Starting phenix.real_space_refine
on Thu May 15 08:13:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w7a_37337/05_2025/8w7a_37337.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w7a_37337/05_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_37337/05_2025/8w7a_37337.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w7a_37337/05_2025/8w7a_37337.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w7a_37337/05_2025/8w7a_37337.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w7a_37337/05_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-5687/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: 7.56, per 1000 atoms: 0.58
  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: 3.21
  Conformation dependent library (CDL) restraints added in 1.7 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: 1.43
  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: 3.76 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:             0.860
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.570
  Check model and map are aligned:         0.100
  Set scattering table:                    0.140
  Process input model:                     29.900
  Find NCS groups from input model:        0.790
  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:             0.010
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.190
-------------------------------------------------------------------------------
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  : 1.578 
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: 0.2427
  time to fit residues: 89.5517
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  : 1.361 
-------------------------------------------------------------------------------
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 = 24338.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.153312 restraints weight = 15819.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.155512 restraints weight = 11754.760|
|-----------------------------------------------------------------------------|
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  : 1.502 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.7137 (p90) cc_final: 0.5808 (p90)
REVERT: A  249 ARG cc_start: 0.7106 (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: 0.6876 (t80) cc_final: 0.6353 (t80)
REVERT: B  770 TYR cc_start: 0.5476 (m-80) cc_final: 0.5097 (m-80)
REVERT: B  863 LEU cc_start: 0.4361 (OUTLIER) cc_final: 0.4004 (mt)
  outliers start: 19
  outliers final: 10
  residues processed: 207
  average time/residue: 0.2282
  time to fit residues: 70.6543
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  : 1.498 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 5 optimal weight:    0.0570
   chunk 19 optimal weight:    0.9980
   chunk 108 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0570
   chunk 43 optimal weight:    5.9990
   chunk 100 optimal weight:    9.9990
   chunk 51 optimal weight:    9.9990
   chunk 73 optimal weight:    0.8980
   chunk 24 optimal weight:   10.0000
   chunk 153 optimal weight:    0.9990
   overall best weight:    0.6018

-------------------------------------------------------------------------------
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 = 0.4520 r_free = 0.4520 target = 0.181577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.155747 restraints weight = 24378.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.159157 restraints weight = 15777.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.161510 restraints weight = 11580.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.4301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6598
moved from start:          0.2378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  13331  Z= 0.119
  Angle     :  0.708   8.827  18034  Z= 0.366
  Chirality :  0.046   0.258   1939
  Planarity :  0.005   0.094   2281
  Dihedral  :  6.865  78.803   1739
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.84 %
    Allowed  : 10.41 %
    Favored  : 88.75 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 14.51 %
    Favored  : 83.58 %
  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: -3.54 (0.19), residues: 1556
  helix: -1.64 (0.19), residues: 637
  sheet: -2.51 (0.65), residues: 57
  loop : -3.02 (0.19), residues: 862

