Starting phenix.real_space_refine
on Wed Jun 11 14:34:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w7a_37337/06_2025/8w7a_37337.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w7a_37337/06_2025/8w7a_37337.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w7a_37337/06_2025/8w7a_37337.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w7a_37337/06_2025/8w7a_37337.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w7a_37337/06_2025/8w7a_37337.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w7a_37337/06_2025/8w7a_37337.cif"
  }
  resolution = 3.77
  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=   0.003 sd=   0.056
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      30      5.16       5
     C    8419      2.51       5
     N    2142      2.21       5
     O    2423      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 54 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 13017
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 6404
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 782, 6404
          Classifications: {'peptide': 782}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 23, 'TRANS': 758}
          Chain breaks: 7
    Chain: "B"
      Number of atoms: 6581
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 804, 6581
          Classifications: {'peptide': 804}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 22, 'TRANS': 781}
          Chain breaks: 6
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 8.11, per 1000 atoms: 0.62
  Number of scatterers: 13017
  At special positions: 0
  Unit cell: (102.102, 104.676, 135.564, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      30     16.00
     P       3     15.00
     O    2423      8.00
     N    2142      7.00
     C    8419      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.17
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2960

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 9 sheets defined
      40.6% alpha, 3.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 71 through 78
      removed outlier: 3.683A  pdb=" N   ASP A  75 " --> pdb=" O   GLU A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 100
    Processing helix  chain 'A' and resid 126 through 133
      removed outlier: 3.916A  pdb=" N   GLU A 130 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 272
      removed outlier: 3.779A  pdb=" N   ALA A 266 " --> pdb=" O   SER A 262 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   SER A 267 " --> pdb=" O   GLU A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 314
    Processing helix  chain 'A' and resid 326 through 342
      removed outlier: 3.632A  pdb=" N   SER A 331 " --> pdb=" O   LEU A 327 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   LYS A 332 " --> pdb=" O   LEU A 328 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   ILE A 333 " --> pdb=" O   ARG A 329 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   ILE A 338 " --> pdb=" O   VAL A 334 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ASN A 342 " --> pdb=" O   ILE A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 413
      removed outlier: 4.905A  pdb=" N   GLY A 407 " --> pdb=" O   ILE A 403 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ILE A 408 " --> pdb=" O   ASP A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 425
      removed outlier: 3.868A  pdb=" N   ASP A 424 " --> pdb=" O   THR A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 431 through 445
      removed outlier: 4.226A  pdb=" N   GLY A 437 " --> pdb=" O   THR A 433 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   LYS A 438 " --> pdb=" O   ARG A 434 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   LYS A 439 " --> pdb=" O   ILE A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 452
    Processing helix  chain 'A' and resid 453 through 461
    Processing helix  chain 'A' and resid 488 through 509
      removed outlier: 4.252A  pdb=" N   ILE A 492 " --> pdb=" O   SER A 488 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ILE A 497 " --> pdb=" O   GLN A 493 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ARG A 501 " --> pdb=" O   ILE A 497 " (cutoff:3.500A)
      removed outlier: 4.671A  pdb=" N   GLY A 502 " --> pdb=" O   LYS A 498 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   PHE A 503 " --> pdb=" O   LEU A 499 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   THR A 504 " --> pdb=" O   LEU A 500 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   THR A 506 " --> pdb=" O   GLY A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 526
      removed outlier: 3.651A  pdb=" N   LEU A 526 " --> pdb=" O   TYR A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 550
      removed outlier: 3.703A  pdb=" N   LEU A 546 " --> pdb=" O   SER A 542 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ALA A 547 " --> pdb=" O   TYR A 543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 572
      removed outlier: 3.884A  pdb=" N   ILE A 561 " --> pdb=" O   ASP A 557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 584 through 595
      removed outlier: 4.437A  pdb=" N   THR A 588 " --> pdb=" O   GLY A 584 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ILE A 589 " --> pdb=" O   LYS A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 597 through 614
      removed outlier: 5.748A  pdb=" N   ILE A 610 " --> pdb=" O   THR A 606 " (cutoff:3.500A)
      removed outlier: 5.408A  pdb=" N   GLU A 611 " --> pdb=" O   THR A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 624 through 639
      removed outlier: 3.993A  pdb=" N   VAL A 631 " --> pdb=" O   GLY A 627 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   GLY A 639 " --> pdb=" O   PHE A 635 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 642 through 661
      removed outlier: 4.093A  pdb=" N   LEU A 650 " --> pdb=" O   GLY A 646 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ILE A 661 " --> pdb=" O   THR A 657 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 691 through 706
      removed outlier: 3.566A  pdb=" N   ALA A 695 " --> pdb=" O   HIS A 691 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU A 697 " --> pdb=" O   GLY A 693 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   TYR A 702 " --> pdb=" O   PHE A 698 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   LYS A 703 " --> pdb=" O   GLY A 699 " (cutoff:3.500A)
      removed outlier: 5.121A  pdb=" N   LEU A 704 " --> pdb=" O   GLU A 700 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 707 through 720
      removed outlier: 3.700A  pdb=" N   LYS A 711 " --> pdb=" O   GLU A 707 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   LEU A 714 " --> pdb=" O   TYR A 710 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   GLU A 715 " --> pdb=" O   LYS A 711 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   LEU A 716 " --> pdb=" O   ASN A 712 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 723
      No H-bonds generated for 'chain 'A' and resid 721 through 723'
    Processing helix  chain 'A' and resid 748 through 759
      removed outlier: 4.366A  pdb=" N   LEU A 752 " --> pdb=" O   GLY A 748 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 764 through 769
    Processing helix  chain 'A' and resid 770 through 778
    Processing helix  chain 'A' and resid 791 through 800
      removed outlier: 3.568A  pdb=" N   ALA A 798 " --> pdb=" O   GLY A 794 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ASN A 799 " --> pdb=" O   LEU A 795 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 808 through 818
      removed outlier: 4.188A  pdb=" N   LYS A 814 " --> pdb=" O   SER A 810 " (cutoff:3.500A)
      removed outlier: 4.878A  pdb=" N   LEU A 815 " --> pdb=" O   GLY A 811 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 819 through 821
      No H-bonds generated for 'chain 'A' and resid 819 through 821'
    Processing helix  chain 'A' and resid 847 through 861
      removed outlier: 3.937A  pdb=" N   VAL A 851 " --> pdb=" O   GLY A 847 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   VAL A 856 " --> pdb=" O   ALA A 852 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   MET A 859 " --> pdb=" O   LEU A 855 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 74
    Processing helix  chain 'B' and resid 77 through 82
      removed outlier: 4.249A  pdb=" N   GLU B  82 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 100
    Processing helix  chain 'B' and resid 123 through 128
      removed outlier: 3.630A  pdb=" N   GLN B 127 " --> pdb=" O   GLU B 123 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   ARG B 128 " --> pdb=" O   SER B 124 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 123 through 128'
