Starting phenix.real_space_refine
on Tue Jul 29 04:34:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ijz_9682/07_2025/6ijz_9682.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ijz_9682/07_2025/6ijz_9682.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ijz_9682/07_2025/6ijz_9682.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ijz_9682/07_2025/6ijz_9682.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ijz_9682/07_2025/6ijz_9682.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ijz_9682/07_2025/6ijz_9682.cif"
  }
  resolution = 3.68
  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=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    7264      2.51       5
     N    1778      2.21       5
     O    1872      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10964
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5482
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 683, 5482
          Classifications: {'peptide': 683}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'CIS': 1, 'PTRANS': 36, 'TRANS': 645}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 61
          Unresolved non-hydrogen dihedrals: 43
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 31
  Restraints were copied for chains:
    B
  Time building chain proxies: 10.94, per 1000 atoms: 1.00
  Number of scatterers: 10964
  At special positions: 0
  Unit cell: (95.411, 139.849, 108.481, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      50     16.00
     O    1872      8.00
     N    1778      7.00
     C    7264      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: 3.12
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2636

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 2 sheets defined
      69.2% alpha, 1.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 30
      removed outlier: 3.804A  pdb=" N   VAL A   9 " --> pdb=" O   GLN A   5 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   VAL A  20 " --> pdb=" O   LEU A  16 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   LEU A  30 " --> pdb=" O   ALA A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 34 through 39
    Processing helix  chain 'A' and resid 39 through 45
    Processing helix  chain 'A' and resid 77 through 81
      removed outlier: 3.656A  pdb=" N   LYS A  81 " --> pdb=" O   GLU A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 91
    Processing helix  chain 'A' and resid 93 through 125
      removed outlier: 3.744A  pdb=" N   VAL A  97 " --> pdb=" O   LEU A  93 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   TYR A 102 " --> pdb=" O   TYR A  98 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   THR A 110 " --> pdb=" O   LEU A 106 " (cutoff:3.500A)
      Proline residue:  A 111  - end of helix
      removed outlier: 3.891A  pdb=" N   VAL A 119 " --> pdb=" O   LEU A 115 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   VAL A 121 " --> pdb=" O   TRP A 117 " (cutoff:3.500A)
      Proline residue:  A 122  - end of helix
    Processing helix  chain 'A' and resid 158 through 193
      removed outlier: 4.010A  pdb=" N   HIS A 162 " --> pdb=" O   ARG A 158 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   VAL A 164 " --> pdb=" O   TRP A 160 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   TRP A 172 " --> pdb=" O   ALA A 168 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   CYS A 174 " --> pdb=" O   THR A 170 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   TYR A 181 " --> pdb=" O   LEU A 177 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ALA A 185 " --> pdb=" O   TYR A 181 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   MET A 187 " --> pdb=" O   THR A 183 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ALA A 193 " --> pdb=" O   LEU A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 229
      removed outlier: 4.040A  pdb=" N   LEU A 220 " --> pdb=" O   SER A 216 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   VAL A 227 " --> pdb=" O   HIS A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 267
      removed outlier: 3.546A  pdb=" N   GLN A 263 " --> pdb=" O   LEU A 259 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   TYR A 266 " --> pdb=" O   TYR A 262 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ALA A 267 " --> pdb=" O   GLN A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 310
      removed outlier: 5.250A  pdb=" N   ALA A 296 " --> pdb=" O   GLU A 292 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   SER A 306 " --> pdb=" O   SER A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 337
      removed outlier: 3.562A  pdb=" N   ALA A 333 " --> pdb=" O   THR A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 369
      No H-bonds generated for 'chain 'A' and resid 367 through 369'
    Processing helix  chain 'A' and resid 370 through 389
      removed outlier: 3.595A  pdb=" N   ARG A 374 " --> pdb=" O   SER A 370 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   VAL A 380 " --> pdb=" O   LEU A 376 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   PHE A 382 " --> pdb=" O   MET A 378 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   PHE A 387 " --> pdb=" O   PHE A 383 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   PHE A 389 " --> pdb=" O   LEU A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 401
      removed outlier: 3.508A  pdb=" N   ILE A 393 " --> pdb=" O   PHE A 389 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   VAL A 396 " --> pdb=" O   PRO A 392 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   LEU A 399 " --> pdb=" O   PHE A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 407
    Processing helix  chain 'A' and resid 420 through 428
    Processing helix  chain 'A' and resid 428 through 438
    Processing helix  chain 'A' and resid 440 through 452
      removed outlier: 3.961A  pdb=" N   GLU A 452 " --> pdb=" O   MET A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 456 through 475
      removed outlier: 4.215A  pdb=" N   ARG A 462 " --> pdb=" O   SER A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 489
      removed outlier: 3.822A  pdb=" N   ALA A 483 " --> pdb=" O   ALA A 479 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ALA A 486 " --> pdb=" O   ILE A 482 " (cutoff:3.500A)
      removed outlier: 4.920A  pdb=" N   PHE A 487 " --> pdb=" O   ALA A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 496
      removed outlier: 3.609A  pdb=" N   GLN A 496 " --> pdb=" O   SER A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 500 through 512
      removed outlier: 3.739A  pdb=" N   ILE A 505 " --> pdb=" O   ILE A 501 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ILE A 509 " --> pdb=" O   ILE A 505 " (cutoff:3.500A)
      Proline residue:  A 510  - end of helix
    Processing helix  chain 'A' and resid 513 through 523
    Processing helix  chain 'A' and resid 524 through 530
    Processing helix  chain 'A' and resid 534 through 547
      removed outlier: 4.112A  pdb=" N   MET A 540 " --> pdb=" O   LYS A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 560
      removed outlier: 3.514A  pdb=" N   ALA A 558 " --> pdb=" O   ARG A 555 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   MET A 559 " --> pdb=" O   GLU A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 569 through 583
      removed outlier: 3.848A  pdb=" N   ILE A 573 " --> pdb=" O   GLY A 569 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   GLN A 574 " --> pdb=" O   GLU A 570 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   TYR A 583 " --> pdb=" O   LEU A 579 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 590 through 612
      removed outlier: 3.948A  pdb=" N   ILE A 603 " --> pdb=" O   ALA A 599 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 647
      removed outlier: 3.773A  pdb=" N   GLY A 629 " --> pdb=" O   PRO A 625 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   GLY A 644 " --> pdb=" O   LEU A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 651 through 655
      removed outlier: 3.838A  pdb=" N   ALA A 654 " --> pdb=" O   ALA A 651 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ALA A 655 " --> pdb=" O   ALA A 652 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 651 through 655'
    Processing helix  chain 'A' and resid 659 through 676
      removed outlier: 3.852A  pdb=" N   VAL A 663 " --> pdb=" O   ILE A 659 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ILE A 666 " --> pdb=" O   PRO A 662 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLY A 674 " --> pdb=" O   HIS A 670 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 677 through 680
    Processing helix  chain 'A' and resid 684 through 699
      removed outlier: 3.636A  pdb=" N   ASP A 692 " --> pdb=" O   ALA A 688 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 704 through 709
      removed outlier: 3.582A  pdb=" N   GLN A 709 " --> pdb=" O   LYS A 705 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 30
      removed outlier: 3.804A  pdb=" N   VAL B   9 " --> pdb=" O   GLN B   5 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   VAL B  20 " --> pdb=" O   LEU B  16 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   LEU B  30 " --> pdb=" O   ALA B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 39
    Processing helix  chain 'B' and resid 39 through 45
    Processing helix  chain 'B' and resid 77 through 81
      removed outlier: 3.656A  pdb=" N   LYS B  81 " --> pdb=" O   GLU B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 91
    Processing helix  chain 'B' and resid 93 through 125
      removed outlier: 3.744A  pdb=" N   VAL B  97 " --> pdb=" O   LEU B  93 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   TYR B 102 " --> pdb=" O   TYR B  98 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   THR B 110 " --> pdb=" O   LEU B 106 " (cutoff:3.500A)
      Proline residue:  B 111  - end of helix
      removed outlier: 3.891A  pdb=" N   VAL B 119 " --> pdb=" O   LEU B 115 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   VAL B 121 " --> pdb=" O   TRP B 117 " (cutoff:3.500A)
      Proline residue:  B 122  - end of helix
    Processing helix  chain 'B' and resid 158 through 193
      removed outlier: 4.009A  pdb=" N   HIS B 162 " --> pdb=" O   ARG B 158 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   VAL B 164 " --> pdb=" O   TRP B 160 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   TRP B 172 " --> pdb=" O   ALA B 168 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   CYS B 174 " --> pdb=" O   THR B 170 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   TYR B 181 " --> pdb=" O   LEU B 177 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ALA B 185 " --> pdb=" O   TYR B 181 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   MET B 187 " --> pdb=" O   THR B 183 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ALA B 193 " --> pdb=" O   LEU B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 229
      removed outlier: 4.040A  pdb=" N   LEU B 220 " --> pdb=" O   SER B 216 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   VAL B 227 " --> pdb=" O   HIS B 223 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 242 through 267
      removed outlier: 3.546A  pdb=" N   GLN B 263 " --> pdb=" O   LEU B 259 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   TYR B 266 " --> pdb=" O   TYR B 262 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ALA B 267 " --> pdb=" O   GLN B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 310
      removed outlier: 5.250A  pdb=" N   ALA B 296 " --> pdb=" O   GLU B 292 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   SER B 306 " --> pdb=" O   SER B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 337
      removed outlier: 3.561A  pdb=" N   ALA B 333 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 369
      No H-bonds generated for 'chain 'B' and resid 367 through 369'
    Processing helix  chain 'B' and resid 370 through 389
      removed outlier: 3.596A  pdb=" N   ARG B 374 " --> pdb=" O   SER B 370 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   VAL B 380 " --> pdb=" O   LEU B 376 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   PHE B 382 " --> pdb=" O   MET B 378 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   PHE B 387 " --> pdb=" O   PHE B 383 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   PHE B 389 " --> pdb=" O   LEU B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 389 through 401
      removed outlier: 3.508A  pdb=" N   ILE B 393 " --> pdb=" O   PHE B 389 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   VAL B 396 " --> pdb=" O   PRO B 392 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   LEU B 399 " --> pdb=" O   PHE B 395 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 402 through 407
    Processing helix  chain 'B' and resid 420 through 428
    Processing helix  chain 'B' and resid 428 through 438
    Processing helix  chain 'B' and resid 440 through 452
      removed outlier: 3.961A  pdb=" N   GLU B 452 " --> pdb=" O   MET B 448 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 456 through 475
      removed outlier: 4.215A  pdb=" N   ARG B 462 " --> pdb=" O   SER B 458 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 477 through 489
      removed outlier: 3.822A  pdb=" N   ALA B 483 " --> pdb=" O   ALA B 479 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ALA B 486 " --> pdb=" O   ILE B 482 " (cutoff:3.500A)
      removed outlier: 4.920A  pdb=" N   PHE B 487 " --> pdb=" O   ALA B 483 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 489 through 496
      removed outlier: 3.608A  pdb=" N   GLN B 496 " --> pdb=" O   SER B 492 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 500 through 512
      removed outlier: 3.739A  pdb=" N   ILE B 505 " --> pdb=" O   ILE B 501 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ILE B 509 " --> pdb=" O   ILE B 505 " (cutoff:3.500A)
      Proline residue:  B 510  - end of helix
    Processing helix  chain 'B' and resid 513 through 523
    Processing helix  chain 'B' and resid 524 through 530
    Processing helix  chain 'B' and resid 534 through 547
      removed outlier: 4.112A  pdb=" N   MET B 540 " --> pdb=" O   LYS B 536 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 560
      removed outlier: 3.514A  pdb=" N   ALA B 558 " --> pdb=" O   ARG B 555 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   MET B 559 " --> pdb=" O   GLU B 556 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 569 through 583
      removed outlier: 3.848A  pdb=" N   ILE B 573 " --> pdb=" O   GLY B 569 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   GLN B 574 " --> pdb=" O   GLU B 570 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   TYR B 583 " --> pdb=" O   LEU B 579 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 590 through 612
      removed outlier: 3.947A  pdb=" N   ILE B 603 " --> pdb=" O   ALA B 599 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 623 through 647
      removed outlier: 3.773A  pdb=" N   GLY B 629 " --> pdb=" O   PRO B 625 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   GLY B 644 " --> pdb=" O   LEU B 640 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 651 through 655
      removed outlier: 3.837A  pdb=" N   ALA B 654 " --> pdb=" O   ALA B 651 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ALA B 655 " --> pdb=" O   ALA B 652 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 651 through 655'
    Processing helix  chain 'B' and resid 659 through 676
      removed outlier: 3.852A  pdb=" N   VAL B 663 " --> pdb=" O   ILE B 659 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ILE B 666 " --> pdb=" O   PRO B 662 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLY B 674 " --> pdb=" O   HIS B 670 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 677 through 680
    Processing helix  chain 'B' and resid 684 through 699
      removed outlier: 3.636A  pdb=" N   ASP B 692 " --> pdb=" O   ALA B 688 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 704 through 709
      removed outlier: 3.581A  pdb=" N   GLN B 709 " --> pdb=" O   LYS B 705 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 203 through 205
      removed outlier: 4.859A  pdb=" N   VAL A 239 " --> pdb=" O   MET A 320 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 203 through 205
      removed outlier: 4.860A  pdb=" N   VAL B 239 " --> pdb=" O   MET B 320 " (cutoff:3.500A)