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   0.034   0.001   PHE B 344 
 TYR   0.015   0.001   TYR A  45 
 ARG   0.003   0.000   ARG A 654 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03957 (  342)
  hydrogen bonds       : angle       5.13472 (  981)
  covalent geometry    : bond        0.00247 (13331)
  covalent geometry    : angle       0.70763 (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
  232 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 205
  time to evaluate  : 1.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.7156 (p90) cc_final: 0.5801 (p90)
REVERT: A  249 ARG cc_start: 0.7167 (ppt170) cc_final: 0.6743 (ppt170)
REVERT: A  417 MET cc_start: 0.5069 (mtt) cc_final: 0.4824 (mtt)
REVERT: A  532 ILE cc_start: 0.7735 (mm) cc_final: 0.7027 (mp)
REVERT: A  559 TYR cc_start: 0.7448 (m-80) cc_final: 0.7247 (m-80)
REVERT: A  648 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7456 (pp20)
REVERT: A  712 ASN cc_start: 0.6351 (m110) cc_final: 0.5810 (t0)
REVERT: A  776 ARG cc_start: 0.7850 (mmp80) cc_final: 0.6652 (ttm-80)
REVERT: B  557 ASP cc_start: 0.7638 (p0) cc_final: 0.6918 (p0)
REVERT: B  656 TYR cc_start: 0.6709 (t80) cc_final: 0.6266 (t80)
REVERT: B  860 ASP cc_start: 0.6458 (m-30) cc_final: 0.6028 (m-30)
  outliers start: 27
  outliers final: 12
  residues processed: 224
  average time/residue: 0.2309
  time to fit residues: 76.8815
Evaluate side-chains
  191 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 178
  time to evaluate  : 1.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 LEU
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 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:    0.8980
   chunk 40 optimal weight:   20.0000
   chunk 44 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 117 optimal weight:    0.7980
   chunk 118 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 76 optimal weight:    4.9990
   chunk 157 optimal weight:    9.9990
   chunk 29 optimal weight:    0.9990
   chunk 147 optimal weight:    0.6980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A  39 ASN
A 527 ASN
B 432 GLN
B 522 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.178532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.152774 restraints weight = 24166.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.155993 restraints weight = 15656.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.158266 restraints weight = 11606.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.4266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6659
moved from start:          0.2771

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= 0.124
  Angle     :  0.697   8.791  18034  Z= 0.359
  Chirality :  0.046   0.305   1939
  Planarity :  0.005   0.053   2281
  Dihedral  :  6.600  77.143   1739
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.71 %
    Allowed  : 10.99 %
    Favored  : 88.30 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 16.99 %
    Favored  : 80.40 %
  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: -3.31 (0.19), residues: 1556
  helix: -1.35 (0.19), residues: 651
  sheet: -2.07 (0.63), residues: 57
  loop : -3.02 (0.19), residues: 848

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 204 
 HIS   0.007   0.001   HIS B  81 
 PHE   0.034   0.001   PHE B 200 
 TYR   0.015   0.001   TYR B 660 
 ARG   0.003   0.000   ARG A 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03771 (  342)
  hydrogen bonds       : angle       4.99393 (  981)
  covalent geometry    : bond        0.00268 (13331)
  covalent geometry    : angle       0.69662 (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
  226 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 189
  time to evaluate  : 1.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 LYS cc_start: 0.6069 (mmtm) cc_final: 0.5760 (mmtp)
REVERT: A  140 TYR cc_start: 0.6864 (p90) cc_final: 0.5622 (p90)
REVERT: A  249 ARG cc_start: 0.7271 (ppt170) cc_final: 0.6802 (ppt170)
REVERT: A  417 MET cc_start: 0.5220 (mtt) cc_final: 0.5011 (mtt)
REVERT: A  434 ARG cc_start: 0.7131 (tmm-80) cc_final: 0.6575 (ptm160)
REVERT: A  648 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7830 (pp20)
REVERT: A  712 ASN cc_start: 0.6544 (m110) cc_final: 0.6056 (t0)
REVERT: A  776 ARG cc_start: 0.7882 (mmp80) cc_final: 0.6738 (ttm110)
REVERT: B  539 ILE cc_start: 0.8560 (mm) cc_final: 0.8300 (mm)
REVERT: B  654 ARG cc_start: 0.8573 (mmm-85) cc_final: 0.8204 (tpp-160)
REVERT: B  656 TYR cc_start: 0.6641 (t80) cc_final: 0.6216 (t80)
REVERT: B  711 LYS cc_start: 0.8423 (pptt) cc_final: 0.8167 (pptt)
REVERT: B  860 ASP cc_start: 0.6539 (m-30) cc_final: 0.6135 (m-30)
REVERT: B  863 LEU cc_start: 0.4443 (OUTLIER) cc_final: 0.4142 (mt)
  outliers start: 37
  outliers final: 18
  residues processed: 211
  average time/residue: 0.2225
  time to fit residues: 70.5450
Evaluate side-chains
  191 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 171
  time to evaluate  : 1.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 ILE
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  648 GLU
Chi-restraints excluded: chain A residue  773 SER
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  356 LEU
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  742 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:    0.9990
   chunk 107 optimal weight:    4.9990
   chunk 25 optimal weight:    8.9990
   chunk 18 optimal weight:    9.9990
   chunk 64 optimal weight:    7.9990
   chunk 15 optimal weight:   30.0000
   chunk 79 optimal weight:   10.0000
   chunk 13 optimal weight:    2.9990
   chunk 83 optimal weight:    4.9990
   chunk 73 optimal weight:    3.9990
   chunk 152 optimal weight:   10.0000
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 527 ASN
** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 432 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 = 0.4363 r_free = 0.4363 target = 0.166987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.138935 restraints weight = 23971.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.142181 restraints weight = 15230.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.144415 restraints weight = 11244.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.4101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6953
moved from start:          0.3503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  13331  Z= 0.239
  Angle     :  0.848   9.740  18034  Z= 0.442
  Chirality :  0.052   0.273   1939
  Planarity :  0.005   0.050   2281
  Dihedral  :  7.307  79.164   1739
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 15.23
  Ramachandran Plot:
    Outliers :  0.71 %
    Allowed  : 12.53 %
    Favored  : 86.76 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 18.47 %
    Favored  : 78.49 %
  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: -3.56 (0.19), residues: 1556
  helix: -1.52 (0.19), residues: 660
  sheet: -2.33 (0.65), residues: 51
  loop : -3.19 (0.19), residues: 845