    Processing helix  chain 'B' and resid 260 through 265
    Processing helix  chain 'B' and resid 270 through 275
      removed outlier: 3.889A  pdb=" N   LEU B 275 " --> pdb=" O   ALA B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 313
      removed outlier: 3.765A  pdb=" N   THR B 311 " --> pdb=" O   ASN B 307 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 335 through 344
      removed outlier: 3.819A  pdb=" N   ASN B 342 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 412
      removed outlier: 3.607A  pdb=" N   ILE B 411 " --> pdb=" O   GLY B 407 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ALA B 412 " --> pdb=" O   ILE B 408 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 407 through 412'
    Processing helix  chain 'B' and resid 420 through 425
      removed outlier: 3.898A  pdb=" N   ASP B 424 " --> pdb=" O   THR B 421 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 431 through 445
      removed outlier: 5.022A  pdb=" N   GLY B 437 " --> pdb=" O   THR B 433 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   LYS B 438 " --> pdb=" O   ARG B 434 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   LYS B 439 " --> pdb=" O   ILE B 435 " (cutoff:3.500A)
      removed outlier: 4.781A  pdb=" N   LEU B 440 " --> pdb=" O   GLU B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 465
      removed outlier: 3.902A  pdb=" N   ASP B 452 " --> pdb=" O   ARG B 448 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   TYR B 453 " --> pdb=" O   GLU B 449 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   LEU B 461 " --> pdb=" O   LEU B 457 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 488 through 498
      removed outlier: 3.816A  pdb=" N   ILE B 492 " --> pdb=" O   SER B 488 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   PHE B 495 " --> pdb=" O   ASP B 491 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   ILE B 496 " --> pdb=" O   ILE B 492 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 500 through 505
    Processing helix  chain 'B' and resid 507 through 512
    Processing helix  chain 'B' and resid 536 through 550
      removed outlier: 3.527A  pdb=" N   LEU B 540 " --> pdb=" O   ASP B 536 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLN B 544 " --> pdb=" O   LEU B 540 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   GLN B 545 " --> pdb=" O   TRP B 541 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LEU B 546 " --> pdb=" O   SER B 542 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LYS B 549 " --> pdb=" O   GLN B 545 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   VAL B 550 " --> pdb=" O   LEU B 546 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 557 through 571
      removed outlier: 3.953A  pdb=" N   ILE B 561 " --> pdb=" O   ASP B 557 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   GLU B 568 " --> pdb=" O   GLN B 564 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   VAL B 570 " --> pdb=" O   ILE B 566 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 584 through 596
      removed outlier: 3.871A  pdb=" N   THR B 588 " --> pdb=" O   GLY B 584 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   ILE B 592 " --> pdb=" O   THR B 588 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   TYR B 593 " --> pdb=" O   ILE B 589 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 598 through 616
      removed outlier: 3.623A  pdb=" N   VAL B 602 " --> pdb=" O   ILE B 598 " (cutoff:3.500A)
      removed outlier: 5.325A  pdb=" N   GLU B 611 " --> pdb=" O   THR B 607 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 625 through 639
    Processing helix  chain 'B' and resid 643 through 661
      removed outlier: 3.556A  pdb=" N   LEU B 658 " --> pdb=" O   ARG B 654 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 663 through 667
      removed outlier: 3.691A  pdb=" N   THR B 666 " --> pdb=" O   ASN B 663 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   PHE B 667 " --> pdb=" O   PRO B 664 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 663 through 667'
    Processing helix  chain 'B' and resid 691 through 705
      removed outlier: 3.686A  pdb=" N   LYS B 703 " --> pdb=" O   GLY B 699 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LEU B 704 " --> pdb=" O   GLU B 700 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   THR B 705 " --> pdb=" O   ALA B 701 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 708 through 710
      No H-bonds generated for 'chain 'B' and resid 708 through 710'
    Processing helix  chain 'B' and resid 711 through 722
      removed outlier: 4.019A  pdb=" N   GLU B 715 " --> pdb=" O   LYS B 711 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   LEU B 716 " --> pdb=" O   ASN B 712 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 748 through 757
      removed outlier: 4.077A  pdb=" N   LEU B 752 " --> pdb=" O   GLY B 748 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   LEU B 753 " --> pdb=" O   SER B 749 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   ASN B 757 " --> pdb=" O   LEU B 753 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 770 through 778
      removed outlier: 3.582A  pdb=" N   LEU B 774 " --> pdb=" O   TYR B 770 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 792 through 799
      removed outlier: 3.755A  pdb=" N   GLU B 796 " --> pdb=" O   PHE B 792 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   ASN B 799 " --> pdb=" O   LEU B 795 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 808 through 813
    Processing helix  chain 'B' and resid 814 through 819
    Processing helix  chain 'B' and resid 847 through 860
      removed outlier: 3.947A  pdb=" N   VAL B 851 " --> pdb=" O   GLY B 847 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   VAL B 856 " --> pdb=" O   ALA B 852 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ILE B 858 " --> pdb=" O   GLY B 854 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   MET B 859 " --> pdb=" O   LEU B 855 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 62
      removed outlier: 3.718A  pdb=" N   ILE A  60 " --> pdb=" O   CYS A 115 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   CYS A 115 " --> pdb=" O   ILE A  60 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   ILE A  62 " --> pdb=" O   ILE A 113 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   ILE A 113 " --> pdb=" O   ILE A  62 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LYS A  88 " --> pdb=" O   THR A 114 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 224 through 225
      removed outlier: 4.191A  pdb=" N   ARG A 224 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ILE A 231 " --> pdb=" O   ARG A 224 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   GLY A 230 " --> pdb=" O   GLU A 247 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 304 through 305
    Processing sheet with id=AA4, first strand: chain 'A' and resid 725 through 727
      removed outlier: 3.515A  pdb=" N   LYS A 726 " --> pdb=" O   GLN A 734 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   GLN A 734 " --> pdb=" O   LYS A 726 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   GLN A 737 " --> pdb=" O   ARG A 740 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ARG A 740 " --> pdb=" O   GLN A 737 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 823 through 825
      removed outlier: 3.648A  pdb=" N   CYS A 824 " --> pdb=" O   VAL A 831 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   VAL A 831 " --> pdb=" O   CYS A 824 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 37
      removed outlier: 3.501A  pdb=" N   HIS B  35 " --> pdb=" O   TYR B  47 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   TYR B  47 " --> pdb=" O   HIS B  35 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TYR B  45 " --> pdb=" O   VAL B  37 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 233 through 234
      removed outlier: 3.706A  pdb=" N   LEU B 296 " --> pdb=" O   LYS B 246 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   PHE B 295 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   GLY B 288 " --> pdb=" O   PHE B 295 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   TRP B 286 " --> pdb=" O   GLY B 297 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   GLU B 299 " --> pdb=" O   ILE B 284 " (cutoff:3.500A)
      removed outlier: 7.542A  pdb=" N   ILE B 284 " --> pdb=" O   GLU B 299 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 304 through 305
    Processing sheet with id=AA9, first strand: chain 'B' and resid 350 through 351

    342 hydrogen bonds defined for protein.
    981 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: 3.25