    557 hydrogen bonds defined for protein.
    1653 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.45

  Time building geometry restraints manager: 3.32 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 3027
        1.33 -     1.45: 2070
        1.45 -     1.57: 6083
        1.57 -     1.69: 0
        1.69 -     1.81: 92
  Bond restraints: 11272
  Sorted by residual:
  bond pdb=" CB  TRP A 624 "
       pdb=" CG  TRP A 624 "
    ideal  model  delta    sigma   weight residual
    1.498  1.404  0.094 3.10e-02 1.04e+03 9.10e+00
  bond pdb=" CB  TRP B 624 "
       pdb=" CG  TRP B 624 "
    ideal  model  delta    sigma   weight residual
    1.498  1.405  0.093 3.10e-02 1.04e+03 9.04e+00
  bond pdb=" CB  PRO B 111 "
       pdb=" CG  PRO B 111 "
    ideal  model  delta    sigma   weight residual
    1.492  1.398  0.094 5.00e-02 4.00e+02 3.54e+00
  bond pdb=" CB  PRO A 111 "
       pdb=" CG  PRO A 111 "
    ideal  model  delta    sigma   weight residual
    1.492  1.398  0.094 5.00e-02 4.00e+02 3.54e+00
  bond pdb=" CB  TRP B 172 "
       pdb=" CG  TRP B 172 "
    ideal  model  delta    sigma   weight residual
    1.498  1.443  0.055 3.10e-02 1.04e+03 3.15e+00
  ... (remaining 11267 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.32: 14665
        2.32 -     4.64: 541
        4.64 -     6.97: 96
        6.97 -     9.29: 40
        9.29 -    11.61: 6
  Bond angle restraints: 15348
  Sorted by residual:
  angle pdb=" C   SER B 619 "
        pdb=" N   ALA B 620 "
        pdb=" CA  ALA B 620 "
      ideal   model   delta    sigma   weight residual
     121.70  133.31  -11.61 1.80e+00 3.09e-01 4.16e+01
  angle pdb=" C   SER A 619 "
        pdb=" N   ALA A 620 "
        pdb=" CA  ALA A 620 "
      ideal   model   delta    sigma   weight residual
     121.70  133.31  -11.61 1.80e+00 3.09e-01 4.16e+01
  angle pdb=" C   VAL A 206 "
        pdb=" N   ARG A 207 "
        pdb=" CA  ARG A 207 "
      ideal   model   delta    sigma   weight residual
     121.54  130.94   -9.40 1.91e+00 2.74e-01 2.42e+01
  angle pdb=" C   VAL B 206 "
        pdb=" N   ARG B 207 "
        pdb=" CA  ARG B 207 "
      ideal   model   delta    sigma   weight residual
     121.54  130.89   -9.35 1.91e+00 2.74e-01 2.40e+01
  angle pdb=" CA  TRP B 624 "
        pdb=" CB  TRP B 624 "
        pdb=" CG  TRP B 624 "
      ideal   model   delta    sigma   weight residual
     113.60  104.68    8.92 1.90e+00 2.77e-01 2.20e+01
  ... (remaining 15343 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.25: 5910
       12.25 -    24.50: 580
       24.50 -    36.75: 120
       36.75 -    49.00: 32
       49.00 -    61.25: 4
  Dihedral angle restraints: 6646
    sinusoidal: 2596
      harmonic: 4050
  Sorted by residual:
  dihedral pdb=" CA  GLN B 135 "
           pdb=" C   GLN B 135 "
           pdb=" N   LEU B 136 "
           pdb=" CA  LEU B 136 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -131.79  -48.21     0      5.00e+00 4.00e-02 9.29e+01
  dihedral pdb=" CA  GLN A 135 "
           pdb=" C   GLN A 135 "
           pdb=" N   LEU A 136 "
           pdb=" CA  LEU A 136 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -131.83  -48.17     0      5.00e+00 4.00e-02 9.28e+01
  dihedral pdb=" CA  LYS A 134 "
           pdb=" C   LYS A 134 "
           pdb=" N   GLN A 135 "
           pdb=" CA  GLN A 135 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.87   31.13     0      5.00e+00 4.00e-02 3.88e+01
  ... (remaining 6643 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 1371
       0.073 -    0.146: 326
       0.146 -    0.218: 34
       0.218 -    0.291: 11
       0.291 -    0.364: 2
  Chirality restraints: 1744
  Sorted by residual:
  chirality pdb=" CB  VAL A 206 "
            pdb=" CA  VAL A 206 "
            pdb=" CG1 VAL A 206 "
            pdb=" CG2 VAL A 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.27   -0.36 2.00e-01 2.50e+01 3.31e+00
  chirality pdb=" CB  VAL B 206 "
            pdb=" CA  VAL B 206 "
            pdb=" CG1 VAL B 206 "
            pdb=" CG2 VAL B 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.27   -0.36 2.00e-01 2.50e+01 3.27e+00
  chirality pdb=" CA  TYR A 613 "
            pdb=" N   TYR A 613 "
            pdb=" C   TYR A 613 "
            pdb=" CB  TYR A 613 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.65e+00
  ... (remaining 1741 not shown)