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 590 
 HIS   0.011   0.002   HIS A   9 
 PHE   0.023   0.002   PHE A  13 
 TYR   0.020   0.002   TYR A 350 
 ARG   0.014   0.001   ARG B 821 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04786 (  342)
  hydrogen bonds       : angle       5.49580 (  981)
  covalent geometry    : bond        0.00543 (13331)
  covalent geometry    : angle       0.84835 (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
  220 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 177
  time to evaluate  : 1.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.7110 (p90) cc_final: 0.5823 (p90)
REVERT: A  518 PHE cc_start: 0.6534 (OUTLIER) cc_final: 0.5785 (t80)
REVERT: A  712 ASN cc_start: 0.6716 (m110) cc_final: 0.6340 (t0)
REVERT: A  776 ARG cc_start: 0.7952 (mmp80) cc_final: 0.6660 (ttm-80)
REVERT: B  539 ILE cc_start: 0.8913 (mm) cc_final: 0.8648 (mm)
REVERT: B  656 TYR cc_start: 0.6961 (t80) cc_final: 0.6315 (t80)
REVERT: B  711 LYS cc_start: 0.8382 (pptt) cc_final: 0.8067 (pptt)
REVERT: B  770 TYR cc_start: 0.5512 (m-80) cc_final: 0.5117 (m-80)
REVERT: B  820 TYR cc_start: 0.7347 (OUTLIER) cc_final: 0.7116 (m-80)
REVERT: B  860 ASP cc_start: 0.6679 (m-30) cc_final: 0.6296 (m-30)
REVERT: B  863 LEU cc_start: 0.4500 (OUTLIER) cc_final: 0.4082 (mp)
  outliers start: 43
  outliers final: 23
  residues processed: 208
  average time/residue: 0.2184
  time to fit residues: 68.2287
Evaluate side-chains
  184 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 158
  time to evaluate  : 1.360 
-------------------------------------------------------------------------------
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  581 LEU
Chi-restraints excluded: chain A residue  670 VAL
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  773 SER
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   30 LEU
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  367 ILE
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  592 ILE
Chi-restraints excluded: chain B residue  633 LEU
Chi-restraints excluded: chain B residue  788 LEU
Chi-restraints excluded: chain B residue  815 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:    0.9990
   chunk 63 optimal weight:    7.9990
   chunk 65 optimal weight:   10.0000
   chunk 51 optimal weight:    3.9990
   chunk 130 optimal weight:    0.9990
   chunk 156 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 148 optimal weight:   10.0000
   chunk 124 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 7 optimal weight:    0.0170
   overall best weight:    1.6026

