Starting phenix.real_space_refine
on Thu Jul 31 21:58:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6que_4637/07_2025/6que_4637.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6que_4637/07_2025/6que_4637.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6que_4637/07_2025/6que_4637.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6que_4637/07_2025/6que_4637.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6que_4637/07_2025/6que_4637.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6que_4637/07_2025/6que_4637.cif"
  }
  resolution = 3.7
  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=   0.002 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       7      5.49       5
     S      80      5.16       5
     C    8822      2.51       5
     N    2283      2.21       5
     O    2599      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13791
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 7620
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1038, 7620
          Classifications: {'peptide': 1038}
          Link IDs: {'PTRANS': 51, 'TRANS': 986}
    Chain: "B"
      Number of atoms: 6035
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 827, 6035
          Classifications: {'peptide': 827}
          Link IDs: {'PTRANS': 39, 'TRANS': 787}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 92
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 92
          Unusual residues: {'NAD': 1, 'NAP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Unusual residues: {'NAD': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 9.47, per 1000 atoms: 0.69
  Number of scatterers: 13791
  At special positions: 0
  Unit cell: (140.58, 130.995, 132.06, 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      80     16.00
     P       7     15.00
     O    2599      8.00
     N    2283      7.00
     C    8822      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: 4.62
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  3718 Ramachandran restraints generated.
    1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3308

  Finding SS restraints...
    Secondary structure from input PDB file:
      78 helices and 10 sheets defined
      57.3% alpha, 5.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.92
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 13
      removed outlier: 3.665A  pdb=" N   GLN A  13 " --> pdb=" O   PRO A  10 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 10 through 13'
    Processing helix  chain 'A' and resid 59 through 67
      removed outlier: 3.508A  pdb=" N   TYR A  63 " --> pdb=" O   SER A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 78
      removed outlier: 3.678A  pdb=" N   ALA A  78 " --> pdb=" O   LYS A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 127
      removed outlier: 3.737A  pdb=" N   LEU A 121 " --> pdb=" O   ASN A 117 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   LYS A 123 " --> pdb=" O   ASP A 119 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ARG A 127 " --> pdb=" O   LYS A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 165
      removed outlier: 3.713A  pdb=" N   VAL A 161 " --> pdb=" O   GLY A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 206
    Processing helix  chain 'A' and resid 216 through 227
      removed outlier: 3.739A  pdb=" N   LEU A 220 " --> pdb=" O   ARG A 216 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   GLU A 221 " --> pdb=" O   ALA A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 265
    Processing helix  chain 'A' and resid 287 through 292
    Processing helix  chain 'A' and resid 333 through 336
    Processing helix  chain 'A' and resid 337 through 357
      removed outlier: 4.053A  pdb=" N   SER A 357 " --> pdb=" O   LEU A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 384
      removed outlier: 3.511A  pdb=" N   VAL A 379 " --> pdb=" O   THR A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 420
      removed outlier: 3.975A  pdb=" N   LEU A 415 " --> pdb=" O   THR A 411 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   GLU A 416 " --> pdb=" O   VAL A 412 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ALA A 417 " --> pdb=" O   ALA A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 423
      No H-bonds generated for 'chain 'A' and resid 421 through 423'
    Processing helix  chain 'A' and resid 424 through 449
      removed outlier: 3.969A  pdb=" N   VAL A 435 " --> pdb=" O   THR A 431 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   TYR A 436 " --> pdb=" O   SER A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 475
      removed outlier: 3.935A  pdb=" N   SER A 456 " --> pdb=" O   ASN A 452 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   TRP A 474 " --> pdb=" O   TYR A 470 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   GLY A 475 " --> pdb=" O   HIS A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 479
      No H-bonds generated for 'chain 'A' and resid 477 through 479'
    Processing helix  chain 'A' and resid 480 through 492
      removed outlier: 3.705A  pdb=" N   SER A 486 " --> pdb=" O   SER A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 502
      removed outlier: 3.739A  pdb=" N   GLY A 498 " --> pdb=" O   LEU A 494 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   VAL A 501 " --> pdb=" O   VAL A 497 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   LEU A 502 " --> pdb=" O   GLY A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 511 through 540
      removed outlier: 3.731A  pdb=" N   ALA A 518 " --> pdb=" O   GLN A 514 " (cutoff:3.500A)
      removed outlier: 4.945A  pdb=" N   THR A 521 " --> pdb=" O   ALA A 517 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   VAL A 526 " --> pdb=" O   PHE A 522 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   ASN A 527 " --> pdb=" O   ILE A 523 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ILE A 528 " --> pdb=" O   SER A 524 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   ALA A 529 " --> pdb=" O   SER A 525 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ASP A 540 " --> pdb=" O   GLN A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 554