  Planarity restraints: 1914
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 233 "    0.016 2.00e-02 2.50e+03   3.20e-02 1.03e+01
        pdb=" C   TYR B 233 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   TYR B 233 "    0.021 2.00e-02 2.50e+03
        pdb=" N   LEU B 234 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 233 "   -0.016 2.00e-02 2.50e+03   3.19e-02 1.02e+01
        pdb=" C   TYR A 233 "    0.055 2.00e-02 2.50e+03
        pdb=" O   TYR A 233 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   LEU A 234 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 612 "    0.014 2.00e-02 2.50e+03   3.01e-02 9.03e+00
        pdb=" C   VAL A 612 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   VAL A 612 "    0.020 2.00e-02 2.50e+03
        pdb=" N   TYR A 613 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1911 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 52
        2.58 -     3.16: 8901
        3.16 -     3.74: 16886
        3.74 -     4.32: 22900
        4.32 -     4.90: 37417
  Nonbonded interactions: 86156
  Sorted by model distance:
  nonbonded pdb=" O   VAL B 612 "
            pdb=" CD1 TYR B 613 "
     model   vdw
     2.000 3.340
  nonbonded pdb=" O   VAL A 612 "
            pdb=" CD1 TYR A 613 "
     model   vdw
     2.001 3.340
  nonbonded pdb=" OG  SER A 216 "
            pdb=" OE1 GLU A 219 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OG  SER B 216 "
            pdb=" OE1 GLU B 219 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" O   PHE B 420 "
            pdb=" OG  SER B 423 "
     model   vdw
     2.314 3.040
  ... (remaining 86151 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.420
  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:          0.400
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     31.940
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
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      :  0.008   0.094  11272  Z= 0.323
  Angle     :  1.110  11.610  15348  Z= 0.589
  Chirality :  0.064   0.364   1744
  Planarity :  0.009   0.068   1914
  Dihedral  : 10.644  61.249   4010
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 10.93 %
    Favored  : 88.77 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  3.45 %
    Favored  : 95.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.16 %
    Twisted Proline : 2.78 %
    Twisted General : 0.31 %

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: -5.03 (0.17), residues: 1354
  helix: -2.86 (0.13), residues: 860
  sheet: -3.31 (1.09), residues: 20
  loop : -4.03 (0.23), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.004   TRP A 525 
 HIS   0.009   0.002   HIS A 162 
 PHE   0.029   0.003   PHE A  21 
 TYR   0.048   0.003   TYR A 181 
 ARG   0.007   0.001   ARG A 630 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15687 (  557)
  hydrogen bonds       : angle       6.99577 ( 1653)
  covalent geometry    : bond        0.00764 (11272)
  covalent geometry    : angle       1.10977 (15348)

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

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

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  384 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 376
  time to evaluate  : 1.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ASN cc_start: 0.7948 (m-40) cc_final: 0.7405 (m110)
REVERT: A  165 MET cc_start: 0.8984 (mmm) cc_final: 0.8551 (mpp)
REVERT: A  370 SER cc_start: 0.9131 (p) cc_final: 0.8818 (t)
REVERT: A  397 GLN cc_start: 0.8925 (mp10) cc_final: 0.8443 (mp10)
REVERT: A  415 ILE cc_start: 0.7030 (mm) cc_final: 0.6711 (mm)
REVERT: A  428 PHE cc_start: 0.9116 (t80) cc_final: 0.8820 (t80)
REVERT: A  446 MET cc_start: 0.8927 (tpt) cc_final: 0.8697 (tpp)
REVERT: A  512 LYS cc_start: 0.9126 (tttp) cc_final: 0.8792 (ttmm)
REVERT: A  521 MET cc_start: 0.7940 (mmt) cc_final: 0.7468 (mmt)
REVERT: A  574 GLN cc_start: 0.8580 (mt0) cc_final: 0.8362 (mt0)
REVERT: A  581 LEU cc_start: 0.8919 (mt) cc_final: 0.8698 (mt)
REVERT: A  589 MET cc_start: 0.8154 (mmm) cc_final: 0.7795 (mmm)
REVERT: A  612 VAL cc_start: 0.8839 (t) cc_final: 0.8499 (p)
REVERT: A  682 ARG cc_start: 0.8161 (mtm180) cc_final: 0.7957 (mtm-85)
REVERT: A  709 GLN cc_start: 0.8693 (tm-30) cc_final: 0.8245 (tm-30)
REVERT: A  712 TYR cc_start: 0.8591 (m-80) cc_final: 0.8236 (m-80)
REVERT: B   14 ASN cc_start: 0.7948 (m-40) cc_final: 0.7390 (m110)
REVERT: B  165 MET cc_start: 0.8986 (mmm) cc_final: 0.8565 (mpp)
REVERT: B  303 LYS cc_start: 0.7984 (mttt) cc_final: 0.7779 (mttt)
REVERT: B  378 MET cc_start: 0.8575 (mmt) cc_final: 0.8103 (mmt)
REVERT: B  397 GLN cc_start: 0.8824 (mp10) cc_final: 0.8383 (mp10)
REVERT: B  446 MET cc_start: 0.8921 (tpt) cc_final: 0.8698 (tpt)
REVERT: B  448 MET cc_start: 0.8808 (ttt) cc_final: 0.8244 (ttt)
REVERT: B  459 SER cc_start: 0.8685 (m) cc_final: 0.8211 (t)
REVERT: B  521 MET cc_start: 0.7893 (mmt) cc_final: 0.7396 (mmt)
REVERT: B  589 MET cc_start: 0.8254 (mmm) cc_final: 0.7968 (mmm)
REVERT: B  645 LEU cc_start: 0.8316 (mt) cc_final: 0.8105 (mm)
REVERT: B  690 MET cc_start: 0.8038 (ttm) cc_final: 0.7739 (ttm)
REVERT: B  709 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8441 (tm-30)
REVERT: B  712 TYR cc_start: 0.8704 (m-80) cc_final: 0.8406 (m-80)
  outliers start: 8
  outliers final: 6
  residues processed: 379
  average time/residue: 0.2200
  time to fit residues: 117.4992
Evaluate side-chains
  268 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 262
  time to evaluate  : 1.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  533 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 114 optimal weight:    9.9990
   chunk 103 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 69 optimal weight:    7.9990
   chunk 55 optimal weight:    0.6980
   chunk 106 optimal weight:    0.9980
   chunk 41 optimal weight:    0.6980
   chunk 64 optimal weight:    0.8980
   chunk 79 optimal weight:    5.9990
   chunk 123 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 151 ASN
A 232 HIS
A 489 GLN
A 542 HIS
A 607 HIS
A 608 GLN
B 151 ASN
B 232 HIS
B 340 GLN
B 489 GLN
B 495 ASN
B 567 ASN
B 607 HIS

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.143583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.115415 restraints weight = 18451.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.118659 restraints weight = 9824.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.120705 restraints weight = 6668.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.2345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11272  Z= 0.151
  Angle     :  0.720   8.415  15348  Z= 0.376
  Chirality :  0.045   0.174   1744
  Planarity :  0.006   0.058   1914
  Dihedral  :  7.268  49.420   1478
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.12 %
    Favored  : 89.88 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 10.17 %
    Favored  : 86.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -3.50 (0.20), residues: 1354
  helix: -1.48 (0.16), residues: 870
  sheet: -3.23 (1.07), residues: 30
  loop : -3.81 (0.24), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 525 
 HIS   0.006   0.002   HIS A 379 
 PHE   0.016   0.001   PHE B 428 
 TYR   0.022   0.002   TYR B 181 
 ARG   0.008   0.001   ARG A 698 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04084 (  557)
  hydrogen bonds       : angle       4.53465 ( 1653)
  covalent geometry    : bond        0.00343 (11272)
  covalent geometry    : angle       0.71968 (15348)