  Time building geometry restraints manager: 3.56 seconds

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

  Histogram of bond lengths:
        1.10 -     1.24: 1767
        1.24 -     1.39: 3681
        1.39 -     1.53: 7034
        1.53 -     1.68: 805
        1.68 -     1.82: 44
  Bond restraints: 13331
  Sorted by residual:
  bond pdb=" CG  PRO A 139 "
       pdb=" CD  PRO A 139 "
    ideal  model  delta    sigma   weight residual
    1.503  1.101  0.402 3.40e-02 8.65e+02 1.40e+02
  bond pdb=" C   ARG B 249 "
       pdb=" N   PRO B 250 "
    ideal  model  delta    sigma   weight residual
    1.332  1.397 -0.065 1.12e-02 7.97e+03 3.37e+01
  bond pdb=" CG  PRO A 867 "
       pdb=" CD  PRO A 867 "
    ideal  model  delta    sigma   weight residual
    1.503  1.363  0.140 3.40e-02 8.65e+02 1.71e+01
  bond pdb=" N   PRO A 139 "
       pdb=" CA  PRO A 139 "
    ideal  model  delta    sigma   weight residual
    1.469  1.511 -0.042 1.28e-02 6.10e+03 1.09e+01
  bond pdb=" CA  LEU B  30 "
       pdb=" CB  LEU B  30 "
    ideal  model  delta    sigma   weight residual
    1.526  1.549 -0.022 9.30e-03 1.16e+04 5.72e+00
  ... (remaining 13326 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.44: 17745
        4.44 -     8.87: 255
        8.87 -    13.31: 26
       13.31 -    17.74: 5
       17.74 -    22.18: 3
  Bond angle restraints: 18034
  Sorted by residual:
  angle pdb=" N   PRO A 139 "
        pdb=" CD  PRO A 139 "
        pdb=" CG  PRO A 139 "
      ideal   model   delta    sigma   weight residual
     103.20   81.02   22.18 1.50e+00 4.44e-01 2.19e+02
  angle pdb=" CA  PRO A 139 "
        pdb=" CB  PRO A 139 "
        pdb=" CG  PRO A 139 "
      ideal   model   delta    sigma   weight residual
     104.50   85.03   19.47 1.90e+00 2.77e-01 1.05e+02
  angle pdb=" N   ILE A 844 "
        pdb=" CA  ILE A 844 "
        pdb=" C   ILE A 844 "
      ideal   model   delta    sigma   weight residual
     112.29  104.61    7.68 9.40e-01 1.13e+00 6.68e+01
  angle pdb=" CA  GLN B  27 "
        pdb=" CB  GLN B  27 "
        pdb=" CG  GLN B  27 "
      ideal   model   delta    sigma   weight residual
     114.10  129.00  -14.90 2.00e+00 2.50e-01 5.55e+01
  angle pdb=" C   PRO B  10 "
        pdb=" N   PHE B  11 "
        pdb=" CA  PHE B  11 "
      ideal   model   delta    sigma   weight residual
     121.54  135.69  -14.15 1.91e+00 2.74e-01 5.49e+01
  ... (remaining 18029 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 6925
       17.87 -    35.74: 754
       35.74 -    53.62: 117
       53.62 -    71.49: 17
       71.49 -    89.36: 15
  Dihedral angle restraints: 7828
    sinusoidal: 3203
      harmonic: 4625
  Sorted by residual:
  dihedral pdb=" CA  TYR B 429 "
           pdb=" C   TYR B 429 "
           pdb=" N   VAL B 430 "
           pdb=" CA  VAL B 430 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  139.02   40.98     0      5.00e+00 4.00e-02 6.72e+01
  dihedral pdb=" CA  PHE A 613 "
           pdb=" C   PHE A 613 "
           pdb=" N   GLU A 614 "
           pdb=" CA  GLU A 614 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -145.11  -34.89     0      5.00e+00 4.00e-02 4.87e+01
  dihedral pdb=" CA  VAL B  76 "
           pdb=" C   VAL B  76 "
           pdb=" N   ALA B  77 "
           pdb=" CA  ALA B  77 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.77   33.23     0      5.00e+00 4.00e-02 4.42e+01
  ... (remaining 7825 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.085: 1625
       0.085 -    0.169: 262
       0.169 -    0.254: 38
       0.254 -    0.338: 9
       0.338 -    0.423: 5
  Chirality restraints: 1939
  Sorted by residual:
  chirality pdb=" CB  ILE A 561 "
            pdb=" CA  ILE A 561 "
            pdb=" CG1 ILE A 561 "
            pdb=" CG2 ILE A 561 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.22    0.42 2.00e-01 2.50e+01 4.47e+00
  chirality pdb=" CB  ILE A 801 "
            pdb=" CA  ILE A 801 "
            pdb=" CG1 ILE A 801 "
            pdb=" CG2 ILE A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.25    0.40 2.00e-01 2.50e+01 3.91e+00
  chirality pdb=" CB  ILE A 661 "
            pdb=" CA  ILE A 661 "
            pdb=" CG1 ILE A 661 "
            pdb=" CG2 ILE A 661 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.25    0.39 2.00e-01 2.50e+01 3.90e+00
  ... (remaining 1936 not shown)

  Planarity restraints: 2281
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 138 "   -0.127 5.00e-02 4.00e+02   1.87e-01 5.61e+01
        pdb=" N   PRO A 139 "    0.323 5.00e-02 4.00e+02
        pdb=" CA  PRO A 139 "   -0.114 5.00e-02 4.00e+02
        pdb=" CD  PRO A 139 "   -0.082 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B  26 "    0.026 2.00e-02 2.50e+03   5.18e-02 2.69e+01
        pdb=" C   TYR B  26 "   -0.090 2.00e-02 2.50e+03
        pdb=" O   TYR B  26 "    0.034 2.00e-02 2.50e+03
        pdb=" N   GLN B  27 "    0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 150 "    0.068 5.00e-02 4.00e+02   1.01e-01 1.63e+01
        pdb=" N   PRO A 151 "   -0.174 5.00e-02 4.00e+02
        pdb=" CA  PRO A 151 "    0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO A 151 "    0.056 5.00e-02 4.00e+02
  ... (remaining 2278 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 3044
        2.79 -     3.32: 11334
        3.32 -     3.84: 20718
        3.84 -     4.37: 23039
        4.37 -     4.90: 39665
  Nonbonded interactions: 97800
  Sorted by model distance:
  nonbonded pdb=" O   CYS A 783 "
            pdb=" OH  TYR A 822 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" O   CYS B 783 "
            pdb=" OH  TYR B 822 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" O   ALA A 701 "
            pdb=" OG1 THR A 705 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" OD2 ASP B 583 "
            pdb=" OH  TYR B 681 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   LYS B 585 "
            pdb=" OG1 THR B 588 "
     model   vdw
     2.303 3.040
  ... (remaining 97795 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 4 through 154 or resid 222 through 869))
  selection = (chain 'B' and (resid 4 through 117 or resid 121 through 142 or resid 146 throug \ 
h 153 or resid 201 or resid 222 through 233 or resid 241 through 670 or resid 67 \ 
5 through 869))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.350
  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:             0.030
  Extract box with map and model:          0.510
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     30.470
  Find NCS groups from input model:        0.540
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6519
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.402  13331  Z= 0.305
  Angle     :  1.373  22.175  18034  Z= 0.770
  Chirality :  0.068   0.423   1939
  Planarity :  0.009   0.187   2281
  Dihedral  : 15.090  89.362   4868
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.96 %
    Allowed  : 10.67 %
    Favored  : 88.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.39 %

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: -4.55 (0.17), residues: 1556
  helix: -3.09 (0.15), residues: 606
  sheet: -2.53 (0.65), residues: 63
  loop : -3.11 (0.17), residues: 887

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.003   TRP B 204 
 HIS   0.020   0.002   HIS A 413 
 PHE   0.037   0.003   PHE A   5 
 TYR   0.034   0.003   TYR B 140 
 ARG   0.006   0.001   ARG A 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22672 (  342)
  hydrogen bonds       : angle       8.30379 (  981)
  covalent geometry    : bond        0.00662 (13331)
  covalent geometry    : angle       1.37255 (18034)

