.043   0.197   2108
  Planarity :  0.004   0.060   2455
  Dihedral  :  6.971  89.716   1934
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  :  9.42 %
    Favored  : 90.11 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 31.10 %
    Favored  : 64.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.13 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.51 (0.20), residues: 1699
  helix:  1.03 (0.20), residues: 738
  sheet: -0.99 (0.40), residues: 182
  loop : -3.20 (0.18), residues: 779

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C 114 
 HIS   0.005   0.001   HIS A 676 
 PHE   0.016   0.002   PHE A  32 
 TYR   0.012   0.001   TYR C 155 
 ARG   0.003   0.000   ARG B 359 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05242 (  550)
  hydrogen bonds       : angle       4.66067 ( 1614)
  covalent geometry    : bond        0.00351 (14293)
  covalent geometry    : angle       0.63217 (19216)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  380 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 308
  time to evaluate  : 1.651 
Fit side-chains
REVERT: A  137 TYR cc_start: 0.6837 (OUTLIER) cc_final: 0.5909 (t80)
REVERT: A  303 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7185 (mp0)
REVERT: A  311 ASP cc_start: 0.7475 (t0) cc_final: 0.7127 (t70)
REVERT: A  380 VAL cc_start: 0.8655 (m) cc_final: 0.8449 (t)
REVERT: A  491 LYS cc_start: 0.8168 (tmtt) cc_final: 0.7952 (tttp)
REVERT: A  493 GLN cc_start: 0.8452 (tm-30) cc_final: 0.8036 (tm-30)
REVERT: B   52 ASP cc_start: 0.8253 (t0) cc_final: 0.7922 (m-30)
REVERT: B   81 GLU cc_start: 0.7165 (mp0) cc_final: 0.6955 (mp0)
REVERT: B  277 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7443 (pt)
REVERT: B  324 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7686 (mt-10)
REVERT: B  385 ASP cc_start: 0.7784 (p0) cc_final: 0.7507 (p0)
REVERT: B  461 GLN cc_start: 0.7692 (mt0) cc_final: 0.7478 (mt0)
REVERT: B  522 VAL cc_start: 0.8694 (OUTLIER) cc_final: 0.8471 (p)
REVERT: B  555 GLU cc_start: 0.6904 (tm-30) cc_final: 0.6480 (tm-30)
REVERT: B  613 ASP cc_start: 0.7334 (p0) cc_final: 0.7103 (p0)
REVERT: B  641 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7545 (mppt)
REVERT: C   14 ASP cc_start: 0.8261 (p0) cc_final: 0.8031 (p0)
REVERT: K  525 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7496 (tt)
  outliers start: 72
  outliers final: 47
  residues processed: 356
  average time/residue: 0.2863
  time to fit residues: 144.0629
Evaluate side-chains
  354 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 301
  time to evaluate  : 1.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue   81 GLU
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  137 TYR
Chi-restraints excluded: chain A residue  171 HIS
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  303 GLU
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  521 CYS
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain A residue  562 ASN
Chi-restraints excluded: chain A residue  574 LYS
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  612 ARG
Chi-restraints excluded: chain A residue  692 GLU
Chi-restraints excluded: chain B residue   32 PHE
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  468 SER
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain B residue  522 VAL
Chi-restraints excluded: chain B residue  564 CYS
Chi-restraints excluded: chain B residue  579 THR
Chi-restraints excluded: chain B residue  583 ARG
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain B residue  591 ILE
Chi-restraints excluded: chain B residue  617 MET
Chi-restraints excluded: chain B residue  632 HIS
Chi-restraints excluded: chain B residue  641 LYS
Chi-restraints excluded: chain C residue   27 SER
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain C residue  194 CYS
Chi-restraints excluded: chain K residue  524 GLN
Chi-restraints excluded: chain K residue  525 LEU
Chi-restraints excluded: chain K residue  577 LEU
Chi-restraints excluded: chain K residue  588 LEU
Chi-restraints excluded: chain K residue  592 ILE
Chi-restraints excluded: chain K residue  595 PHE
Chi-restraints excluded: chain K residue  697 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 167 optimal weight:    1.9990
   chunk 83 optimal weight:    0.7980
   chunk 99 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 109 optimal weight:    0.6980
   chunk 133 optimal weight:   30.0000
   chunk 0 optimal weight:    2.9990
   chunk 143 optimal weight:    8.9990
   chunk 21 optimal weight:    0.0070
   chunk 129 optimal weight:    1.9990
   chunk 130 optimal weight:    0.9980
   overall best weight:    0.6998