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

Flipped N/Q/H residues before XYZ refinement:
B 544 GLN
B 615 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.171832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.145022 restraints weight = 24116.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.148126 restraints weight = 15563.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.150410 restraints weight = 11616.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.4175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6826
moved from start:          0.3532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  13331  Z= 0.143
  Angle     :  0.742  11.979  18034  Z= 0.382
  Chirality :  0.047   0.231   1939
  Planarity :  0.005   0.052   2281
  Dihedral  :  6.823  78.804   1739
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 12.67
  Ramachandran Plot:
    Outliers :  0.71 %
    Allowed  : 11.50 %
    Favored  : 87.79 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 20.10 %
    Favored  : 77.07 %
  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: -3.32 (0.19), residues: 1556
  helix: -1.22 (0.20), residues: 651
  sheet: -2.18 (0.66), residues: 51
  loop : -3.15 (0.19), residues: 854

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A 590 
 HIS   0.006   0.001   HIS B  81 
 PHE   0.024   0.002   PHE B 200 
 TYR   0.017   0.002   TYR B 660 
 ARG   0.003   0.000   ARG A 562 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03917 (  342)
  hydrogen bonds       : angle       5.17756 (  981)
  covalent geometry    : bond        0.00319 (13331)
  covalent geometry    : angle       0.74169 (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
  221 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 181
  time to evaluate  : 1.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.6897 (p90) cc_final: 0.5696 (p90)
REVERT: A  153 TYR cc_start: 0.5389 (m-80) cc_final: 0.5126 (m-80)
REVERT: A  712 ASN cc_start: 0.6606 (m110) cc_final: 0.6279 (t0)
REVERT: A  776 ARG cc_start: 0.7900 (mmp80) cc_final: 0.6667 (ttm-80)
REVERT: B  416 TYR cc_start: 0.6912 (OUTLIER) cc_final: 0.5068 (m-80)
REVERT: B  539 ILE cc_start: 0.8794 (mm) cc_final: 0.8555 (mm)
REVERT: B  557 ASP cc_start: 0.7855 (p0) cc_final: 0.7260 (p0)
REVERT: B  654 ARG cc_start: 0.8599 (mmm-85) cc_final: 0.8191 (tpp-160)
REVERT: B  656 TYR cc_start: 0.6820 (t80) cc_final: 0.6241 (t80)
REVERT: B  711 LYS cc_start: 0.8350 (pptt) cc_final: 0.8014 (pptt)
REVERT: B  770 TYR cc_start: 0.5651 (m-80) cc_final: 0.5168 (m-80)
REVERT: B  820 TYR cc_start: 0.7263 (OUTLIER) cc_final: 0.7061 (m-80)
REVERT: B  860 ASP cc_start: 0.6567 (m-30) cc_final: 0.6240 (m-30)
REVERT: B  863 LEU cc_start: 0.4389 (OUTLIER) cc_final: 0.4036 (mt)
  outliers start: 40
  outliers final: 23
  residues processed: 207
  average time/residue: 0.2250
  time to fit residues: 69.1307
Evaluate side-chains
  186 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 160
  time to evaluate  : 1.402 
-------------------------------------------------------------------------------
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  451 ILE
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  722 LEU
Chi-restraints excluded: chain A residue  843 ASP
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  416 TYR
Chi-restraints excluded: chain B residue  504 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  742 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 19 optimal weight:    9.9990
   chunk 90 optimal weight:   10.0000
   chunk 47 optimal weight:    4.9990
   chunk 157 optimal weight:    5.9990
   chunk 69 optimal weight:    8.9990
   chunk 143 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 117 optimal weight:    6.9990
   chunk 63 optimal weight:    9.9990
   chunk 27 optimal weight:    9.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    3.1988