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

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

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  354 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 315
  time to evaluate  : 1.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ASN cc_start: 0.8001 (m-40) cc_final: 0.7590 (m110)
REVERT: A   36 ARG cc_start: 0.8224 (tpp-160) cc_final: 0.7782 (tpp-160)
REVERT: A  200 ASP cc_start: 0.8082 (t0) cc_final: 0.7762 (t0)
REVERT: A  257 ASN cc_start: 0.8761 (m-40) cc_final: 0.8464 (m110)
REVERT: A  370 SER cc_start: 0.8938 (p) cc_final: 0.8620 (t)
REVERT: A  415 ILE cc_start: 0.6866 (mm) cc_final: 0.6611 (mm)
REVERT: A  436 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8703 (mm)
REVERT: A  446 MET cc_start: 0.9108 (tpt) cc_final: 0.8644 (tpp)
REVERT: A  613 TYR cc_start: 0.9169 (OUTLIER) cc_final: 0.7056 (m-10)
REVERT: A  712 TYR cc_start: 0.8471 (m-80) cc_final: 0.8099 (m-80)
REVERT: B   36 ARG cc_start: 0.8251 (tpp-160) cc_final: 0.7754 (tpp-160)
REVERT: B  103 TRP cc_start: 0.7866 (t-100) cc_final: 0.7550 (t-100)
REVERT: B  182 GLU cc_start: 0.8171 (tt0) cc_final: 0.7916 (tt0)
REVERT: B  204 VAL cc_start: 0.9556 (t) cc_final: 0.9314 (m)
REVERT: B  257 ASN cc_start: 0.8737 (m-40) cc_final: 0.8481 (m110)
REVERT: B  415 ILE cc_start: 0.6578 (mm) cc_final: 0.6270 (mm)
REVERT: B  422 LYS cc_start: 0.8720 (ttpt) cc_final: 0.8206 (ttpt)
REVERT: B  446 MET cc_start: 0.9136 (tpt) cc_final: 0.8592 (tpp)
REVERT: B  459 SER cc_start: 0.8538 (m) cc_final: 0.8179 (t)
REVERT: B  712 TYR cc_start: 0.8601 (m-80) cc_final: 0.8261 (m-80)
  outliers start: 39
  outliers final: 26
  residues processed: 334
  average time/residue: 0.2192
  time to fit residues: 105.0826
Evaluate side-chains
  286 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 258
  time to evaluate  : 1.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  401 THR
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  449 SER
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  613 TYR
Chi-restraints excluded: chain A residue  694 LEU
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  112 ILE
Chi-restraints excluded: chain B residue  240 CYS
Chi-restraints excluded: chain B residue  258 TRP
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  370 SER
Chi-restraints excluded: chain B residue  384 PHE
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  401 THR
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  533 LEU
Chi-restraints excluded: chain B residue  587 THR
Chi-restraints excluded: chain B residue  613 TYR
Chi-restraints excluded: chain B residue  670 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 99 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 115 optimal weight:    7.9990
   chunk 20 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9980
   chunk 75 optimal weight:    0.6980
   chunk 47 optimal weight:    6.9990
   chunk 42 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 93 optimal weight:    7.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 151 ASN
A 567 ASN
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 151 ASN
B 340 GLN
B 567 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.141772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.114088 restraints weight = 18636.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.117347 restraints weight = 9869.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.119400 restraints weight = 6622.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.3004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11272  Z= 0.134
  Angle     :  0.664   8.582  15348  Z= 0.346
  Chirality :  0.044   0.175   1744
  Planarity :  0.006   0.057   1914
  Dihedral  :  6.768  53.259   1478
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  9.23 %
    Favored  : 90.62 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 14.74 %
    Favored  : 81.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -2.57 (0.22), residues: 1354
  helix: -0.75 (0.17), residues: 896
  sheet: -2.98 (1.12), residues: 30
  loop : -3.60 (0.26), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 525 
 HIS   0.005   0.001   HIS A 628 
 PHE   0.021   0.001   PHE B 428 
 TYR   0.018   0.002   TYR B 181 
 ARG   0.006   0.001   ARG A 698 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03437 (  557)
  hydrogen bonds       : angle       4.03024 ( 1653)
  covalent geometry    : bond        0.00309 (11272)
  covalent geometry    : angle       0.66362 (15348)

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

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

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  323 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 283
  time to evaluate  : 1.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ASN cc_start: 0.7950 (m-40) cc_final: 0.7519 (m110)
REVERT: A   36 ARG cc_start: 0.8332 (tpp-160) cc_final: 0.7541 (mmm160)
REVERT: A   78 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7536 (tm-30)
REVERT: A  182 GLU cc_start: 0.8188 (tt0) cc_final: 0.7911 (tt0)
REVERT: A  257 ASN cc_start: 0.8690 (m-40) cc_final: 0.8442 (m110)
REVERT: A  415 ILE cc_start: 0.6515 (mm) cc_final: 0.6090 (mm)
REVERT: A  446 MET cc_start: 0.9131 (tpt) cc_final: 0.8598 (tpp)
REVERT: A  459 SER cc_start: 0.8592 (m) cc_final: 0.8286 (t)
REVERT: A  488 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7999 (mt-10)
REVERT: A  512 LYS cc_start: 0.9119 (tttp) cc_final: 0.8799 (ttpt)
REVERT: A  531 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7878 (tm-30)
REVERT: A  570 GLU cc_start: 0.9121 (tm-30) cc_final: 0.8674 (tm-30)
REVERT: A  613 TYR cc_start: 0.9133 (OUTLIER) cc_final: 0.6962 (m-10)
REVERT: A  712 TYR cc_start: 0.8565 (m-80) cc_final: 0.8185 (m-80)
REVERT: B   36 ARG cc_start: 0.8418 (tpp-160) cc_final: 0.7544 (mmm160)
REVERT: B   78 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7465 (tm-30)
REVERT: B  103 TRP cc_start: 0.7898 (t-100) cc_final: 0.7665 (t-100)
REVERT: B  182 GLU cc_start: 0.8123 (tt0) cc_final: 0.7860 (tt0)
REVERT: B  415 ILE cc_start: 0.6441 (mm) cc_final: 0.5985 (mm)
REVERT: B  421 MET cc_start: 0.8092 (tpp) cc_final: 0.7694 (mmt)
REVERT: B  422 LYS cc_start: 0.8587 (ttpt) cc_final: 0.8239 (ttpt)
REVERT: B  440 PHE cc_start: 0.7760 (m-80) cc_final: 0.7535 (m-10)
REVERT: B  446 MET cc_start: 0.9095 (tpt) cc_final: 0.8611 (tpp)
REVERT: B  459 SER cc_start: 0.8571 (m) cc_final: 0.8226 (t)
REVERT: B  505 ILE cc_start: 0.8459 (tt) cc_final: 0.8256 (tt)
REVERT: B  531 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8389 (tm-30)
REVERT: B  613 TYR cc_start: 0.9075 (OUTLIER) cc_final: 0.7106 (m-10)
REVERT: B  712 TYR cc_start: 0.8613 (m-80) cc_final: 0.8221 (m-80)
  outliers start: 40
  outliers final: 20
  residues processed: 300
  average time/residue: 0.2074
  time to fit residues: 90.4678
Evaluate side-chains
  278 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 254
  time to evaluate  : 1.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  240 CYS
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  384 PHE
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  613 TYR
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  112 ILE
Chi-restraints excluded: chain B residue  240 CYS
Chi-restraints excluded: chain B residue  258 TRP
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  533 LEU
Chi-restraints excluded: chain B residue  587 THR
Chi-restraints excluded: chain B residue  613 TYR
Chi-restraints excluded: chain B residue  670 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 118 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 113 optimal weight:    0.8980
   chunk 120 optimal weight:    9.9990
   chunk 54 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 98 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0970
   chunk 114 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 122 optimal weight:    0.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 151 ASN
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 151 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.141851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.114372 restraints weight = 18510.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.117580 restraints weight = 9895.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.119591 restraints weight = 6670.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.3340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11272  Z= 0.138
  Angle     :  0.649   7.822  15348  Z= 0.335
  Chirality :  0.044   0.171   1744
  Planarity :  0.005   0.049   1914
  Dihedral  :  6.583  56.169   1478
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.04 %
    Favored  : 89.96 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 16.81 %
    Favored  : 80.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.16 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -1.95 (0.23), residues: 1354
  helix: -0.25 (0.17), residues: 890
  sheet: -2.85 (1.11), residues: 30
  loop : -3.38 (0.27), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 525 
 HIS   0.005   0.001   HIS A 628 
 PHE   0.023   0.001   PHE A 428 
 TYR   0.015   0.002   TYR A 181 
 ARG   0.008   0.001   ARG A 698 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03223 (  557)
  hydrogen bonds       : angle       3.89501 ( 1653)
  covalent geometry    : bond        0.00323 (11272)
  covalent geometry    : angle       0.64880 (15348)