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

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

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 252
  time to evaluate  : 1.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.7187 (p90) cc_final: 0.5859 (p90)
REVERT: A  153 TYR cc_start: 0.5377 (m-80) cc_final: 0.5062 (m-80)
REVERT: A  249 ARG cc_start: 0.7324 (ppt170) cc_final: 0.7123 (ppt170)
REVERT: A  532 ILE cc_start: 0.7787 (mm) cc_final: 0.7443 (pt)
REVERT: A  846 SER cc_start: 0.7997 (m) cc_final: 0.7793 (m)
REVERT: B  557 ASP cc_start: 0.7595 (p0) cc_final: 0.7250 (p0)
REVERT: B  615 ASN cc_start: 0.8194 (p0) cc_final: 0.7323 (p0)
REVERT: B  656 TYR cc_start: 0.7066 (t80) cc_final: 0.6498 (t80)
REVERT: B  660 TYR cc_start: 0.7740 (t80) cc_final: 0.7300 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 252
  average time/residue: 0.2287
  time to fit residues: 84.9234
Evaluate side-chains
  177 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 1.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 133 optimal weight:    0.5980
   chunk 119 optimal weight:    0.9980
   chunk 66 optimal weight:    0.6980
   chunk 40 optimal weight:   20.0000
   chunk 80 optimal weight:   10.0000
   chunk 63 optimal weight:   10.0000
   chunk 123 optimal weight:    0.8980
   chunk 47 optimal weight:    9.9990
   chunk 75 optimal weight:    6.9990
   chunk 92 optimal weight:    8.9990
   chunk 143 optimal weight:    9.9990
   overall best weight:    2.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 345 HIS
A 608 HIS
** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 691 HIS
A 868 GLN
B  74 GLN
** B  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 544 GLN
B 663 ASN
B 712 ASN
B 737 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.176281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.150068 restraints weight = 24338.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.153310 restraints weight = 15821.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.155512 restraints weight = 11757.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.4229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6739
moved from start:          0.2017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  13331  Z= 0.171
  Angle     :  0.814  10.106  18034  Z= 0.425
  Chirality :  0.049   0.313   1939
  Planarity :  0.006   0.130   2281
  Dihedral  :  7.487  77.712   1739
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 12.94
  Ramachandran Plot:
    Outliers :  0.84 %
    Allowed  : 10.73 %
    Favored  : 88.43 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 10.76 %
    Favored  : 87.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -3.93 (0.18), residues: 1556
  helix: -2.18 (0.18), residues: 642
  sheet: -2.65 (0.63), residues: 63
  loop : -3.05 (0.19), residues: 851

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 204 
 HIS   0.006   0.001   HIS B 345 
 PHE   0.024   0.002   PHE B 200 
 TYR   0.022   0.002   TYR A 416 
 ARG   0.006   0.001   ARG B 758 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04897 (  342)
  hydrogen bonds       : angle       5.70077 (  981)
  covalent geometry    : bond        0.00376 (13331)
  covalent geometry    : angle       0.81374 (18034)

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

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

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 193
  time to evaluate  : 1.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.7138 (p90) cc_final: 0.5807 (p90)
REVERT: A  249 ARG cc_start: 0.7107 (ppt170) cc_final: 0.6787 (ppt170)
REVERT: A  417 MET cc_start: 0.5085 (mtt) cc_final: 0.4771 (mtt)
REVERT: A  532 ILE cc_start: 0.7897 (mm) cc_final: 0.7651 (mm)
REVERT: A  776 ARG cc_start: 0.7726 (mmp80) cc_final: 0.6600 (ttm-80)
REVERT: B  557 ASP cc_start: 0.7578 (p0) cc_final: 0.7093 (p0)
REVERT: B  656 TYR cc_start: 0.6877 (t80) cc_final: 0.6353 (t80)
REVERT: B  770 TYR cc_start: 0.5477 (m-80) cc_final: 0.5097 (m-80)
REVERT: B  863 LEU cc_start: 0.4362 (OUTLIER) cc_final: 0.4004 (mt)
  outliers start: 19
  outliers final: 10
  residues processed: 207
  average time/residue: 0.2273
  time to fit residues: 70.7622
Evaluate side-chains
  179 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 168
  time to evaluate  : 1.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  793 CYS
Chi-restraints excluded: chain A residue  806 ASP
Chi-restraints excluded: chain A residue  817 GLU
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  592 ILE
Chi-restraints excluded: chain B residue  633 LEU
Chi-restraints excluded: chain B residue  784 VAL
Chi-restraints excluded: chain B residue  863 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 145 optimal weight:   10.0000
   chunk 5 optimal weight:    0.2980
   chunk 19 optimal weight:    2.9990
   chunk 108 optimal weight:    0.1980
   chunk 57 optimal weight:    0.9980
   chunk 43 optimal weight:    5.9990
   chunk 100 optimal weight:   10.0000
   chunk 51 optimal weight:    9.9990
   chunk 73 optimal weight:    0.9980
   chunk 24 optimal weight:    9.9990
   chunk 153 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B  81 HIS
** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 571 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4510 r_free = 0.4510 target = 0.180682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.153852 restraints weight = 24379.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.157534 restraints weight = 15230.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.160117 restraints weight = 10943.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.4281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6627
moved from start:          0.2359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13331  Z= 0.120
  Angle     :  0.713   8.877  18034  Z= 0.369
  Chirality :  0.046   0.258   1939
  Planarity :  0.005   0.095   2281
  Dihedral  :  6.916  78.817   1739
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.84 %
    Allowed  : 10.60 %
    Favored  : 88.56 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 14.37 %
    Favored  : 83.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

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: -3.56 (0.19), residues: 1556
  helix: -1.67 (0.19), residues: 637
  sheet: -2.55 (0.61), residues: 67
  loop : -3.01 (0.19), residues: 852

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 204 
 HIS   0.005   0.001   HIS B 522 
 PHE   0.033   0.001   PHE B 344 
 TYR   0.015   0.001   TYR A  45 
 ARG   0.002   0.000   ARG B 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04035 (  342)
  hydrogen bonds       : angle       5.16895 (  981)
  covalent geometry    : bond        0.00252 (13331)
  covalent geometry    : angle       0.71281 (18034)

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

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

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 199
  time to evaluate  : 1.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.7187 (p90) cc_final: 0.5827 (p90)
REVERT: A  249 ARG cc_start: 0.7164 (ppt170) cc_final: 0.6734 (ppt170)
REVERT: A  417 MET cc_start: 0.5060 (mtt) cc_final: 0.4813 (mtt)
REVERT: A  532 ILE cc_start: 0.7693 (mm) cc_final: 0.6939 (mp)
REVERT: A  559 TYR cc_start: 0.7545 (m-80) cc_final: 0.7339 (m-80)
REVERT: A  648 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7570 (pp20)
REVERT: A  776 ARG cc_start: 0.7851 (mmp80) cc_final: 0.6638 (ttm-80)
REVERT: B  557 ASP cc_start: 0.7610 (p0) cc_final: 0.7050 (p0)
REVERT: B  656 TYR cc_start: 0.6788 (t80) cc_final: 0.6326 (t80)
REVERT: B  770 TYR cc_start: 0.5511 (m-80) cc_final: 0.4933 (m-80)
REVERT: B  860 ASP cc_start: 0.6482 (m-30) cc_final: 0.6032 (m-30)
  outliers start: 28
  outliers final: 15
  residues processed: 219
  average time/residue: 0.2284
  time to fit residues: 74.8310
Evaluate side-chains
  191 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 175
  time to evaluate  : 1.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  648 GLU
Chi-restraints excluded: chain A residue  793 CYS
Chi-restraints excluded: chain A residue  817 GLU
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  447 THR
Chi-restraints excluded: chain B residue  534 PHE
Chi-restraints excluded: chain B residue  592 ILE
Chi-restraints excluded: chain B residue  633 LEU
Chi-restraints excluded: chain B residue  863 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 45 optimal weight:    9.9990
   chunk 40 optimal weight:   20.0000
   chunk 44 optimal weight:    0.9980
   chunk 8 optimal weight:   10.0000
   chunk 117 optimal weight:    0.9980
   chunk 118 optimal weight:    3.9990
   chunk 5 optimal weight:    6.9990
   chunk 76 optimal weight:    2.9990
   chunk 157 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 147 optimal weight:    3.9990
   overall best weight:    2.3986