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

Flipped N/Q/H residues before XYZ refinement:
A 100 ASN
** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 461 GLN
A 523 GLN
A 601 ASN
B 461 GLN
B 609 GLN
** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C   9 HIS
C 130 ASN
C 253 ASN
K 585 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.152740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.121037 restraints weight = 20260.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 2.38
r_work: 0.3305 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3136 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.1709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062  14293  Z= 0.148
  Angle     :  0.623  13.073  19216  Z= 0.325
  Chirality :  0.043   0.199   2108
  Planarity :  0.004   0.062   2455
  Dihedral  :  6.910  88.268   1934
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  :  9.18 %
    Favored  : 90.35 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 31.36 %
    Favored  : 63.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.13 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (0.20), residues: 1699
  helix:  1.04 (0.20), residues: 743
  sheet: -0.96 (0.39), residues: 188
  loop : -3.18 (0.18), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C 114 
 HIS   0.004   0.001   HIS B 676 
 PHE   0.015   0.001   PHE A  32 
 TYR   0.011   0.001   TYR C 155 
 ARG   0.003   0.000   ARG B 359 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05060 (  550)
  hydrogen bonds       : angle       4.60481 ( 1614)
  covalent geometry    : bond        0.00343 (14293)
  covalent geometry    : angle       0.62334 (19216)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  385 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 310
  time to evaluate  : 1.510 
Fit side-chains
REVERT: A  137 TYR cc_start: 0.6948 (OUTLIER) cc_final: 0.6010 (t80)
REVERT: A  311 ASP cc_start: 0.7543 (t0) cc_final: 0.7261 (t0)
REVERT: A  380 VAL cc_start: 0.8655 (m) cc_final: 0.8454 (t)
REVERT: A  423 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.8001 (mttm)
REVERT: A  491 LYS cc_start: 0.8190 (tmtt) cc_final: 0.7972 (tttm)
REVERT: A  574 LYS cc_start: 0.7398 (OUTLIER) cc_final: 0.6980 (mtmt)
REVERT: B   52 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7840 (m-30)
REVERT: B   80 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7407 (tm-30)
REVERT: B   81 GLU cc_start: 0.7205 (mp0) cc_final: 0.6909 (mp0)
REVERT: B  164 SER cc_start: 0.8951 (p) cc_final: 0.8735 (p)
REVERT: B  188 ASP cc_start: 0.7252 (p0) cc_final: 0.6981 (p0)
REVERT: B  219 LYS cc_start: 0.7557 (mmmt) cc_final: 0.7303 (mmmt)
REVERT: B  277 ILE cc_start: 0.7663 (OUTLIER) cc_final: 0.7440 (pt)
REVERT: B  324 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7704 (mt-10)
REVERT: B  364 ASP cc_start: 0.8021 (p0) cc_final: 0.7705 (p0)
REVERT: B  368 GLU cc_start: 0.7188 (pm20) cc_final: 0.6476 (pm20)
REVERT: B  385 ASP cc_start: 0.7777 (p0) cc_final: 0.7503 (p0)
REVERT: B  424 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7922 (mm-30)
REVERT: B  555 GLU cc_start: 0.6868 (tm-30) cc_final: 0.6508 (tm-30)
REVERT: B  613 ASP cc_start: 0.7285 (p0) cc_final: 0.7054 (p0)
REVERT: B  641 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7509 (mppt)
REVERT: C   14 ASP cc_start: 0.8294 (p0) cc_final: 0.8059 (p0)
REVERT: K  525 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7552 (tt)
  outliers start: 75
  outliers final: 48
  residues processed: 362
  average time/residue: 0.2889
  time to fit residues: 147.2055
Evaluate side-chains
  357 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 300
  time to evaluate  : 1.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  126 ILE
Chi-restraints excluded: chain A residue  137 TYR
Chi-restraints excluded: chain A residue  171 HIS
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  423 LYS
Chi-restraints excluded: chain A residue  461 GLN
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain A residue  562 ASN
Chi-restraints excluded: chain A residue  574 LYS
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  612 ARG
Chi-restraints excluded: chain A residue  632 HIS
Chi-restraints excluded: chain B residue   32 PHE
Chi-restraints excluded: chain B residue   52 ASP
Chi-restraints excluded: chain B residue   80 GLN
Chi-restraints excluded: chain B residue   97 ASP
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  159 SER
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  424 GLU
Chi-restraints excluded: chain B residue  468 SER
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain B residue  564 CYS
Chi-restraints excluded: chain B residue  579 THR
Chi-restraints excluded: chain B residue  583 ARG
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain B residue  591 ILE
Chi-restraints excluded: chain B residue  632 HIS
Chi-restraints excluded: chain B residue  641 LYS
Chi-restraints excluded: chain C residue   27 SER
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain C residue  194 CYS
Chi-restraints excluded: chain C residue  243 THR
Chi-restraints excluded: chain K residue  524 GLN
Chi-restraints excluded: chain K residue  525 LEU
Chi-restraints excluded: chain K residue  573 ILE
Chi-restraints excluded: chain K residue  577 LEU
Chi-restraints excluded: chain K residue  588 LEU
Chi-restraints excluded: chain K residue  592 ILE
Chi-restraints excluded: chain K residue  697 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 107 optimal weight:    0.7980
   chunk 79 optimal weight:    0.5980
   chunk 167 optimal weight:    3.9990
   chunk 114 optimal weight:    1.9990
   chunk 147 optimal weight:   10.0000
   chunk 163 optimal weight:    0.0170
   chunk 25 optimal weight:    0.6980
   chunk 49 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 137 optimal weight:    1.9990
   overall best weight:    0.8220