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

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

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 266
  time to evaluate  : 1.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ASN cc_start: 0.7982 (m-40) cc_final: 0.7520 (m110)
REVERT: A   36 ARG cc_start: 0.8397 (tpp-160) cc_final: 0.7300 (mmm160)
REVERT: A   78 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7486 (tm-30)
REVERT: A  182 GLU cc_start: 0.8180 (tt0) cc_final: 0.7890 (tt0)
REVERT: A  190 GLN cc_start: 0.8266 (tp40) cc_final: 0.7959 (tp40)
REVERT: A  257 ASN cc_start: 0.8656 (m-40) cc_final: 0.8444 (m110)
REVERT: A  397 GLN cc_start: 0.8983 (mp10) cc_final: 0.8704 (mm-40)
REVERT: A  446 MET cc_start: 0.9156 (tpt) cc_final: 0.8685 (tpp)
REVERT: A  459 SER cc_start: 0.8631 (m) cc_final: 0.8309 (t)
REVERT: A  488 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7684 (mt-10)
REVERT: A  521 MET cc_start: 0.8892 (mmm) cc_final: 0.8482 (mmm)
REVERT: A  531 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8059 (tm-30)
REVERT: A  570 GLU cc_start: 0.9213 (tm-30) cc_final: 0.8807 (tm-30)
REVERT: A  613 TYR cc_start: 0.9087 (OUTLIER) cc_final: 0.7100 (m-10)
REVERT: A  712 TYR cc_start: 0.8539 (m-80) cc_final: 0.8154 (m-80)
REVERT: B   14 ASN cc_start: 0.7653 (m110) cc_final: 0.7405 (m110)
REVERT: B   36 ARG cc_start: 0.8418 (tpp-160) cc_final: 0.7294 (mmm160)
REVERT: B   78 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7402 (tm-30)
REVERT: B  182 GLU cc_start: 0.8198 (tt0) cc_final: 0.7931 (tt0)
REVERT: B  299 ASP cc_start: 0.6964 (m-30) cc_final: 0.6755 (t0)
REVERT: B  307 LYS cc_start: 0.8305 (mttt) cc_final: 0.8100 (ttmt)
REVERT: B  378 MET cc_start: 0.8567 (mmt) cc_final: 0.8253 (mmt)
REVERT: B  446 MET cc_start: 0.9160 (tpt) cc_final: 0.8717 (tpp)
REVERT: B  448 MET cc_start: 0.8636 (ttp) cc_final: 0.8295 (ttp)
REVERT: B  459 SER cc_start: 0.8580 (m) cc_final: 0.8256 (t)
REVERT: B  531 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8411 (tm-30)
REVERT: B  613 TYR cc_start: 0.9055 (OUTLIER) cc_final: 0.7030 (m-10)
REVERT: B  712 TYR cc_start: 0.8619 (m-80) cc_final: 0.8213 (m-80)
  outliers start: 36
  outliers final: 25
  residues processed: 289
  average time/residue: 0.1921
  time to fit residues: 82.3439
Evaluate side-chains
  280 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 251
  time to evaluate  : 1.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  240 CYS
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  384 PHE
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  613 TYR
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain A residue  690 MET
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  112 ILE
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  240 CYS
Chi-restraints excluded: chain B residue  258 TRP
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain B residue  384 PHE
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  533 LEU
Chi-restraints excluded: chain B residue  587 THR
Chi-restraints excluded: chain B residue  613 TYR
Chi-restraints excluded: chain B residue  670 HIS
Chi-restraints excluded: chain B residue  690 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 71 optimal weight:    0.8980
   chunk 119 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 88 optimal weight:    6.9990
   chunk 54 optimal weight:    0.7980
   chunk 114 optimal weight:    3.9990
   chunk 135 optimal weight:    0.7980
   chunk 89 optimal weight:    5.9990
   chunk 58 optimal weight:    0.5980
   chunk 66 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   overall best weight:    1.4182

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

Flipped N/Q/H residues before XYZ refinement:
** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 151 ASN
B 397 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.140142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.112407 restraints weight = 18533.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.115565 restraints weight = 10025.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.117539 restraints weight = 6811.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.3498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11272  Z= 0.157
  Angle     :  0.666   8.912  15348  Z= 0.339
  Chirality :  0.044   0.165   1744
  Planarity :  0.005   0.088   1914
  Dihedral  :  6.466  59.775   1478
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.49 %
    Favored  : 89.51 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 17.33 %
    Favored  : 78.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.16 %
    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: -1.58 (0.23), residues: 1354
  helix:  0.07 (0.18), residues: 890
  sheet: -2.81 (1.12), residues: 30
  loop : -3.30 (0.28), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 525 
 HIS   0.005   0.001   HIS A 628 
 PHE   0.024   0.001   PHE A 428 
 TYR   0.016   0.002   TYR A 468 
 ARG   0.005   0.001   ARG A 698 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03256 (  557)
  hydrogen bonds       : angle       3.83807 ( 1653)
  covalent geometry    : bond        0.00372 (11272)
  covalent geometry    : angle       0.66617 (15348)

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

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

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  311 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 262
  time to evaluate  : 1.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ASN cc_start: 0.8028 (m-40) cc_final: 0.7570 (m110)
REVERT: A   36 ARG cc_start: 0.8441 (tpp-160) cc_final: 0.7592 (mmm160)
REVERT: A   47 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.6905 (pp)
REVERT: A   78 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7466 (tm-30)
REVERT: A  182 GLU cc_start: 0.8162 (tt0) cc_final: 0.7860 (tt0)
REVERT: A  190 GLN cc_start: 0.8314 (tp40) cc_final: 0.7991 (tp40)
REVERT: A  397 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8806 (mm110)
REVERT: A  436 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8609 (mm)
REVERT: A  446 MET cc_start: 0.9189 (tpt) cc_final: 0.8784 (tpp)
REVERT: A  459 SER cc_start: 0.8680 (m) cc_final: 0.8366 (t)
REVERT: A  488 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7685 (mt-10)
REVERT: A  531 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8151 (tm-30)
REVERT: A  570 GLU cc_start: 0.9208 (tm-30) cc_final: 0.8852 (tm-30)
REVERT: A  591 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8897 (mp)
REVERT: A  613 TYR cc_start: 0.9109 (OUTLIER) cc_final: 0.7057 (m-10)
REVERT: A  712 TYR cc_start: 0.8617 (m-80) cc_final: 0.8159 (m-80)
REVERT: B   14 ASN cc_start: 0.7790 (m110) cc_final: 0.7491 (m110)
REVERT: B   36 ARG cc_start: 0.8422 (tpp-160) cc_final: 0.7544 (mmm160)
REVERT: B   47 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.6959 (pp)
REVERT: B   78 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7422 (tm-30)
REVERT: B  182 GLU cc_start: 0.8189 (tt0) cc_final: 0.7918 (tt0)
REVERT: B  190 GLN cc_start: 0.8324 (tp40) cc_final: 0.8025 (tp40)
REVERT: B  299 ASP cc_start: 0.7093 (m-30) cc_final: 0.6842 (t0)
REVERT: B  446 MET cc_start: 0.9211 (tpt) cc_final: 0.8832 (tpp)
REVERT: B  459 SER cc_start: 0.8630 (m) cc_final: 0.8332 (t)
REVERT: B  488 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8114 (mp0)
REVERT: B  531 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8229 (tm-30)
REVERT: B  591 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8982 (mp)
REVERT: B  613 TYR cc_start: 0.9174 (OUTLIER) cc_final: 0.7018 (m-10)
REVERT: B  712 TYR cc_start: 0.8642 (m-80) cc_final: 0.8190 (m-80)
  outliers start: 49
  outliers final: 29
  residues processed: 291
  average time/residue: 0.2166
  time to fit residues: 92.3726
Evaluate side-chains
  291 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 252
  time to evaluate  : 1.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  240 CYS
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  384 PHE
Chi-restraints excluded: chain A residue  386 THR
Chi-restraints excluded: chain A residue  397 GLN
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  613 TYR
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain A residue  661 LEU
Chi-restraints excluded: chain A residue  690 MET
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  112 ILE
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  240 CYS
Chi-restraints excluded: chain B residue  258 TRP
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain B residue  384 PHE
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  533 LEU
Chi-restraints excluded: chain B residue  587 THR
Chi-restraints excluded: chain B residue  591 LEU
Chi-restraints excluded: chain B residue  613 TYR
Chi-restraints excluded: chain B residue  670 HIS
Chi-restraints excluded: chain B residue  690 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 134 optimal weight:    0.2980
   chunk 79 optimal weight:    5.9990
   chunk 6 optimal weight:    6.9990
   chunk 92 optimal weight:    8.9990
   chunk 38 optimal weight:    1.9990
   chunk 87 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 96 optimal weight:    0.5980
   chunk 75 optimal weight:    0.9990
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
A 151 ASN
** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 151 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.139031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.111233 restraints weight = 18699.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.114464 restraints weight = 9950.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.116512 restraints weight = 6697.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.3736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11272  Z= 0.134
  Angle     :  0.658   9.024  15348  Z= 0.334
  Chirality :  0.044   0.162   1744
  Planarity :  0.005   0.081   1914
  Dihedral  :  6.193  55.070   1478
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.68 %
    Favored  : 90.32 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 18.28 %
    Favored  : 77.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.16 %
    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: -1.38 (0.23), residues: 1354
  helix:  0.25 (0.18), residues: 894
  sheet: -2.76 (1.12), residues: 30
  loop : -3.32 (0.28), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 525 
 HIS   0.005   0.001   HIS A 628 
 PHE   0.025   0.001   PHE A 428 
 TYR   0.014   0.002   TYR A 468 
 ARG   0.006   0.001   ARG A 698 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03124 (  557)
  hydrogen bonds       : angle       3.81013 ( 1653)
  covalent geometry    : bond        0.00316 (11272)
  covalent geometry    : angle       0.65832 (15348)