-------------------------------------------------------------------------------
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 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 481 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.166095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.138251 restraints weight = 24224.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.141634 restraints weight = 15251.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.143831 restraints weight = 11214.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.4094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6960
moved from start:          0.3893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  13331  Z= 0.217
  Angle     :  0.820  10.989  18034  Z= 0.427
  Chirality :  0.050   0.218   1939
  Planarity :  0.005   0.051   2281
  Dihedral  :  7.130  78.256   1739
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 16.01
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  : 13.11 %
    Favored  : 86.25 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 20.74 %
    Favored  : 75.94 %
  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: -3.51 (0.19), residues: 1556
  helix: -1.37 (0.19), residues: 665
  sheet: -2.28 (0.64), residues: 51
  loop : -3.29 (0.18), residues: 840

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 590 
 HIS   0.009   0.002   HIS A   9 
 PHE   0.038   0.002   PHE A  13 
 TYR   0.020   0.002   TYR A 260 
 ARG   0.005   0.001   ARG B  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04521 (  342)
  hydrogen bonds       : angle       5.49997 (  981)
  covalent geometry    : bond        0.00500 (13331)
  covalent geometry    : angle       0.82039 (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
  208 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 161
  time to evaluate  : 1.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.7114 (p90) cc_final: 0.5886 (p90)
REVERT: A  153 TYR cc_start: 0.5262 (m-80) cc_final: 0.5004 (m-80)
REVERT: A  518 PHE cc_start: 0.6409 (OUTLIER) cc_final: 0.5741 (t80)
REVERT: A  712 ASN cc_start: 0.6682 (m110) cc_final: 0.6371 (t0)
REVERT: B  416 TYR cc_start: 0.7019 (OUTLIER) cc_final: 0.5265 (m-80)
REVERT: B  539 ILE cc_start: 0.8906 (mm) cc_final: 0.8677 (mm)
REVERT: B  557 ASP cc_start: 0.7804 (p0) cc_final: 0.7241 (p0)
REVERT: B  711 LYS cc_start: 0.8387 (pptt) cc_final: 0.8048 (pptt)
REVERT: B  770 TYR cc_start: 0.5527 (m-80) cc_final: 0.5128 (m-80)
REVERT: B  820 TYR cc_start: 0.7459 (OUTLIER) cc_final: 0.7185 (m-80)
REVERT: B  860 ASP cc_start: 0.6728 (m-30) cc_final: 0.6396 (m-30)
REVERT: B  863 LEU cc_start: 0.4411 (OUTLIER) cc_final: 0.3948 (mt)
  outliers start: 47
  outliers final: 29
  residues processed: 192
  average time/residue: 0.2233
  time to fit residues: 64.7828
Evaluate side-chains
  189 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 156
  time to evaluate  : 1.477 
-------------------------------------------------------------------------------
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   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  286 TRP
Chi-restraints excluded: chain A residue  426 THR
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  704 LEU
Chi-restraints excluded: chain B residue   12 PHE
Chi-restraints excluded: chain B residue   27 GLN
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  416 TYR
Chi-restraints excluded: chain B residue  504 THR
Chi-restraints excluded: chain B residue  534 PHE
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  645 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 139 optimal weight:    8.9990
   chunk 118 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 63 optimal weight:    9.9990
   chunk 132 optimal weight:    4.9990
   chunk 153 optimal weight:    0.8980
   chunk 157 optimal weight:    1.9990
   chunk 116 optimal weight:    9.9990
   chunk 123 optimal weight:    6.9990
   chunk 42 optimal weight:    2.9990
   chunk 119 optimal weight:    0.8980
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
B 385 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.169634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.142862 restraints weight = 23815.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.146044 restraints weight = 15529.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.148186 restraints weight = 11567.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.4149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6877
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      :  0.004   0.036  13331  Z= 0.160
  Angle     :  0.758  10.935  18034  Z= 0.393
  Chirality :  0.048   0.206   1939
  Planarity :  0.005   0.053   2281
  Dihedral  :  6.880  78.998   1739
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 13.64
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  : 11.83 %
    Favored  : 87.53 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 22.22 %
    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: -3.37 (0.19), residues: 1556
  helix: -1.23 (0.19), residues: 665
  sheet: -2.20 (0.64), residues: 51
  loop : -3.22 (0.19), residues: 840