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

Flipped N/Q/H residues before XYZ refinement:
A 100 ASN
** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 523 GLN
A 601 ASN
B 609 GLN
** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 130 ASN
K 585 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.152113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.118227 restraints weight = 20423.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.3433 rms_B_bonded: 2.65
r_work: 0.3283 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7316
moved from start:          0.1785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  14293  Z= 0.162
  Angle     :  0.635  13.731  19216  Z= 0.331
  Chirality :  0.043   0.194   2108
  Planarity :  0.004   0.062   2455
  Dihedral  :  6.944  89.517   1934
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  9.12 %
    Favored  : 90.35 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 32.00 %
    Favored  : 62.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.13 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.43 (0.20), residues: 1699
  helix:  1.04 (0.20), residues: 743
  sheet: -0.91 (0.39), residues: 190
  loop : -3.16 (0.18), residues: 766

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C 114 
 HIS   0.004   0.001   HIS A 676 
 PHE   0.018   0.002   PHE A  32 
 TYR   0.012   0.001   TYR A 373 
 ARG   0.003   0.000   ARG B 359 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05273 (  550)
  hydrogen bonds       : angle       4.60562 ( 1614)
  covalent geometry    : bond        0.00381 (14293)
  covalent geometry    : angle       0.63498 (19216)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  394 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 82
    poor density    : 312
  time to evaluate  : 1.579 
Fit side-chains
REVERT: A  137 TYR cc_start: 0.6745 (OUTLIER) cc_final: 0.5806 (t80)
REVERT: A  303 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7162 (mp0)
REVERT: A  311 ASP cc_start: 0.7364 (t0) cc_final: 0.7051 (t0)
REVERT: A  380 VAL cc_start: 0.8596 (m) cc_final: 0.8395 (t)
REVERT: A  423 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7888 (mttm)
REVERT: A  443 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7319 (mt-10)
REVERT: A  491 LYS cc_start: 0.8051 (tmtt) cc_final: 0.7843 (tttm)
REVERT: A  639 ARG cc_start: 0.7986 (tmm160) cc_final: 0.7781 (ttp80)
REVERT: B   52 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7701 (m-30)
REVERT: B   80 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7245 (tm-30)
REVERT: B   81 GLU cc_start: 0.7032 (mp0) cc_final: 0.6793 (mp0)
REVERT: B  164 SER cc_start: 0.8883 (p) cc_final: 0.8675 (p)
REVERT: B  188 ASP cc_start: 0.7049 (p0) cc_final: 0.6805 (p0)
REVERT: B  277 ILE cc_start: 0.7613 (OUTLIER) cc_final: 0.7397 (pt)
REVERT: B  324 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7491 (mt-10)
REVERT: B  364 ASP cc_start: 0.7953 (p0) cc_final: 0.7653 (p0)
REVERT: B  368 GLU cc_start: 0.6980 (pm20) cc_final: 0.6303 (pm20)
REVERT: B  385 ASP cc_start: 0.7554 (p0) cc_final: 0.7278 (p0)
REVERT: B  522 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.8357 (p)
REVERT: B  555 GLU cc_start: 0.6770 (tm-30) cc_final: 0.6336 (tm-30)
REVERT: B  613 ASP cc_start: 0.7026 (p0) cc_final: 0.6801 (p0)
REVERT: B  641 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7324 (mppt)
REVERT: C   14 ASP cc_start: 0.8158 (p0) cc_final: 0.7944 (p0)
REVERT: K  525 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7515 (tt)
  outliers start: 82
  outliers final: 55
  residues processed: 372
  average time/residue: 0.2954
  time to fit residues: 154.5712
Evaluate side-chains
  364 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 300
  time to evaluate  : 1.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  126 ILE
Chi-restraints excluded: chain A residue  137 TYR
Chi-restraints excluded: chain A residue  171 HIS
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  303 GLU
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  423 LYS
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  521 CYS
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain A residue  562 ASN
Chi-restraints excluded: chain A residue  574 LYS
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  612 ARG
Chi-restraints excluded: chain A residue  632 HIS
Chi-restraints excluded: chain B residue   32 PHE
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue   52 ASP
Chi-restraints excluded: chain B residue   80 GLN
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  159 SER
Chi-restraints excluded: chain B residue  175 ILE
Chi-restraints excluded: chain B residue  214 THR
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  277 ILE
Chi-restraints excluded: chain B residue  468 SER
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain B residue  522 VAL
Chi-restraints excluded: chain B residue  564 CYS
Chi-restraints excluded: chain B residue  579 THR
Chi-restraints excluded: chain B residue  583 ARG
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain B residue  591 ILE
Chi-restraints excluded: chain B residue  617 MET
Chi-restraints excluded: chain B residue  632 HIS
Chi-restraints excluded: chain B residue  641 LYS
Chi-restraints excluded: chain C residue   27 SER
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  130 ASN
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain C residue  194 CYS
Chi-restraints excluded: chain C residue  243 THR
Chi-restraints excluded: chain K residue  524 GLN
Chi-restraints excluded: chain K residue  525 LEU
Chi-restraints excluded: chain K residue  573 ILE
Chi-restraints excluded: chain K residue  577 LEU
Chi-restraints excluded: chain K residue  588 LEU
Chi-restraints excluded: chain K residue  592 ILE
Chi-restraints excluded: chain K residue  595 PHE
Chi-restraints excluded: chain K residue  648 GLU
Chi-restraints excluded: chain K residue  697 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 69 optimal weight:    0.5980
   chunk 83 optimal weight:    0.1980
   chunk 158 optimal weight:    1.9990
   chunk 109 optimal weight:    0.0970
   chunk 113 optimal weight:    0.0870
   chunk 110 optimal weight:    1.9990
   chunk 80 optimal weight:    0.7980
   chunk 75 optimal weight:    0.3980
   chunk 111 optimal weight:    0.1980
   chunk 140 optimal weight:   10.0000
   chunk 64 optimal weight:    1.9990
   overall best weight:    0.1956