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

Flipped N/Q/H residues before XYZ refinement:
A  39 ASN
** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4415 r_free = 0.4415 target = 0.171565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.144818 restraints weight = 24404.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.147953 restraints weight = 15974.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.150135 restraints weight = 11968.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.4167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6852
moved from start:          0.3003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  13331  Z= 0.178
  Angle     :  0.767   9.475  18034  Z= 0.400
  Chirality :  0.049   0.320   1939
  Planarity :  0.005   0.055   2281
  Dihedral  :  7.038  78.489   1739
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 13.68
  Ramachandran Plot:
    Outliers :  0.71 %
    Allowed  : 11.31 %
    Favored  : 87.98 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 17.06 %
    Favored  : 80.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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 (0.19), residues: 1556
  helix: -1.51 (0.19), residues: 657
  sheet: -2.15 (0.67), residues: 53
  loop : -3.13 (0.19), residues: 846

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 204 
 HIS   0.008   0.001   HIS B  81 
 PHE   0.034   0.002   PHE B 200 
 TYR   0.018   0.002   TYR A  47 
 ARG   0.004   0.001   ARG B  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04365 (  342)
  hydrogen bonds       : angle       5.30710 (  981)
  covalent geometry    : bond        0.00400 (13331)
  covalent geometry    : angle       0.76719 (18034)

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

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

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 188
  time to evaluate  : 1.554 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 LYS cc_start: 0.6323 (mmtp) cc_final: 0.6094 (mmtp)
REVERT: A  140 TYR cc_start: 0.6952 (p90) cc_final: 0.5684 (p90)
REVERT: A  249 ARG cc_start: 0.7242 (ppt170) cc_final: 0.6814 (ppt170)
REVERT: A  712 ASN cc_start: 0.6592 (m110) cc_final: 0.6102 (t0)
REVERT: A  776 ARG cc_start: 0.7920 (mmp80) cc_final: 0.6702 (ttm110)
REVERT: B  539 ILE cc_start: 0.8689 (mm) cc_final: 0.8414 (mm)
REVERT: B  557 ASP cc_start: 0.7682 (p0) cc_final: 0.7024 (p0)
REVERT: B  564 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8775 (mt0)
REVERT: B  656 TYR cc_start: 0.6663 (t80) cc_final: 0.6193 (t80)
REVERT: B  711 LYS cc_start: 0.8385 (pptt) cc_final: 0.8133 (pptt)
REVERT: B  770 TYR cc_start: 0.5665 (m-80) cc_final: 0.5196 (m-80)
REVERT: B  860 ASP cc_start: 0.6518 (m-30) cc_final: 0.6078 (m-30)
REVERT: B  863 LEU cc_start: 0.4519 (OUTLIER) cc_final: 0.4130 (mt)
  outliers start: 40
  outliers final: 22
  residues processed: 214
  average time/residue: 0.2371
  time to fit residues: 76.6149
Evaluate side-chains
  193 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 169
  time to evaluate  : 1.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  589 ILE
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  793 CYS
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  447 THR
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  504 THR
Chi-restraints excluded: chain B residue  534 PHE
Chi-restraints excluded: chain B residue  564 GLN
Chi-restraints excluded: chain B residue  592 ILE
Chi-restraints excluded: chain B residue  633 LEU
Chi-restraints excluded: chain B residue  788 LEU
Chi-restraints excluded: chain B residue  863 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 35 optimal weight:    0.4980
   chunk 107 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 18 optimal weight:    9.9990
   chunk 64 optimal weight:    6.9990
   chunk 15 optimal weight:    8.9990
   chunk 79 optimal weight:    0.9990
   chunk 13 optimal weight:   20.0000
   chunk 83 optimal weight:    6.9990
   chunk 73 optimal weight:    0.6980
   chunk 152 optimal weight:    7.9990
   overall best weight:    2.2386

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

Flipped N/Q/H residues before XYZ refinement:
A 137 ASN
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 571 ASN
B 615 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.170660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.143775 restraints weight = 23686.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.146907 restraints weight = 15541.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.149077 restraints weight = 11612.588|
|-----------------------------------------------------------------------------|
r_work (final): 0.4163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6851
moved from start:          0.3295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  13331  Z= 0.168
  Angle     :  0.755   9.836  18034  Z= 0.391
  Chirality :  0.048   0.260   1939
  Planarity :  0.005   0.051   2281
  Dihedral  :  6.954  79.093   1739
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 12.94
  Ramachandran Plot:
    Outliers :  0.71 %
    Allowed  : 11.89 %
    Favored  : 87.40 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 18.90 %
    Favored  : 78.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -3.42 (0.19), residues: 1556
  helix: -1.29 (0.19), residues: 648
  sheet: -2.31 (0.66), residues: 51
  loop : -3.20 (0.18), residues: 857

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 590 
 HIS   0.007   0.001   HIS A   9 
 PHE   0.016   0.002   PHE B 344 
 TYR   0.018   0.002   TYR B 660 
 ARG   0.005   0.000   ARG B 821 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04250 (  342)
  hydrogen bonds       : angle       5.26916 (  981)
  covalent geometry    : bond        0.00378 (13331)
  covalent geometry    : angle       0.75464 (18034)

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

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

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 186
  time to evaluate  : 1.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.6926 (p90) cc_final: 0.5737 (p90)
REVERT: A  153 TYR cc_start: 0.5441 (m-80) cc_final: 0.5233 (m-80)
REVERT: A  712 ASN cc_start: 0.6580 (m110) cc_final: 0.6199 (t0)
REVERT: A  776 ARG cc_start: 0.7919 (mmp80) cc_final: 0.6700 (ttm-80)
REVERT: B  510 TRP cc_start: 0.8033 (t-100) cc_final: 0.7764 (t-100)
REVERT: B  539 ILE cc_start: 0.8765 (mm) cc_final: 0.8521 (mm)
REVERT: B  557 ASP cc_start: 0.7687 (p0) cc_final: 0.7461 (t0)
REVERT: B  656 TYR cc_start: 0.6852 (t80) cc_final: 0.6275 (t80)
REVERT: B  711 LYS cc_start: 0.8373 (pptt) cc_final: 0.8080 (pptt)
REVERT: B  770 TYR cc_start: 0.5644 (m-80) cc_final: 0.5170 (m-80)
REVERT: B  820 TYR cc_start: 0.7296 (OUTLIER) cc_final: 0.7079 (m-80)
REVERT: B  860 ASP cc_start: 0.6626 (m-30) cc_final: 0.6253 (m-30)
REVERT: B  863 LEU cc_start: 0.4461 (OUTLIER) cc_final: 0.4115 (mt)
  outliers start: 41
  outliers final: 26
  residues processed: 212
  average time/residue: 0.2240
  time to fit residues: 71.5031
Evaluate side-chains
  190 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 162
  time to evaluate  : 1.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  589 ILE
Chi-restraints excluded: chain A residue  670 VAL
Chi-restraints excluded: chain A residue  704 LEU
Chi-restraints excluded: chain A residue  722 LEU
Chi-restraints excluded: chain A residue  773 SER
Chi-restraints excluded: chain B residue   12 PHE
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  504 THR
Chi-restraints excluded: chain B residue  534 PHE
Chi-restraints excluded: chain B residue  564 GLN
Chi-restraints excluded: chain B residue  592 ILE
Chi-restraints excluded: chain B residue  633 LEU
Chi-restraints excluded: chain B residue  788 LEU
Chi-restraints excluded: chain B residue  820 TYR
Chi-restraints excluded: chain B residue  863 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 63 optimal weight:    9.9990
   chunk 65 optimal weight:    6.9990
   chunk 51 optimal weight:    7.9990
   chunk 130 optimal weight:    7.9990
   chunk 156 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 148 optimal weight:    9.9990
   chunk 124 optimal weight:    4.9990
   chunk 13 optimal weight:    9.9990
   chunk 7 optimal weight:    7.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 481 HIS
B 544 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.164101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.136219 restraints weight = 24775.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.139496 restraints weight = 15704.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.141726 restraints weight = 11584.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.4065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7014
moved from start:          0.3962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  13331  Z= 0.249
  Angle     :  0.860  11.165  18034  Z= 0.449
  Chirality :  0.052   0.238   1939
  Planarity :  0.006   0.051   2281
  Dihedral  :  7.510  78.765   1739
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 16.78
  Ramachandran Plot:
    Outliers :  0.71 %
    Allowed  : 13.24 %
    Favored  : 86.05 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 19.53 %
    Favored  : 76.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -3.64 (0.19), residues: 1556
  helix: -1.54 (0.19), residues: 653
  sheet: -2.46 (0.63), residues: 51
  loop : -3.27 (0.19), residues: 852