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 590 
 HIS   0.006   0.001   HIS A   9 
 PHE   0.027   0.002   PHE A  13 
 TYR   0.017   0.002   TYR A 260 
 ARG   0.003   0.000   ARG B  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04061 (  342)
  hydrogen bonds       : angle       5.30573 (  981)
  covalent geometry    : bond        0.00361 (13331)
  covalent geometry    : angle       0.75772 (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
  224 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 181
  time to evaluate  : 1.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.6967 (p90) cc_final: 0.5790 (p90)
REVERT: A  153 TYR cc_start: 0.5250 (m-80) cc_final: 0.4994 (m-80)
REVERT: A  415 LEU cc_start: 0.6328 (mm) cc_final: 0.5727 (tp)
REVERT: A  712 ASN cc_start: 0.6765 (m110) cc_final: 0.6420 (t0)
REVERT: B  260 TYR cc_start: 0.7337 (m-80) cc_final: 0.6579 (t80)
REVERT: B  416 TYR cc_start: 0.6927 (OUTLIER) cc_final: 0.5174 (m-80)
REVERT: B  539 ILE cc_start: 0.8852 (mm) cc_final: 0.8612 (mm)
REVERT: B  557 ASP cc_start: 0.7716 (p0) cc_final: 0.7213 (p0)
REVERT: B  711 LYS cc_start: 0.8375 (pptt) cc_final: 0.8066 (pptt)
REVERT: B  770 TYR cc_start: 0.5677 (m-80) cc_final: 0.5260 (m-80)
REVERT: B  820 TYR cc_start: 0.7267 (OUTLIER) cc_final: 0.6989 (m-80)
REVERT: B  860 ASP cc_start: 0.6712 (m-30) cc_final: 0.6404 (m-30)
  outliers start: 43
  outliers final: 30
  residues processed: 208
  average time/residue: 0.2333
  time to fit residues: 72.6858
Evaluate side-chains
  197 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 165
  time to evaluate  : 1.484 
-------------------------------------------------------------------------------
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  426 THR
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  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   60 ILE
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  568 GLU
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  755 LEU
Chi-restraints excluded: chain B residue  788 LEU
Chi-restraints excluded: chain B residue  809 PHE
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 101 optimal weight:    8.9990
   chunk 25 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 77 optimal weight:    5.9990
   chunk 115 optimal weight:    0.0570
   chunk 45 optimal weight:    8.9990
   chunk 136 optimal weight:   10.0000
   chunk 90 optimal weight:    6.9990
   chunk 102 optimal weight:    5.9990
   chunk 50 optimal weight:    0.8980
   overall best weight:    2.1904

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.168864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.141245 restraints weight = 23953.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.144639 restraints weight = 15063.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.146964 restraints weight = 11032.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.4133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6899
moved from start:          0.4089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13331  Z= 0.174
  Angle     :  0.786  10.649  18034  Z= 0.408
  Chirality :  0.049   0.197   1939
  Planarity :  0.005   0.053   2281
  Dihedral  :  6.908  76.745   1739
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 14.30
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  : 12.60 %
    Favored  : 86.89 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 22.72 %
    Favored  : 74.24 %
  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: -3.36 (0.19), residues: 1556
  helix: -1.21 (0.19), residues: 666
  sheet: -2.19 (0.63), residues: 51
  loop : -3.22 (0.19), residues: 839