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

Flipped N/Q/H residues before XYZ refinement:
A 100 ASN
** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 585 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.155531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.122025 restraints weight = 20354.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3500 rms_B_bonded: 2.56
r_work: 0.3359 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7230
moved from start:          0.2188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.087  14293  Z= 0.114
  Angle     :  0.598  14.866  19216  Z= 0.308
  Chirality :  0.041   0.191   2108
  Planarity :  0.004   0.073   2455
  Dihedral  :  6.562  83.000   1934
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  :  8.30 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 33.42 %
    Favored  : 62.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.20), residues: 1699
  helix:  1.27 (0.20), residues: 731
  sheet: -0.77 (0.39), residues: 191
  loop : -3.02 (0.19), residues: 777

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP C 114 
 HIS   0.005   0.001   HIS B 676 
 PHE   0.009   0.001   PHE A  39 
 TYR   0.011   0.001   TYR C 155 
 ARG   0.004   0.000   ARG C 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03958 (  550)
  hydrogen bonds       : angle       4.45629 ( 1614)
  covalent geometry    : bond        0.00255 (14293)
  covalent geometry    : angle       0.59767 (19216)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  359 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 299
  time to evaluate  : 1.670 
Fit side-chains
REVERT: A  137 TYR cc_start: 0.6523 (OUTLIER) cc_final: 0.5906 (t80)
REVERT: A  311 ASP cc_start: 0.7335 (t0) cc_final: 0.6996 (t0)
REVERT: A  328 GLU cc_start: 0.7497 (pt0) cc_final: 0.7109 (pt0)
REVERT: A  491 LYS cc_start: 0.8006 (tmtt) cc_final: 0.7801 (tttm)
REVERT: A  549 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.6120 (mp0)
REVERT: B   52 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7639 (m-30)
REVERT: B   80 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7303 (tm-30)
REVERT: B   81 GLU cc_start: 0.6787 (mp0) cc_final: 0.6573 (mp0)
REVERT: B  188 ASP cc_start: 0.7039 (p0) cc_final: 0.6789 (p0)
REVERT: B  364 ASP cc_start: 0.7884 (p0) cc_final: 0.7602 (p0)
REVERT: B  368 GLU cc_start: 0.6922 (pm20) cc_final: 0.6283 (pm20)
REVERT: B  385 ASP cc_start: 0.7452 (p0) cc_final: 0.7180 (p0)
REVERT: B  555 GLU cc_start: 0.6611 (tm-30) cc_final: 0.6225 (tm-30)
REVERT: B  613 ASP cc_start: 0.6976 (p0) cc_final: 0.6771 (p0)
REVERT: B  641 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7384 (mppt)
REVERT: C   14 ASP cc_start: 0.8081 (p0) cc_final: 0.7838 (p0)
REVERT: K  525 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7366 (tt)
REVERT: K  564 MET cc_start: 0.7689 (tpp) cc_final: 0.7175 (tpp)
REVERT: K  650 MET cc_start: 0.7305 (ttm) cc_final: 0.6936 (mtt)
  outliers start: 60
  outliers final: 40
  residues processed: 343
  average time/residue: 0.3208
  time to fit residues: 154.8316
Evaluate side-chains
  338 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 292
  time to evaluate  : 1.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  137 TYR
Chi-restraints excluded: chain A residue  171 HIS
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain A residue  481 LYS
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain A residue  549 GLU
Chi-restraints excluded: chain A residue  562 ASN
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  612 ARG
Chi-restraints excluded: chain A residue  632 HIS
Chi-restraints excluded: chain B residue   23 GLN
Chi-restraints excluded: chain B residue   32 PHE
Chi-restraints excluded: chain B residue   52 ASP
Chi-restraints excluded: chain B residue   80 GLN
Chi-restraints excluded: chain B residue   97 ASP
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  159 SER
Chi-restraints excluded: chain B residue  468 SER
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain B residue  579 THR
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain B residue  591 ILE
Chi-restraints excluded: chain B residue  632 HIS
Chi-restraints excluded: chain B residue  641 LYS
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain C residue  194 CYS
Chi-restraints excluded: chain C residue  243 THR
Chi-restraints excluded: chain K residue  524 GLN
Chi-restraints excluded: chain K residue  525 LEU
Chi-restraints excluded: chain K residue  544 ILE
Chi-restraints excluded: chain K residue  573 ILE
Chi-restraints excluded: chain K residue  577 LEU
Chi-restraints excluded: chain K residue  588 LEU
Chi-restraints excluded: chain K residue  592 ILE
Chi-restraints excluded: chain K residue  648 GLU
Chi-restraints excluded: chain K residue  697 LEU
Chi-restraints excluded: chain K residue  724 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 115 optimal weight:    0.0000
   chunk 52 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 95 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 152 optimal weight:   10.0000
   chunk 25 optimal weight:    0.0270
   overall best weight:    0.7444