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 590 
 HIS   0.011   0.002   HIS A   9 
 PHE   0.039   0.002   PHE A  13 
 TYR   0.021   0.002   TYR A 260 
 ARG   0.009   0.001   ARG B 821 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04977 (  342)
  hydrogen bonds       : angle       5.71273 (  981)
  covalent geometry    : bond        0.00569 (13331)
  covalent geometry    : angle       0.86005 (18034)

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

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

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 175
  time to evaluate  : 1.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.7070 (p90) cc_final: 0.5868 (p90)
REVERT: A  153 TYR cc_start: 0.5298 (m-80) cc_final: 0.5056 (m-80)
REVERT: A  518 PHE cc_start: 0.6563 (OUTLIER) cc_final: 0.5780 (t80)
REVERT: A  712 ASN cc_start: 0.6721 (m110) cc_final: 0.6386 (t0)
REVERT: A  776 ARG cc_start: 0.7995 (mmp80) cc_final: 0.6692 (ttm-80)
REVERT: B  416 TYR cc_start: 0.7057 (OUTLIER) cc_final: 0.5131 (m-80)
REVERT: B  539 ILE cc_start: 0.8959 (mm) cc_final: 0.8705 (mm)
REVERT: B  557 ASP cc_start: 0.7861 (p0) cc_final: 0.7311 (p0)
REVERT: B  711 LYS cc_start: 0.8393 (pptt) cc_final: 0.8040 (pptt)
REVERT: B  770 TYR cc_start: 0.5592 (m-80) cc_final: 0.5263 (m-80)
REVERT: B  820 TYR cc_start: 0.7596 (OUTLIER) cc_final: 0.7351 (m-80)
  outliers start: 55
  outliers final: 34
  residues processed: 218
  average time/residue: 0.2288
  time to fit residues: 74.1310
Evaluate side-chains
  193 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 156
  time to evaluate  : 1.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   87 PHE
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  589 ILE
Chi-restraints excluded: chain A residue  670 VAL
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  762 ILE
Chi-restraints excluded: chain A residue  773 SER
Chi-restraints excluded: chain A residue  797 VAL
Chi-restraints excluded: chain B residue   12 PHE
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   47 TYR
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  345 HIS
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain B residue  416 TYR
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  504 THR
Chi-restraints excluded: chain B residue  534 PHE
Chi-restraints excluded: chain B residue  564 GLN
Chi-restraints excluded: chain B residue  589 ILE
Chi-restraints excluded: chain B residue  592 ILE
Chi-restraints excluded: chain B residue  633 LEU
Chi-restraints excluded: chain B residue  645 LEU
Chi-restraints excluded: chain B residue  788 LEU
Chi-restraints excluded: chain B residue  820 TYR
Chi-restraints excluded: chain B residue  863 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 19 optimal weight:    9.9990
   chunk 90 optimal weight:    0.4980
   chunk 47 optimal weight:    5.9990
   chunk 157 optimal weight:    0.9980
   chunk 69 optimal weight:    4.9990
   chunk 143 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 117 optimal weight:    6.9990
   chunk 63 optimal weight:    9.9990
   chunk 27 optimal weight:    0.9980
   chunk 76 optimal weight:    1.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  33 ASN
B 355 HIS
B 385 HIS
B 545 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.172361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.146146 restraints weight = 23863.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.149324 restraints weight = 15331.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.151593 restraints weight = 11325.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.4191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6791
moved from start:          0.3841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13331  Z= 0.133
  Angle     :  0.742  12.494  18034  Z= 0.381
  Chirality :  0.047   0.215   1939
  Planarity :  0.005   0.053   2281
  Dihedral  :  6.840  79.216   1739
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  : 11.25 %
    Favored  : 88.11 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 21.59 %
    Favored  : 75.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -3.35 (0.20), residues: 1556
  helix: -1.24 (0.19), residues: 665
  sheet: -2.48 (0.60), residues: 61
  loop : -3.16 (0.19), residues: 830

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 204 
 HIS   0.006   0.001   HIS B 522 
 PHE   0.016   0.001   PHE B 344 
 TYR   0.017   0.001   TYR A 822 
 ARG   0.004   0.000   ARG A 821 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03913 (  342)
  hydrogen bonds       : angle       5.23901 (  981)
  covalent geometry    : bond        0.00290 (13331)
  covalent geometry    : angle       0.74166 (18034)

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

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

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 191
  time to evaluate  : 1.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.6918 (p90) cc_final: 0.5745 (p90)
REVERT: A  153 TYR cc_start: 0.5381 (m-80) cc_final: 0.5139 (m-80)
REVERT: A  712 ASN cc_start: 0.6704 (m110) cc_final: 0.6348 (t0)
REVERT: B  416 TYR cc_start: 0.6836 (OUTLIER) cc_final: 0.5173 (m-80)
REVERT: B  539 ILE cc_start: 0.8739 (mm) cc_final: 0.8482 (mm)
REVERT: B  557 ASP cc_start: 0.7680 (p0) cc_final: 0.7463 (t0)
REVERT: B  711 LYS cc_start: 0.8356 (pptt) cc_final: 0.8055 (pptt)
REVERT: B  770 TYR cc_start: 0.5680 (m-80) cc_final: 0.5187 (m-80)
REVERT: B  820 TYR cc_start: 0.7444 (OUTLIER) cc_final: 0.7192 (m-80)
REVERT: B  860 ASP cc_start: 0.6646 (m-30) cc_final: 0.6330 (m-30)
REVERT: B  863 LEU cc_start: 0.4484 (OUTLIER) cc_final: 0.4131 (mt)
  outliers start: 40
  outliers final: 24
  residues processed: 217
  average time/residue: 0.2292
  time to fit residues: 74.7689
Evaluate side-chains
  195 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 168
  time to evaluate  : 1.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue   87 PHE
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  704 LEU
Chi-restraints excluded: chain A residue  722 LEU
Chi-restraints excluded: chain A residue  773 SER
Chi-restraints excluded: chain B residue   12 PHE
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  411 ILE
Chi-restraints excluded: chain B residue  416 TYR
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  534 PHE
Chi-restraints excluded: chain B residue  564 GLN
Chi-restraints excluded: chain B residue  592 ILE
Chi-restraints excluded: chain B residue  633 LEU
Chi-restraints excluded: chain B residue  788 LEU
Chi-restraints excluded: chain B residue  820 TYR
Chi-restraints excluded: chain B residue  856 VAL
Chi-restraints excluded: chain B residue  863 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 139 optimal weight:    8.9990
   chunk 118 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 63 optimal weight:   10.0000
   chunk 132 optimal weight:    5.9990
   chunk 153 optimal weight:    2.9990
   chunk 157 optimal weight:    1.9990
   chunk 116 optimal weight:    0.6980
   chunk 123 optimal weight:    7.9990
   chunk 42 optimal weight:    1.9990
   chunk 119 optimal weight:    0.7980
   overall best weight:    1.2984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.172528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.146294 restraints weight = 23823.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.149433 restraints weight = 15364.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.151682 restraints weight = 11412.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.4191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6797
moved from start:          0.3943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13331  Z= 0.139
  Angle     :  0.745  11.629  18034  Z= 0.382
  Chirality :  0.047   0.197   1939
  Planarity :  0.005   0.059   2281
  Dihedral  :  6.714  77.741   1739
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  : 11.95 %
    Favored  : 87.47 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 22.58 %
    Favored  : 74.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -3.33 (0.20), residues: 1556
  helix: -1.17 (0.20), residues: 671
  sheet: -2.39 (0.60), residues: 61
  loop : -3.23 (0.19), residues: 824