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 590 
 HIS   0.007   0.001   HIS A   9 
 PHE   0.030   0.002   PHE A  13 
 TYR   0.019   0.002   TYR A 744 
 ARG   0.007   0.000   ARG A 758 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04292 (  342)
  hydrogen bonds       : angle       5.36811 (  981)
  covalent geometry    : bond        0.00398 (13331)
  covalent geometry    : angle       0.78558 (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
  217 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 174
  time to evaluate  : 1.553 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.7058 (p90) cc_final: 0.5859 (p90)
REVERT: A  153 TYR cc_start: 0.5223 (m-80) cc_final: 0.4965 (m-80)
REVERT: A  415 LEU cc_start: 0.6178 (mm) cc_final: 0.5679 (tp)
REVERT: A  505 LEU cc_start: 0.7390 (mt) cc_final: 0.7075 (mp)
REVERT: A  712 ASN cc_start: 0.6722 (m110) cc_final: 0.6370 (t0)
REVERT: B   71 GLU cc_start: 0.7688 (mp0) cc_final: 0.7457 (mt-10)
REVERT: B  416 TYR cc_start: 0.6870 (OUTLIER) cc_final: 0.5273 (m-80)
REVERT: B  539 ILE cc_start: 0.8846 (mm) cc_final: 0.8618 (mm)
REVERT: B  557 ASP cc_start: 0.7754 (p0) cc_final: 0.7305 (p0)
REVERT: B  590 TRP cc_start: 0.5370 (p-90) cc_final: 0.5053 (p-90)
REVERT: B  711 LYS cc_start: 0.8367 (pptt) cc_final: 0.8033 (pptt)
REVERT: B  770 TYR cc_start: 0.5564 (m-80) cc_final: 0.5142 (m-80)
REVERT: B  820 TYR cc_start: 0.7354 (OUTLIER) cc_final: 0.7074 (m-80)
REVERT: B  860 ASP cc_start: 0.6758 (m-30) cc_final: 0.6436 (m-30)
  outliers start: 43
  outliers final: 36
  residues processed: 199
  average time/residue: 0.2334
  time to fit residues: 69.7303
Evaluate side-chains
  204 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 166
  time to evaluate  : 1.599 
-------------------------------------------------------------------------------
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   90 LEU
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  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  648 GLU
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  797 VAL
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   60 ILE
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  504 THR
Chi-restraints excluded: chain B residue  534 PHE
Chi-restraints excluded: chain B residue  568 GLU
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  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:    4.9990
   chunk 83 optimal weight:    6.9990
   chunk 48 optimal weight:    0.6980
   chunk 154 optimal weight:    1.9990
   chunk 100 optimal weight:    8.9990
   chunk 7 optimal weight:    0.7980
   chunk 58 optimal weight:    0.6980
   chunk 103 optimal weight:    7.9990
   chunk 59 optimal weight:    6.9990
   overall best weight:    1.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 790 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.170157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.143728 restraints weight = 25051.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.146934 restraints weight = 16116.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.149126 restraints weight = 11992.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.4152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6872
moved from start:          0.4157

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= 0.159
  Angle     :  0.775  10.886  18034  Z= 0.401
  Chirality :  0.048   0.205   1939
  Planarity :  0.005   0.065   2281
  Dihedral  :  6.801  75.065   1739
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 13.56
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  : 12.79 %
    Favored  : 86.70 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 23.57 %
    Favored  : 73.96 %
  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: -3.30 (0.20), residues: 1556
  helix: -1.19 (0.20), residues: 666
  sheet: -2.10 (0.72), residues: 44
  loop : -3.17 (0.19), residues: 846