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

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

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 261
  time to evaluate  : 1.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ASN cc_start: 0.8021 (m-40) cc_final: 0.7544 (m110)
REVERT: A   36 ARG cc_start: 0.8472 (tpp-160) cc_final: 0.7564 (mmm160)
REVERT: A   47 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.6972 (pp)
REVERT: A   78 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7444 (tm-30)
REVERT: A  190 GLN cc_start: 0.8374 (tp40) cc_final: 0.8025 (tp40)
REVERT: A  250 LYS cc_start: 0.8885 (tttt) cc_final: 0.8648 (ttpt)
REVERT: A  307 LYS cc_start: 0.8452 (mttt) cc_final: 0.8133 (ttmt)
REVERT: A  378 MET cc_start: 0.8293 (mmm) cc_final: 0.8074 (mmm)
REVERT: A  397 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8758 (mm-40)
REVERT: A  436 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8590 (mm)
REVERT: A  446 MET cc_start: 0.9141 (tpt) cc_final: 0.8717 (tpp)
REVERT: A  459 SER cc_start: 0.8666 (m) cc_final: 0.8346 (t)
REVERT: A  488 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7740 (mt-10)
REVERT: A  531 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8196 (tm-30)
REVERT: A  570 GLU cc_start: 0.9219 (tm-30) cc_final: 0.8905 (tm-30)
REVERT: A  613 TYR cc_start: 0.9096 (OUTLIER) cc_final: 0.7043 (m-10)
REVERT: A  712 TYR cc_start: 0.8614 (m-80) cc_final: 0.8128 (m-80)
REVERT: B   14 ASN cc_start: 0.7912 (m110) cc_final: 0.7508 (m110)
REVERT: B   36 ARG cc_start: 0.8411 (tpp-160) cc_final: 0.7609 (mmm160)
REVERT: B   47 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.6932 (pp)
REVERT: B   78 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7341 (tm-30)
REVERT: B  182 GLU cc_start: 0.8217 (tt0) cc_final: 0.7944 (tt0)
REVERT: B  190 GLN cc_start: 0.8395 (tp40) cc_final: 0.8039 (tp40)
REVERT: B  299 ASP cc_start: 0.6985 (m-30) cc_final: 0.6774 (t0)
REVERT: B  421 MET cc_start: 0.8157 (tpp) cc_final: 0.7814 (mmt)
REVERT: B  446 MET cc_start: 0.9200 (tpt) cc_final: 0.8784 (tpp)
REVERT: B  459 SER cc_start: 0.8638 (m) cc_final: 0.8332 (t)
REVERT: B  488 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7017 (mt-10)
REVERT: B  512 LYS cc_start: 0.9088 (tttp) cc_final: 0.8333 (tttp)
REVERT: B  521 MET cc_start: 0.9100 (mmp) cc_final: 0.8859 (mmm)
REVERT: B  531 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8208 (tm-30)
REVERT: B  613 TYR cc_start: 0.9126 (OUTLIER) cc_final: 0.6969 (m-10)
REVERT: B  712 TYR cc_start: 0.8616 (m-80) cc_final: 0.8171 (m-80)
  outliers start: 49
  outliers final: 31
  residues processed: 290
  average time/residue: 0.1876
  time to fit residues: 81.1394
Evaluate side-chains
  294 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 255
  time to evaluate  : 1.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  240 CYS
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  384 PHE
Chi-restraints excluded: chain A residue  386 THR
Chi-restraints excluded: chain A residue  397 GLN
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  613 TYR
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain A residue  661 LEU
Chi-restraints excluded: chain A residue  694 LEU
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  112 ILE
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  240 CYS
Chi-restraints excluded: chain B residue  258 TRP
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  384 PHE
Chi-restraints excluded: chain B residue  386 THR
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  501 ILE
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  534 MET
Chi-restraints excluded: chain B residue  587 THR
Chi-restraints excluded: chain B residue  613 TYR
Chi-restraints excluded: chain B residue  645 LEU
Chi-restraints excluded: chain B residue  661 LEU
Chi-restraints excluded: chain B residue  670 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 11 optimal weight:    0.0980
   chunk 5 optimal weight:    0.0020
   chunk 28 optimal weight:    7.9990
   chunk 51 optimal weight:    0.4980
   chunk 77 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 127 optimal weight:    0.6980
   chunk 54 optimal weight:    0.5980
   chunk 87 optimal weight:    0.8980
   chunk 56 optimal weight:    0.8980
   overall best weight:    0.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 151 ASN
** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 151 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.140906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.112947 restraints weight = 18969.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.116266 restraints weight = 9939.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.118383 restraints weight = 6609.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.4000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11272  Z= 0.114
  Angle     :  0.641   9.117  15348  Z= 0.322
  Chirality :  0.043   0.161   1744
  Planarity :  0.005   0.088   1914
  Dihedral  :  5.805  47.323   1476
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.12 %
    Favored  : 89.88 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 20.26 %
    Favored  : 76.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.16 %
    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: -1.06 (0.24), residues: 1354
  helix:  0.52 (0.18), residues: 890
  sheet: -2.71 (1.09), residues: 30
  loop : -3.20 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 525 
 HIS   0.005   0.001   HIS A 628 
 PHE   0.026   0.001   PHE A 428 
 TYR   0.012   0.001   TYR A 468 
 ARG   0.007   0.001   ARG B 698 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02922 (  557)
  hydrogen bonds       : angle       3.75468 ( 1653)
  covalent geometry    : bond        0.00257 (11272)
  covalent geometry    : angle       0.64112 (15348)