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 204 
 HIS   0.005   0.001   HIS B  81 
 PHE   0.022   0.002   PHE A  13 
 TYR   0.016   0.001   TYR A 260 
 ARG   0.005   0.000   ARG B 821 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03980 (  342)
  hydrogen bonds       : angle       5.26873 (  981)
  covalent geometry    : bond        0.00308 (13331)
  covalent geometry    : angle       0.74466 (18034)

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

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

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 184
  time to evaluate  : 1.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.6931 (p90) cc_final: 0.5759 (p90)
REVERT: A  153 TYR cc_start: 0.5278 (m-80) cc_final: 0.5038 (m-80)
REVERT: A  415 LEU cc_start: 0.6259 (mm) cc_final: 0.5870 (tp)
REVERT: A  712 ASN cc_start: 0.6679 (m110) cc_final: 0.6382 (t0)
REVERT: B  402 GLU cc_start: 0.7510 (mp0) cc_final: 0.7227 (mm-30)
REVERT: B  416 TYR cc_start: 0.6857 (OUTLIER) cc_final: 0.5299 (m-80)
REVERT: B  539 ILE cc_start: 0.8740 (mm) cc_final: 0.8476 (mm)
REVERT: B  557 ASP cc_start: 0.7780 (p0) cc_final: 0.7379 (p0)
REVERT: B  654 ARG cc_start: 0.8567 (mmm-85) cc_final: 0.8302 (tpp-160)
REVERT: B  711 LYS cc_start: 0.8452 (pptt) cc_final: 0.8115 (pptt)
REVERT: B  755 LEU cc_start: 0.5316 (OUTLIER) cc_final: 0.5030 (tp)
REVERT: B  770 TYR cc_start: 0.5618 (m-80) cc_final: 0.5178 (m-80)
REVERT: B  860 ASP cc_start: 0.6606 (m-30) cc_final: 0.6289 (m-30)
REVERT: B  863 LEU cc_start: 0.4540 (OUTLIER) cc_final: 0.4158 (mt)
  outliers start: 38
  outliers final: 29
  residues processed: 208
  average time/residue: 0.2322
  time to fit residues: 71.9636
Evaluate side-chains
  203 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 171
  time to evaluate  : 1.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 PHE
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  268 GLU
Chi-restraints excluded: chain A residue  385 HIS
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  534 PHE
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  704 LEU
Chi-restraints excluded: chain A residue  722 LEU
Chi-restraints excluded: chain A residue  773 SER
Chi-restraints excluded: chain A residue  843 ASP
Chi-restraints excluded: chain B residue   12 PHE
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  345 HIS
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  416 TYR
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  534 PHE
Chi-restraints excluded: chain B residue  564 GLN
Chi-restraints excluded: chain B residue  568 GLU
Chi-restraints excluded: chain B residue  592 ILE
Chi-restraints excluded: chain B residue  633 LEU
Chi-restraints excluded: chain B residue  755 LEU
Chi-restraints excluded: chain B residue  788 LEU
Chi-restraints excluded: chain B residue  856 VAL
Chi-restraints excluded: chain B residue  863 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 66 optimal weight:    5.9990
   chunk 101 optimal weight:    9.9990
   chunk 25 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 115 optimal weight:    0.2980
   chunk 45 optimal weight:    0.9990
   chunk 136 optimal weight:    2.9990
   chunk 90 optimal weight:   10.0000
   chunk 102 optimal weight:    9.9990
   chunk 50 optimal weight:    5.9990
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
A 790 ASN
** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 432 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.174403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.148511 restraints weight = 24533.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.151728 restraints weight = 15837.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.153943 restraints weight = 11733.498|
|-----------------------------------------------------------------------------|
r_work (final): 0.4211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6757
moved from start:          0.4007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13331  Z= 0.133
  Angle     :  0.739  11.569  18034  Z= 0.378
  Chirality :  0.047   0.192   1939
  Planarity :  0.005   0.053   2281
  Dihedral  :  6.566  76.012   1739
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  : 11.57 %
    Favored  : 87.92 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 22.51 %
    Favored  : 74.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -3.26 (0.20), residues: 1556
  helix: -1.10 (0.20), residues: 671
  sheet: -2.28 (0.61), residues: 61
  loop : -3.21 (0.19), residues: 824

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 590 
 HIS   0.005   0.001   HIS B  81 
 PHE   0.020   0.002   PHE B 344 
 TYR   0.013   0.001   TYR A  45 
 ARG   0.004   0.000   ARG B 821 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03895 (  342)
  hydrogen bonds       : angle       5.24816 (  981)
  covalent geometry    : bond        0.00296 (13331)
  covalent geometry    : angle       0.73899 (18034)