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

Flipped N/Q/H residues before XYZ refinement:
A 100 ASN
** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 601 ASN
** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 585 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.152570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.118543 restraints weight = 20138.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 2.68
r_work: 0.3293 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7300
moved from start:          0.2102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071  14293  Z= 0.157
  Angle     :  0.641  13.898  19216  Z= 0.332
  Chirality :  0.043   0.230   2108
  Planarity :  0.004   0.059   2455
  Dihedral  :  6.676  87.295   1932
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  :  9.18 %
    Favored  : 90.35 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 32.84 %
    Favored  : 62.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.13 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.20), residues: 1699
  helix:  1.20 (0.20), residues: 735
  sheet: -0.69 (0.40), residues: 187
  loop : -3.00 (0.19), residues: 777

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C 114 
 HIS   0.004   0.001   HIS B 676 
 PHE   0.017   0.002   PHE A  32 
 TYR   0.012   0.001   TYR A 216 
 ARG   0.003   0.000   ARG B 359 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05005 (  550)
  hydrogen bonds       : angle       4.50147 ( 1614)
  covalent geometry    : bond        0.00371 (14293)
  covalent geometry    : angle       0.64107 (19216)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  364 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 298
  time to evaluate  : 1.647 
Fit side-chains
REVERT: A  137 TYR cc_start: 0.6719 (OUTLIER) cc_final: 0.5820 (t80)
REVERT: A  311 ASP cc_start: 0.7349 (t0) cc_final: 0.6972 (t0)
REVERT: A  328 GLU cc_start: 0.7535 (pt0) cc_final: 0.7133 (pt0)
REVERT: A  443 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7328 (mt-10)
REVERT: A  518 ASP cc_start: 0.7289 (m-30) cc_final: 0.6961 (m-30)
REVERT: B   52 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7684 (m-30)
REVERT: B   80 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.7212 (tm-30)
REVERT: B   81 GLU cc_start: 0.7039 (mp0) cc_final: 0.6823 (mp0)
REVERT: B  139 VAL cc_start: 0.7852 (p) cc_final: 0.7507 (m)
REVERT: B  364 ASP cc_start: 0.7894 (p0) cc_final: 0.7624 (p0)
REVERT: B  368 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6699 (pm20)
REVERT: B  385 ASP cc_start: 0.7498 (p0) cc_final: 0.7242 (p0)
REVERT: B  522 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8350 (p)
REVERT: B  555 GLU cc_start: 0.6741 (tm-30) cc_final: 0.6295 (tm-30)
REVERT: B  613 ASP cc_start: 0.6958 (p0) cc_final: 0.6755 (p0)
REVERT: B  641 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7361 (mppt)
REVERT: C   14 ASP cc_start: 0.8154 (p0) cc_final: 0.7914 (p0)
REVERT: C  112 MET cc_start: 0.4253 (mtp) cc_final: 0.4008 (mtp)
REVERT: C  121 LYS cc_start: 0.7286 (OUTLIER) cc_final: 0.7070 (ptpt)
REVERT: K  525 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7493 (tt)
REVERT: K  689 MET cc_start: 0.5026 (ttt) cc_final: 0.4732 (ttt)
  outliers start: 66
  outliers final: 49
  residues processed: 342
  average time/residue: 0.3140
  time to fit residues: 151.0156
Evaluate side-chains
  350 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 293
  time to evaluate  : 1.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  137 TYR