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

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

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 287
  time to evaluate  : 1.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ASN cc_start: 0.7998 (m-40) cc_final: 0.7497 (m110)
REVERT: A   36 ARG cc_start: 0.8376 (tpp-160) cc_final: 0.7208 (mmm160)
REVERT: A   78 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7385 (tm-30)
REVERT: A  182 GLU cc_start: 0.8249 (tt0) cc_final: 0.8005 (tt0)
REVERT: A  250 LYS cc_start: 0.8785 (tttt) cc_final: 0.8498 (ttpp)
REVERT: A  307 LYS cc_start: 0.8323 (mttt) cc_final: 0.8061 (ttmt)
REVERT: A  370 SER cc_start: 0.8988 (p) cc_final: 0.8738 (t)
REVERT: A  422 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8075 (ttpt)
REVERT: A  446 MET cc_start: 0.9033 (tpt) cc_final: 0.8577 (tpp)
REVERT: A  459 SER cc_start: 0.8680 (m) cc_final: 0.8248 (t)
REVERT: A  488 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7884 (mt-10)
REVERT: A  531 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8154 (tm-30)
REVERT: A  570 GLU cc_start: 0.9229 (tm-30) cc_final: 0.8897 (tm-30)
REVERT: A  591 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8657 (mp)
REVERT: A  613 TYR cc_start: 0.8951 (OUTLIER) cc_final: 0.7017 (m-10)
REVERT: A  712 TYR cc_start: 0.8589 (m-80) cc_final: 0.8159 (m-80)
REVERT: B   14 ASN cc_start: 0.8030 (m110) cc_final: 0.7627 (m110)
REVERT: B   36 ARG cc_start: 0.8434 (tpp-160) cc_final: 0.7567 (mmm160)
REVERT: B  190 GLN cc_start: 0.8361 (tp40) cc_final: 0.8006 (tp40)
REVERT: B  420 PHE cc_start: 0.7451 (t80) cc_final: 0.6875 (m-10)
REVERT: B  421 MET cc_start: 0.8151 (tpp) cc_final: 0.7825 (mmt)
REVERT: B  446 MET cc_start: 0.9176 (tpt) cc_final: 0.8740 (tpp)
REVERT: B  459 SER cc_start: 0.8640 (m) cc_final: 0.8286 (t)
REVERT: B  488 GLU cc_start: 0.8408 (mt-10) cc_final: 0.7911 (mt-10)
REVERT: B  531 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8172 (tm-30)
REVERT: B  613 TYR cc_start: 0.8995 (OUTLIER) cc_final: 0.6951 (m-10)
REVERT: B  650 HIS cc_start: 0.5712 (m-70) cc_final: 0.5462 (m90)
REVERT: B  712 TYR cc_start: 0.8657 (m-80) cc_final: 0.8223 (m-80)
  outliers start: 38
  outliers final: 24
  residues processed: 310
  average time/residue: 0.2448
  time to fit residues: 114.9456
Evaluate side-chains
  285 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 255
  time to evaluate  : 1.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  384 PHE
Chi-restraints excluded: chain A residue  386 THR
Chi-restraints excluded: chain A residue  422 LYS
Chi-restraints excluded: chain A residue  501 ILE
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  613 TYR
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain A residue  661 LEU
Chi-restraints excluded: chain B residue   35 ASP
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  240 CYS
Chi-restraints excluded: chain B residue  258 TRP
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  384 PHE
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  501 ILE
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  587 THR
Chi-restraints excluded: chain B residue  613 TYR
Chi-restraints excluded: chain B residue  645 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 32 optimal weight:    0.0030
   chunk 73 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 89 optimal weight:    6.9990
   chunk 61 optimal weight:    4.9990
   chunk 63 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 124 optimal weight:    3.9990
   chunk 31 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.6990

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

Flipped N/Q/H residues before XYZ refinement:
** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 608 GLN
B 151 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.142789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.115249 restraints weight = 18469.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.118523 restraints weight = 9753.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.120582 restraints weight = 6535.820|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.4165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11272  Z= 0.125
  Angle     :  0.662   8.835  15348  Z= 0.333
  Chirality :  0.044   0.154   1744
  Planarity :  0.005   0.071   1914
  Dihedral  :  5.652  42.857   1476
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.19 %
    Favored  : 89.81 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 21.12 %
    Favored  : 75.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.16 %
    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: -0.94 (0.24), residues: 1354
  helix:  0.62 (0.18), residues: 890
  sheet: -2.76 (1.07), residues: 30
  loop : -3.18 (0.28), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 525 
 HIS   0.005   0.001   HIS A 628 
 PHE   0.026   0.001   PHE A 428 
 TYR   0.013   0.001   TYR A 102 
 ARG   0.004   0.000   ARG B 198 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02986 (  557)
  hydrogen bonds       : angle       3.80559 ( 1653)
  covalent geometry    : bond        0.00292 (11272)
  covalent geometry    : angle       0.66164 (15348)

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

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

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 253
  time to evaluate  : 1.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ASN cc_start: 0.7965 (m-40) cc_final: 0.7471 (m110)
REVERT: A   36 ARG cc_start: 0.8266 (tpp-160) cc_final: 0.7652 (tpp80)
REVERT: A   47 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7010 (pp)
REVERT: A   78 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7306 (tm-30)
REVERT: A  161 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8278 (t)
REVERT: A  182 GLU cc_start: 0.8183 (tt0) cc_final: 0.7934 (tt0)
REVERT: A  250 LYS cc_start: 0.8798 (tttt) cc_final: 0.8511 (ttpp)
REVERT: A  307 LYS cc_start: 0.8307 (mttt) cc_final: 0.8072 (ttmt)
REVERT: A  378 MET cc_start: 0.8477 (mmm) cc_final: 0.8138 (mmm)
REVERT: A  422 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8043 (ttpt)
REVERT: A  446 MET cc_start: 0.9088 (tpt) cc_final: 0.8643 (tpp)
REVERT: A  459 SER cc_start: 0.8624 (m) cc_final: 0.8263 (t)
REVERT: A  488 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7810 (mt-10)
REVERT: A  531 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8166 (tm-30)
REVERT: A  570 GLU cc_start: 0.9216 (tm-30) cc_final: 0.8895 (tm-30)
REVERT: A  613 TYR cc_start: 0.8984 (OUTLIER) cc_final: 0.7052 (m-10)
REVERT: A  712 TYR cc_start: 0.8653 (m-80) cc_final: 0.8190 (m-80)
REVERT: B   14 ASN cc_start: 0.7922 (m110) cc_final: 0.7595 (m110)
REVERT: B   36 ARG cc_start: 0.8295 (tpp-160) cc_final: 0.7831 (tpp80)
REVERT: B  190 GLN cc_start: 0.8355 (tp40) cc_final: 0.7983 (tp40)
REVERT: B  421 MET cc_start: 0.8222 (tpp) cc_final: 0.7852 (mmt)
REVERT: B  446 MET cc_start: 0.9206 (tpt) cc_final: 0.8746 (tpp)
REVERT: B  459 SER cc_start: 0.8640 (m) cc_final: 0.8295 (t)
REVERT: B  488 GLU cc_start: 0.8389 (mt-10) cc_final: 0.6960 (mt-10)
REVERT: B  512 LYS cc_start: 0.9145 (tttp) cc_final: 0.8264 (tttp)
REVERT: B  531 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8114 (tm-30)
REVERT: B  613 TYR cc_start: 0.9040 (OUTLIER) cc_final: 0.7412 (m-10)
REVERT: B  712 TYR cc_start: 0.8709 (m-80) cc_final: 0.8249 (m-80)
  outliers start: 42
  outliers final: 28
  residues processed: 280
  average time/residue: 0.2046
  time to fit residues: 85.6189
Evaluate side-chains
  276 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 241
  time to evaluate  : 1.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  240 CYS
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  384 PHE
Chi-restraints excluded: chain A residue  386 THR
Chi-restraints excluded: chain A residue  422 LYS
Chi-restraints excluded: chain A residue  501 ILE
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  534 MET
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  613 TYR
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain A residue  661 LEU
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  101 ILE
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  240 CYS
Chi-restraints excluded: chain B residue  258 TRP
Chi-restraints excluded: chain B residue  264 LEU
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  384 PHE
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  501 ILE
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  587 THR
Chi-restraints excluded: chain B residue  613 TYR
Chi-restraints excluded: chain B residue  645 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 125 optimal weight:    1.9990
   chunk 86 optimal weight:    0.1980
   chunk 13 optimal weight:    0.0870
   chunk 120 optimal weight:    5.9990
   chunk 73 optimal weight:    0.7980
   chunk 9 optimal weight:    0.0980
   chunk 75 optimal weight:    0.5980
   chunk 50 optimal weight:    0.5980
   chunk 68 optimal weight:   10.0000
   chunk 100 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.3158

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

Flipped N/Q/H residues before XYZ refinement:
A  14 ASN
B 151 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.145771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.118244 restraints weight = 18659.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.121492 restraints weight = 9925.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.123531 restraints weight = 6717.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.4402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11272  Z= 0.116
  Angle     :  0.658   9.639  15348  Z= 0.328
  Chirality :  0.043   0.166   1744
  Planarity :  0.005   0.077   1914
  Dihedral  :  5.412  43.860   1474
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.38 %
    Favored  : 90.62 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 22.07 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.16 %
    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: -0.74 (0.24), residues: 1354
  helix:  0.81 (0.18), residues: 878
  sheet: -2.72 (1.08), residues: 30
  loop : -3.09 (0.28), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 525 
 HIS   0.005   0.001   HIS A 628 
 PHE   0.031   0.001   PHE B 428 
 TYR   0.014   0.001   TYR B 102 
 ARG   0.004   0.000   ARG A 198 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02917 (  557)
  hydrogen bonds       : angle       3.82268 ( 1653)
  covalent geometry    : bond        0.00259 (11272)
  covalent geometry    : angle       0.65845 (15348)