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

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

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 182
  time to evaluate  : 1.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.6953 (p90) cc_final: 0.5782 (p90)
REVERT: A  153 TYR cc_start: 0.5282 (m-80) cc_final: 0.5040 (m-80)
REVERT: A  415 LEU cc_start: 0.5759 (mm) cc_final: 0.5491 (tp)
REVERT: A  513 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6385 (mt-10)
REVERT: A  712 ASN cc_start: 0.6673 (m110) cc_final: 0.6410 (t0)
REVERT: B  402 GLU cc_start: 0.7487 (mp0) cc_final: 0.7185 (mm-30)
REVERT: B  416 TYR cc_start: 0.6806 (OUTLIER) cc_final: 0.5373 (m-80)
REVERT: B  539 ILE cc_start: 0.8646 (mm) cc_final: 0.8394 (mm)
REVERT: B  557 ASP cc_start: 0.7855 (p0) cc_final: 0.7524 (t0)
REVERT: B  654 ARG cc_start: 0.8589 (mmm-85) cc_final: 0.8273 (tpp-160)
REVERT: B  711 LYS cc_start: 0.8443 (pptt) cc_final: 0.8070 (pptt)
REVERT: B  755 LEU cc_start: 0.5205 (OUTLIER) cc_final: 0.4915 (tp)
REVERT: B  770 TYR cc_start: 0.5599 (m-80) cc_final: 0.5136 (m-80)
REVERT: B  820 TYR cc_start: 0.7399 (OUTLIER) cc_final: 0.7102 (m-80)
REVERT: B  860 ASP cc_start: 0.6718 (m-30) cc_final: 0.6441 (m-30)
REVERT: B  863 LEU cc_start: 0.4485 (OUTLIER) cc_final: 0.4149 (mt)
  outliers start: 40
  outliers final: 29
  residues processed: 209
  average time/residue: 0.2383
  time to fit residues: 74.4707
Evaluate side-chains
  202 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 169
  time to evaluate  : 1.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   87 PHE
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  268 GLU
Chi-restraints excluded: chain A residue  416 TYR
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  534 PHE
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  704 LEU
Chi-restraints excluded: chain A residue  722 LEU
Chi-restraints excluded: chain A residue  843 ASP
Chi-restraints excluded: chain A residue  859 MET
Chi-restraints excluded: chain B residue   12 PHE
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  345 HIS
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  416 TYR
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  534 PHE
Chi-restraints excluded: chain B residue  564 GLN
Chi-restraints excluded: chain B residue  592 ILE
Chi-restraints excluded: chain B residue  633 LEU
Chi-restraints excluded: chain B residue  755 LEU
Chi-restraints excluded: chain B residue  788 LEU
Chi-restraints excluded: chain B residue  820 TYR
Chi-restraints excluded: chain B residue  856 VAL
Chi-restraints excluded: chain B residue  863 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 78 optimal weight:    6.9990
   chunk 65 optimal weight:    6.9990
   chunk 83 optimal weight:    5.9990
   chunk 48 optimal weight:    5.9990
   chunk 154 optimal weight:    5.9990
   chunk 100 optimal weight:    9.9990
   chunk 7 optimal weight:    5.9990
   chunk 58 optimal weight:   10.0000
   chunk 103 optimal weight:    8.9990
   chunk 59 optimal weight:    0.4980
   overall best weight:    4.8988

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

Flipped N/Q/H residues before XYZ refinement:
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 432 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 = 0.4305 r_free = 0.4305 target = 0.162059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.134277 restraints weight = 24563.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.137487 restraints weight = 15667.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.139626 restraints weight = 11596.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.4039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7060
moved from start:          0.4567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.071  13331  Z= 0.306
  Angle     :  0.935  10.291  18034  Z= 0.489
  Chirality :  0.055   0.243   1939
  Planarity :  0.006   0.054   2281
  Dihedral  :  7.568  75.152   1739
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 20.27
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  : 14.14 %
    Favored  : 85.28 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 22.79 %
    Favored  : 74.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

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: -3.76 (0.19), residues: 1556
  helix: -1.62 (0.18), residues: 667
  sheet: -2.34 (0.62), residues: 51
  loop : -3.39 (0.19), residues: 838

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 590 
 HIS   0.013   0.003   HIS A   9 
 PHE   0.025   0.003   PHE A   5 
 TYR   0.023   0.003   TYR A  45 
 ARG   0.009   0.001   ARG B 821 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05319 (  342)
  hydrogen bonds       : angle       6.00126 (  981)
  covalent geometry    : bond        0.00707 (13331)
  covalent geometry    : angle       0.93524 (18034)

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

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

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3112 Ramachandran restraints generated.
    1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 169
  time to evaluate  : 1.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.7149 (p90) cc_final: 0.5891 (p90)
REVERT: A  153 TYR cc_start: 0.5235 (m-80) cc_final: 0.5002 (m-80)
REVERT: A  337 LEU cc_start: 0.6012 (OUTLIER) cc_final: 0.5760 (mm)
REVERT: A  417 MET cc_start: 0.5470 (mtt) cc_final: 0.5233 (mtt)
REVERT: A  440 LEU cc_start: 0.5125 (OUTLIER) cc_final: 0.4750 (tp)
REVERT: A  518 PHE cc_start: 0.6594 (OUTLIER) cc_final: 0.5766 (t80)
REVERT: A  712 ASN cc_start: 0.6807 (m110) cc_final: 0.6504 (t0)
REVERT: B  416 TYR cc_start: 0.6966 (OUTLIER) cc_final: 0.5243 (m-80)
REVERT: B  539 ILE cc_start: 0.9042 (mm) cc_final: 0.8748 (mm)
REVERT: B  557 ASP cc_start: 0.7851 (p0) cc_final: 0.7473 (p0)
REVERT: B  564 GLN cc_start: 0.9263 (OUTLIER) cc_final: 0.8899 (mp10)
REVERT: B  711 LYS cc_start: 0.8390 (pptt) cc_final: 0.8046 (pptt)
REVERT: B  770 TYR cc_start: 0.5715 (m-80) cc_final: 0.5418 (m-80)
REVERT: B  820 TYR cc_start: 0.7697 (OUTLIER) cc_final: 0.7355 (m-80)
REVERT: B  835 ASP cc_start: 0.6792 (m-30) cc_final: 0.6415 (t0)
REVERT: B  860 ASP cc_start: 0.6980 (m-30) cc_final: 0.6652 (m-30)
  outliers start: 39
  outliers final: 22
  residues processed: 197
  average time/residue: 0.2417
  time to fit residues: 70.1805
Evaluate side-chains
  186 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 158
  time to evaluate  : 1.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  259 THR
Chi-restraints excluded: chain A residue  286 TRP
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  385 HIS
Chi-restraints excluded: chain A residue  416 TYR
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  589 ILE
Chi-restraints excluded: chain A residue  843 ASP
Chi-restraints excluded: chain B residue   12 PHE
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  345 HIS
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain B residue  416 TYR
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  534 PHE
Chi-restraints excluded: chain B residue  564 GLN
Chi-restraints excluded: chain B residue  633 LEU
Chi-restraints excluded: chain B residue  755 LEU
Chi-restraints excluded: chain B residue  788 LEU
Chi-restraints excluded: chain B residue  820 TYR
Chi-restraints excluded: chain B residue  863 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 85 optimal weight:    0.5980
   chunk 20 optimal weight:    5.9990
   chunk 40 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 118 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 47 optimal weight:    9.9990
   chunk 8 optimal weight:    0.9990
   chunk 124 optimal weight:    0.7980
   chunk 155 optimal weight:    0.9980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B 572 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.173483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.147248 restraints weight = 23995.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.150620 restraints weight = 15230.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.152882 restraints weight = 11192.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.4204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6773
moved from start:          0.4316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13331  Z= 0.138
  Angle     :  0.766  11.722  18034  Z= 0.393
  Chirality :  0.048   0.193   1939
  Planarity :  0.005   0.057   2281
  Dihedral  :  6.729  74.062   1739
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 11.94
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  : 11.76 %
    Favored  : 87.72 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 23.43 %
    Favored  : 74.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -3.39 (0.19), residues: 1556
  helix: -1.22 (0.20), residues: 666
  sheet: -2.20 (0.63), residues: 56
  loop : -3.28 (0.19), residues: 834

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 590 
 HIS   0.005   0.001   HIS B  81 
 PHE   0.019   0.002   PHE A   5 
 TYR   0.016   0.001   TYR A  45 
 ARG   0.004   0.000   ARG B  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03977 (  342)
  hydrogen bonds       : angle       5.31344 (  981)
  covalent geometry    : bond        0.00302 (13331)
  covalent geometry    : angle       0.76569 (18034)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3906.95 seconds
wall clock time: 68 minutes 45.02 seconds (4125.02 seconds total)