Chi-restraints excluded: chain A residue  152 ASP
Chi-restraints excluded: chain A residue  171 HIS
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain A residue  481 LYS
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  521 CYS
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain A residue  562 ASN
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  612 ARG
Chi-restraints excluded: chain A residue  632 HIS
Chi-restraints excluded: chain B residue   32 PHE
Chi-restraints excluded: chain B residue   52 ASP
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue   80 GLN
Chi-restraints excluded: chain B residue   97 ASP
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  159 SER
Chi-restraints excluded: chain B residue  368 GLU
Chi-restraints excluded: chain B residue  468 SER
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain B residue  522 VAL
Chi-restraints excluded: chain B residue  543 LEU
Chi-restraints excluded: chain B residue  564 CYS
Chi-restraints excluded: chain B residue  579 THR
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain B residue  591 ILE
Chi-restraints excluded: chain B residue  632 HIS
Chi-restraints excluded: chain B residue  641 LYS
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  121 LYS
Chi-restraints excluded: chain C residue  194 CYS
Chi-restraints excluded: chain C residue  243 THR
Chi-restraints excluded: chain K residue  525 LEU
Chi-restraints excluded: chain K residue  544 ILE
Chi-restraints excluded: chain K residue  573 ILE
Chi-restraints excluded: chain K residue  577 LEU
Chi-restraints excluded: chain K residue  588 LEU
Chi-restraints excluded: chain K residue  592 ILE
Chi-restraints excluded: chain K residue  648 GLU
Chi-restraints excluded: chain K residue  668 MET
Chi-restraints excluded: chain K residue  697 LEU
Chi-restraints excluded: chain K residue  724 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9990
   chunk 134 optimal weight:   30.0000
   chunk 15 optimal weight:    2.9990
   chunk 140 optimal weight:    7.9990
   chunk 99 optimal weight:    0.6980
   chunk 125 optimal weight:    0.9990
   chunk 7 optimal weight:    0.3980
   chunk 141 optimal weight:    1.9990
   overall best weight:    1.0186

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

Flipped N/Q/H residues before XYZ refinement:
A 100 ASN
** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 523 GLN
B 625 HIS
** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 146 GLN
K 585 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.151100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.117664 restraints weight = 20162.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 2.49
r_work: 0.3287 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3113 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.2116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065  14293  Z= 0.188
  Angle     :  0.683  15.473  19216  Z= 0.353
  Chirality :  0.045   0.221   2108
  Planarity :  0.004   0.061   2455
  Dihedral  :  6.911  88.022   1932
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  9.48 %
    Favored  : 90.11 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 32.26 %
    Favored  : 63.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.13 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.35 (0.20), residues: 1699
  helix:  1.11 (0.20), residues: 733
  sheet: -0.97 (0.39), residues: 196
  loop : -3.04 (0.19), residues: 770