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 590 
 HIS   0.006   0.001   HIS A   9 
 PHE   0.026   0.002   PHE A  13 
 TYR   0.015   0.002   TYR A 744 
 ARG   0.007   0.000   ARG A 758 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04200 (  342)
  hydrogen bonds       : angle       5.33731 (  981)
  covalent geometry    : bond        0.00360 (13331)
  covalent geometry    : angle       0.77453 (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
  210 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 175
  time to evaluate  : 1.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 TYR cc_start: 0.6946 (p90) cc_final: 0.5745 (p90)
REVERT: A  153 TYR cc_start: 0.5220 (m-80) cc_final: 0.4985 (m-80)
REVERT: A  415 LEU cc_start: 0.5906 (mm) cc_final: 0.5439 (tp)
REVERT: A  513 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6389 (mt-10)
REVERT: A  712 ASN cc_start: 0.6697 (m110) cc_final: 0.6387 (t0)
REVERT: B  260 TYR cc_start: 0.7297 (m-80) cc_final: 0.6371 (t80)
REVERT: B  416 TYR cc_start: 0.6814 (OUTLIER) cc_final: 0.5258 (m-80)
REVERT: B  539 ILE cc_start: 0.8758 (mm) cc_final: 0.8536 (mm)
REVERT: B  557 ASP cc_start: 0.7672 (p0) cc_final: 0.7297 (p0)
REVERT: B  711 LYS cc_start: 0.8404 (pptt) cc_final: 0.8032 (pptt)
REVERT: B  770 TYR cc_start: 0.5606 (m-80) cc_final: 0.5231 (m-80)
REVERT: B  820 TYR cc_start: 0.7346 (OUTLIER) cc_final: 0.7108 (m-80)
REVERT: B  860 ASP cc_start: 0.6777 (m-30) cc_final: 0.6438 (m-30)
  outliers start: 35
  outliers final: 32
  residues processed: 195
  average time/residue: 0.2197
  time to fit residues: 65.4144
Evaluate side-chains
  198 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 164
  time to evaluate  : 1.479 
-------------------------------------------------------------------------------
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   90 LEU
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  451 ILE
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain A residue  648 GLU
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  797 VAL
Chi-restraints excluded: chain B residue   12 PHE
Chi-restraints excluded: chain B residue   27 GLN
Chi-restraints excluded: chain B residue   60 ILE
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  568 GLU
Chi-restraints excluded: chain B residue  633 LEU
Chi-restraints excluded: chain B residue  742 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 85 optimal weight:    7.9990
   chunk 20 optimal weight:    6.9990
   chunk 40 optimal weight:   20.0000
   chunk 43 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 118 optimal weight:    0.6980
   chunk 80 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 124 optimal weight:    2.9990
   chunk 155 optimal weight:    4.9990
   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 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  33 ASN
B 227 ASN
B 355 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.173753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.147575 restraints weight = 24797.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.150840 restraints weight = 15919.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.153099 restraints weight = 11767.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.4200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6781
moved from start:          0.4158

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= 0.137
  Angle     :  0.749  11.224  18034  Z= 0.387
  Chirality :  0.047   0.196   1939
  Planarity :  0.005   0.058   2281
  Dihedral  :  6.530  72.977   1739
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  : 12.34 %
    Favored  : 87.15 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 23.85 %
    Favored  : 73.89 %
  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: -3.20 (0.20), residues: 1556
  helix: -1.05 (0.20), residues: 670
  sheet: -2.11 (0.63), residues: 56
  loop : -3.17 (0.19), residues: 830

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 291 
 HIS   0.005   0.001   HIS B  81 
 PHE   0.021   0.002   PHE A   5 
 TYR   0.012   0.001   TYR A 744 
 ARG   0.003   0.000   ARG B  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04104 (  342)
  hydrogen bonds       : angle       5.22061 (  981)
  covalent geometry    : bond        0.00302 (13331)
  covalent geometry    : angle       0.74902 (18034)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3788.16 seconds
wall clock time: 67 minutes 21.49 seconds (4041.49 seconds total)