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

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

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 261
  time to evaluate  : 1.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 ARG cc_start: 0.8273 (tpp-160) cc_final: 0.7781 (tpp80)
REVERT: A  161 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8258 (t)
REVERT: A  370 SER cc_start: 0.8912 (p) cc_final: 0.8673 (t)
REVERT: A  422 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.7999 (ttpt)
REVERT: A  446 MET cc_start: 0.9056 (tpt) cc_final: 0.8557 (tpp)
REVERT: A  459 SER cc_start: 0.8627 (m) cc_final: 0.8291 (t)
REVERT: A  511 MET cc_start: 0.8428 (mmm) cc_final: 0.8121 (mmm)
REVERT: A  531 GLU cc_start: 0.8343 (pp20) cc_final: 0.8070 (tm-30)
REVERT: A  570 GLU cc_start: 0.9199 (tm-30) cc_final: 0.8807 (tm-30)
REVERT: A  613 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.7111 (m-10)
REVERT: A  712 TYR cc_start: 0.8613 (m-80) cc_final: 0.8054 (m-80)
REVERT: B   36 ARG cc_start: 0.8197 (tpp-160) cc_final: 0.7723 (tpp80)
REVERT: B  297 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8342 (mm-30)
REVERT: B  378 MET cc_start: 0.6990 (mmt) cc_final: 0.6727 (tpp)
REVERT: B  421 MET cc_start: 0.8114 (tpp) cc_final: 0.7817 (mmt)
REVERT: B  446 MET cc_start: 0.9193 (tpt) cc_final: 0.8646 (tpp)
REVERT: B  459 SER cc_start: 0.8584 (m) cc_final: 0.8250 (t)
REVERT: B  521 MET cc_start: 0.9031 (mmp) cc_final: 0.8447 (mmm)
REVERT: B  531 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8057 (tm-30)
REVERT: B  613 TYR cc_start: 0.8912 (OUTLIER) cc_final: 0.7472 (m-10)
REVERT: B  712 TYR cc_start: 0.8622 (m-80) cc_final: 0.8227 (m-80)
  outliers start: 34
  outliers final: 20
  residues processed: 278
  average time/residue: 0.1964
  time to fit residues: 82.9983
Evaluate side-chains
  272 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 246
  time to evaluate  : 1.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  384 PHE
Chi-restraints excluded: chain A residue  422 LYS
Chi-restraints excluded: chain A residue  501 ILE
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  613 TYR
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain A residue  661 LEU
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  258 TRP
Chi-restraints excluded: chain B residue  264 LEU
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  384 PHE
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  501 ILE
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  587 THR
Chi-restraints excluded: chain B residue  613 TYR
Chi-restraints excluded: chain B residue  645 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   chunk 118 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 99 optimal weight:    0.5980
   chunk 75 optimal weight:    0.3980
   chunk 19 optimal weight:    0.7980
   chunk 55 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** B 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.144270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.116845 restraints weight = 18516.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.120096 restraints weight = 9839.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.122133 restraints weight = 6628.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.4511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11272  Z= 0.129
  Angle     :  0.692   8.977  15348  Z= 0.347
  Chirality :  0.044   0.164   1744
  Planarity :  0.005   0.069   1914
  Dihedral  :  5.278  41.823   1471
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.45 %
    Favored  : 90.55 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 22.16 %
    Favored  : 75.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.16 %
    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: -0.66 (0.24), residues: 1354
  helix:  0.82 (0.18), residues: 888
  sheet: -2.67 (1.08), residues: 30
  loop : -3.01 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 525 
 HIS   0.005   0.001   HIS A 628 
 PHE   0.032   0.001   PHE B 428 
 TYR   0.011   0.001   TYR A 468 
 ARG   0.004   0.000   ARG A 198 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02983 (  557)
  hydrogen bonds       : angle       3.84991 ( 1653)
  covalent geometry    : bond        0.00307 (11272)
  covalent geometry    : angle       0.69211 (15348)

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

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

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2708 Ramachandran restraints generated.
    1354 Oldfield, 0 Emsley, 1354 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 245
  time to evaluate  : 1.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ASN cc_start: 0.8148 (m110) cc_final: 0.7800 (m110)
REVERT: A   36 ARG cc_start: 0.8269 (tpp-160) cc_final: 0.7803 (tpp80)
REVERT: A   47 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7029 (pp)
REVERT: A  126 THR cc_start: 0.8081 (p) cc_final: 0.7847 (t)
REVERT: A  307 LYS cc_start: 0.8267 (mttt) cc_final: 0.7916 (mtpt)
REVERT: A  370 SER cc_start: 0.8948 (p) cc_final: 0.8718 (t)
REVERT: A  422 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8004 (ttpt)
REVERT: A  446 MET cc_start: 0.9068 (tpt) cc_final: 0.8508 (tpp)
REVERT: A  459 SER cc_start: 0.8650 (m) cc_final: 0.8377 (t)
REVERT: A  488 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7640 (mp0)
REVERT: A  511 MET cc_start: 0.8301 (mmm) cc_final: 0.8086 (mmm)
REVERT: A  512 LYS cc_start: 0.9066 (tttp) cc_final: 0.8380 (tptm)
REVERT: A  570 GLU cc_start: 0.9201 (tm-30) cc_final: 0.8921 (tm-30)
REVERT: A  608 GLN cc_start: 0.8571 (mm110) cc_final: 0.8211 (mm-40)
REVERT: A  613 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.7123 (m-10)
REVERT: A  712 TYR cc_start: 0.8640 (m-80) cc_final: 0.8087 (m-80)
REVERT: B   36 ARG cc_start: 0.8220 (tpp-160) cc_final: 0.7752 (tpp80)
REVERT: B   47 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.6935 (pp)
REVERT: B   86 GLU cc_start: 0.8414 (tp30) cc_final: 0.8205 (tp30)
REVERT: B  307 LYS cc_start: 0.8112 (mttt) cc_final: 0.7827 (mtpt)
REVERT: B  421 MET cc_start: 0.8133 (tpp) cc_final: 0.7829 (mmt)
REVERT: B  446 MET cc_start: 0.9192 (tpt) cc_final: 0.8654 (tpp)
REVERT: B  459 SER cc_start: 0.8630 (m) cc_final: 0.8249 (t)
REVERT: B  488 GLU cc_start: 0.8480 (mp0) cc_final: 0.7041 (mp0)
REVERT: B  512 LYS cc_start: 0.9175 (tttp) cc_final: 0.8454 (tppt)
REVERT: B  531 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8061 (tm-30)
REVERT: B  613 TYR cc_start: 0.8956 (OUTLIER) cc_final: 0.7434 (m-10)
REVERT: B  712 TYR cc_start: 0.8696 (m-80) cc_final: 0.8239 (m-80)
  outliers start: 32
  outliers final: 23
  residues processed: 265
  average time/residue: 0.1793
  time to fit residues: 71.5283
Evaluate side-chains
  270 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 241
  time to evaluate  : 1.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  258 TRP
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  384 PHE
Chi-restraints excluded: chain A residue  422 LYS
Chi-restraints excluded: chain A residue  501 ILE
Chi-restraints excluded: chain A residue  587 THR
Chi-restraints excluded: chain A residue  613 TYR
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain A residue  645 LEU
Chi-restraints excluded: chain A residue  661 LEU
Chi-restraints excluded: chain A residue  713 VAL
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  258 TRP
Chi-restraints excluded: chain B residue  264 LEU
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  384 PHE
Chi-restraints excluded: chain B residue  501 ILE
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  587 THR
Chi-restraints excluded: chain B residue  594 ILE
Chi-restraints excluded: chain B residue  613 TYR
Chi-restraints excluded: chain B residue  645 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 97 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 102 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0170
   chunk 122 optimal weight:    0.5980
   chunk 43 optimal weight:    3.9990
   chunk 54 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   chunk 64 optimal weight:    0.3980
   chunk 73 optimal weight:    3.9990
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
B 151 ASN
** B 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.144867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.117553 restraints weight = 18404.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.120789 restraints weight = 9796.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.122847 restraints weight = 6610.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.4608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  11272  Z= 0.122
  Angle     :  0.683   8.780  15348  Z= 0.341
  Chirality :  0.044   0.165   1744
  Planarity :  0.005   0.073   1914
  Dihedral  :  5.195  41.792   1471
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.82 %
    Favored  : 90.18 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 22.84 %
    Favored  : 74.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.16 %
    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: -0.60 (0.24), residues: 1354
  helix:  0.85 (0.18), residues: 888
  sheet: -2.62 (1.09), residues: 30
  loop : -2.94 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 525 
 HIS   0.005   0.001   HIS A 628 
 PHE   0.029   0.001   PHE B 428 
 TYR   0.012   0.001   TYR B 102 
 ARG   0.004   0.000   ARG A 198 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02946 (  557)
  hydrogen bonds       : angle       3.85200 ( 1653)
  covalent geometry    : bond        0.00285 (11272)
  covalent geometry    : angle       0.68293 (15348)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4235.26 seconds
wall clock time: 76 minutes 2.82 seconds (4562.82 seconds total)