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C 114 
 HIS   0.007   0.001   HIS B 676 
 PHE   0.021   0.002   PHE A  32 
 TYR   0.015   0.002   TYR A 485 
 ARG   0.004   0.000   ARG B 359 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05630 (  550)
  hydrogen bonds       : angle       4.59882 ( 1614)
  covalent geometry    : bond        0.00452 (14293)
  covalent geometry    : angle       0.68291 (19216)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  384 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 315
  time to evaluate  : 1.851 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 ILE cc_start: 0.8022 (mm) cc_final: 0.7780 (mt)
REVERT: A  137 TYR cc_start: 0.7070 (OUTLIER) cc_final: 0.6063 (t80)
REVERT: A  303 GLU cc_start: 0.7747 (tp30) cc_final: 0.7378 (mp0)
REVERT: A  311 ASP cc_start: 0.7571 (t0) cc_final: 0.7250 (t0)
REVERT: A  328 GLU cc_start: 0.7792 (pt0) cc_final: 0.7406 (pt0)
REVERT: A  443 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7565 (mt-10)
REVERT: A  518 ASP cc_start: 0.7697 (m-30) cc_final: 0.7355 (m-30)
REVERT: B   52 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7847 (m-30)
REVERT: B   81 GLU cc_start: 0.7291 (mp0) cc_final: 0.7063 (mp0)
REVERT: B  139 VAL cc_start: 0.7961 (p) cc_final: 0.7615 (m)
REVERT: B  364 ASP cc_start: 0.7956 (p0) cc_final: 0.7671 (p0)
REVERT: B  385 ASP cc_start: 0.7697 (p0) cc_final: 0.7447 (p0)
REVERT: B  522 VAL cc_start: 0.8704 (OUTLIER) cc_final: 0.8484 (p)
REVERT: B  555 GLU cc_start: 0.6925 (tm-30) cc_final: 0.6484 (tm-30)
REVERT: B  613 ASP cc_start: 0.7072 (p0) cc_final: 0.6843 (p0)
REVERT: B  641 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7436 (mppt)
REVERT: B  666 SER cc_start: 0.8768 (t) cc_final: 0.8547 (m)
REVERT: C   14 ASP cc_start: 0.8291 (p0) cc_final: 0.8048 (p0)
REVERT: C  112 MET cc_start: 0.5055 (mtp) cc_final: 0.4728 (mtp)
REVERT: K  525 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7727 (tt)
  outliers start: 69
  outliers final: 53
  residues processed: 363
  average time/residue: 0.3547
  time to fit residues: 183.1855
Evaluate side-chains
  365 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 307
  time to evaluate  : 1.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  126 ILE
Chi-restraints excluded: chain A residue  137 TYR
Chi-restraints excluded: chain A residue  152 ASP
Chi-restraints excluded: chain A residue  171 HIS
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain A residue  481 LYS
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  521 CYS
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain A residue  562 ASN
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  612 ARG
Chi-restraints excluded: chain B residue   52 ASP
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue   97 ASP
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  159 SER
Chi-restraints excluded: chain B residue  468 SER
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain B residue  522 VAL
Chi-restraints excluded: chain B residue  543 LEU
Chi-restraints excluded: chain B residue  564 CYS
Chi-restraints excluded: chain B residue  579 THR
Chi-restraints excluded: chain B residue  583 ARG
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain B residue  591 ILE
Chi-restraints excluded: chain B residue  617 MET
Chi-restraints excluded: chain B residue  620 MET
Chi-restraints excluded: chain B residue  625 HIS
Chi-restraints excluded: chain B residue  632 HIS
Chi-restraints excluded: chain B residue  641 LYS
Chi-restraints excluded: chain C residue   27 SER
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain C residue  194 CYS
Chi-restraints excluded: chain C residue  243 THR
Chi-restraints excluded: chain K residue  525 LEU
Chi-restraints excluded: chain K residue  544 ILE
Chi-restraints excluded: chain K residue  573 ILE
Chi-restraints excluded: chain K residue  588 LEU
Chi-restraints excluded: chain K residue  592 ILE
Chi-restraints excluded: chain K residue  595 PHE
Chi-restraints excluded: chain K residue  648 GLU
Chi-restraints excluded: chain K residue  668 MET
Chi-restraints excluded: chain K residue  697 LEU
Chi-restraints excluded: chain K residue  724 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9990
   chunk 142 optimal weight:   30.0000
   chunk 126 optimal weight:    0.1980
   chunk 104 optimal weight:    0.9990
   chunk 52 optimal weight:    0.5980
   chunk 102 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0470
   chunk 33 optimal weight:    0.6980
   chunk 101 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.4878

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

Flipped N/Q/H residues before XYZ refinement:
A 100 ASN
** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 609 GLN
B 625 HIS
** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 146 GLN
K 585 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.152789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.118545 restraints weight = 20112.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 2.69
r_work: 0.3294 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7287
moved from start:          0.2304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074  14293  Z= 0.135
  Angle     :  0.653  14.391  19216  Z= 0.335
  Chirality :  0.043   0.207   2108
  Planarity :  0.004   0.062   2455
  Dihedral  :  6.742  85.090   1932
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  8.89 %
    Favored  : 90.76 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 33.29 %
    Favored  : 63.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.13 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.20), residues: 1699
  helix:  1.19 (0.20), residues: 733
  sheet: -0.74 (0.41), residues: 188
  loop : -3.05 (0.19), residues: 778

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C 114 
 HIS   0.004   0.001   HIS B 632 
 PHE   0.012   0.001   PHE A  32 
 TYR   0.015   0.001   TYR K 566 
 ARG   0.004   0.000   ARG B 359 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04640 (  550)
  hydrogen bonds       : angle       4.51249 ( 1614)
  covalent geometry    : bond        0.00313 (14293)
  covalent geometry    : angle       0.65257 (19216)

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

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

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3398 Ramachandran restraints generated.
    1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  360 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 307
  time to evaluate  : 1.559 
Fit side-chains
   revert: symmetry clash
REVERT: A  137 TYR cc_start: 0.6687 (OUTLIER) cc_final: 0.5740 (t80)
REVERT: A  311 ASP cc_start: 0.7375 (t0) cc_final: 0.7087 (t0)
REVERT: A  328 GLU cc_start: 0.7542 (pt0) cc_final: 0.7151 (pt0)
REVERT: A  430 TYR cc_start: 0.8092 (t80) cc_final: 0.7727 (t80)
REVERT: A  443 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7341 (mt-10)
REVERT: A  518 ASP cc_start: 0.7408 (m-30) cc_final: 0.7024 (m-30)
REVERT: B   52 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7655 (m-30)
REVERT: B  139 VAL cc_start: 0.7781 (p) cc_final: 0.7409 (m)
REVERT: B  364 ASP cc_start: 0.7836 (p0) cc_final: 0.7549 (p0)
REVERT: B  380 VAL cc_start: 0.8118 (t) cc_final: 0.7916 (m)
REVERT: B  385 ASP cc_start: 0.7462 (p0) cc_final: 0.7228 (p0)
REVERT: B  522 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.8320 (t)
REVERT: B  555 GLU cc_start: 0.6783 (tm-30) cc_final: 0.6341 (tm-30)
REVERT: B  562 ASN cc_start: 0.8263 (t0) cc_final: 0.8060 (t0)
REVERT: B  613 ASP cc_start: 0.6917 (p0) cc_final: 0.6710 (p0)
REVERT: B  641 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7404 (mppt)
REVERT: C   14 ASP cc_start: 0.8102 (p0) cc_final: 0.7894 (p0)
REVERT: C  112 MET cc_start: 0.4339 (mtp) cc_final: 0.4082 (mtp)
REVERT: C  129 VAL cc_start: 0.7622 (t) cc_final: 0.7408 (t)
REVERT: K  525 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7558 (tt)
  outliers start: 53
  outliers final: 44
  residues processed: 343
  average time/residue: 0.3878
  time to fit residues: 185.9513
Evaluate side-chains
  350 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 301
  time to evaluate  : 1.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  126 ILE
Chi-restraints excluded: chain A residue  137 TYR
Chi-restraints excluded: chain A residue  152 ASP
Chi-restraints excluded: chain A residue  171 HIS
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  327 LEU
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain A residue  481 LYS
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  521 CYS
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain A residue  562 ASN
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  612 ARG
Chi-restraints excluded: chain B residue   52 ASP
Chi-restraints excluded: chain B residue   97 ASP
Chi-restraints excluded: chain B residue  126 ILE
Chi-restraints excluded: chain B residue  159 SER
Chi-restraints excluded: chain B residue  468 SER
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain B residue  522 VAL
Chi-restraints excluded: chain B residue  543 LEU
Chi-restraints excluded: chain B residue  564 CYS
Chi-restraints excluded: chain B residue  579 THR
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain B residue  591 ILE
Chi-restraints excluded: chain B residue  632 HIS
Chi-restraints excluded: chain B residue  641 LYS
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain C residue   81 LEU
Chi-restraints excluded: chain C residue   84 LEU
Chi-restraints excluded: chain C residue  152 VAL
Chi-restraints excluded: chain C residue  194 CYS
Chi-restraints excluded: chain C residue  243 THR
Chi-restraints excluded: chain K residue  525 LEU
Chi-restraints excluded: chain K residue  544 ILE
Chi-restraints excluded: chain K residue  573 ILE
Chi-restraints excluded: chain K residue  588 LEU
Chi-restraints excluded: chain K residue  592 ILE
Chi-restraints excluded: chain K residue  648 GLU
Chi-restraints excluded: chain K residue  697 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 135 optimal weight:    9.9990
   chunk 118 optimal weight:    0.4980
   chunk 7 optimal weight:    0.7980
   chunk 134 optimal weight:   20.0000
   chunk 109 optimal weight:    0.9990
   chunk 131 optimal weight:   20.0000
   chunk 137 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 97 optimal weight:    0.5980
   chunk 153 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 100 ASN
** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 146 GLN
K 585 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.152198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.118808 restraints weight = 20278.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 2.51
r_work: 0.3309 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3136 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.2328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070  14293  Z= 0.156
  Angle     :  0.665  15.718  19216  Z= 0.343
  Chirality :  0.044   0.242   2108
  Planarity :  0.004   0.062   2455
  Dihedral  :  6.812  88.272   1932
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  9.65 %
    Favored  : 89.94 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 33.68 %
    Favored  : 62.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.13 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.20), residues: 1699
  helix:  1.16 (0.20), residues: 733
  sheet: -0.90 (0.40), residues: 195
  loop : -3.05 (0.19), residues: 771

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C 114 
 HIS   0.005   0.001   HIS B 676 
 PHE   0.017   0.001   PHE A  32 
 TYR   0.011   0.001   TYR B 472 
 ARG   0.004   0.000   ARG B 359 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05010 (  550)
  hydrogen bonds       : angle       4.51029 ( 1614)
  covalent geometry    : bond        0.00369 (14293)
  covalent geometry    : angle       0.66477 (19216)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7716.34 seconds
wall clock time: 136 minutes 55.25 seconds (8215.25 seconds total)