      removed outlier: 3.703A  pdb=" N   LEU A 554 " --> pdb=" O   TYR A 551 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 551 through 554'
    Processing helix  chain 'A' and resid 555 through 572
      removed outlier: 4.176A  pdb=" N   ALA A 559 " --> pdb=" O   TYR A 555 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   THR A 561 " --> pdb=" O   LEU A 557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 576 through 594
      removed outlier: 3.757A  pdb=" N   LEU A 582 " --> pdb=" O   GLN A 578 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   LEU A 592 " --> pdb=" O   CYS A 588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 624
      removed outlier: 4.093A  pdb=" N   GLY A 608 " --> pdb=" O   GLY A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 626 through 649
      removed outlier: 3.610A  pdb=" N   LYS A 649 " --> pdb=" O   LEU A 645 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 682
      removed outlier: 3.689A  pdb=" N   LEU A 659 " --> pdb=" O   ASP A 655 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   SER A 665 " --> pdb=" O   ALA A 661 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   LEU A 666 " --> pdb=" O   ALA A 662 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   VAL A 667 " --> pdb=" O   PHE A 663 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   VAL A 672 " --> pdb=" O   GLY A 668 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   ALA A 677 " --> pdb=" O   LEU A 673 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ILE A 681 " --> pdb=" O   ALA A 677 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 683 through 686
      removed outlier: 3.541A  pdb=" N   PHE A 686 " --> pdb=" O   TYR A 683 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 683 through 686'
    Processing helix  chain 'A' and resid 690 through 692
      No H-bonds generated for 'chain 'A' and resid 690 through 692'
    Processing helix  chain 'A' and resid 693 through 722
      removed outlier: 4.005A  pdb=" N   ALA A 699 " --> pdb=" O   THR A 695 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   THR A 703 " --> pdb=" O   ALA A 699 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   SER A 711 " --> pdb=" O   GLY A 707 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLY A 712 " --> pdb=" O   VAL A 708 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   SER A 713 " --> pdb=" O   THR A 709 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LEU A 720 " --> pdb=" O   ALA A 716 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   GLY A 722 " --> pdb=" O   GLY A 718 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 734 through 748
    Processing helix  chain 'A' and resid 757 through 782
      removed outlier: 3.982A  pdb=" N   ALA A 782 " --> pdb=" O   THR A 778 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 787 through 810
      removed outlier: 4.123A  pdb=" N   VAL A 791 " --> pdb=" O   ASP A 787 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   LEU A 795 " --> pdb=" O   VAL A 791 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ASN A 796 " --> pdb=" O   ILE A 792 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LEU A 803 " --> pdb=" O   SER A 799 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 813 through 837
      removed outlier: 3.888A  pdb=" N   ILE A 817 " --> pdb=" O   ASN A 813 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   SER A 824 " --> pdb=" O   ALA A 820 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   MET A 837 " --> pdb=" O   MET A 833 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 840 through 846
    Processing helix  chain 'A' and resid 870 through 881
    Processing helix  chain 'A' and resid 889 through 895
      removed outlier: 4.338A  pdb=" N   CYS A 893 " --> pdb=" O   GLY A 889 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ALA A 895 " --> pdb=" O   GLY A 891 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 897 through 909
      removed outlier: 3.816A  pdb=" N   ILE A 901 " --> pdb=" O   ALA A 897 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ASP A 903 " --> pdb=" O   TYR A 899 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 928 through 938
      removed outlier: 3.773A  pdb=" N   VAL A 932 " --> pdb=" O   GLY A 928 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 940 through 942
      No H-bonds generated for 'chain 'A' and resid 940 through 942'
    Processing helix  chain 'A' and resid 971 through 976
    Processing helix  chain 'A' and resid 988 through 992
      removed outlier: 3.789A  pdb=" N   SER A 992 " --> pdb=" O   VAL A 989 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1011 through 1015
      removed outlier: 3.836A  pdb=" N   TYR A1015 " --> pdb=" O   PRO A1012 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1025 through 1042
    Processing helix  chain 'B' and resid 32 through 38
      removed outlier: 3.768A  pdb=" N   ALA B  38 " --> pdb=" O   ALA B  34 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 67
      removed outlier: 3.926A  pdb=" N   TYR B  63 " --> pdb=" O   SER B  59 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   GLY B  67 " --> pdb=" O   TYR B  63 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 102
    Processing helix  chain 'B' and resid 113 through 116
    Processing helix  chain 'B' and resid 117 through 127
      removed outlier: 3.643A  pdb=" N   LEU B 121 " --> pdb=" O   ASN B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 165
      removed outlier: 3.656A  pdb=" N   ALA B 165 " --> pdb=" O   VAL B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 207
    Processing helix  chain 'B' and resid 217 through 227
    Processing helix  chain 'B' and resid 250 through 265
    Processing helix  chain 'B' and resid 287 through 292
    Processing helix  chain 'B' and resid 333 through 336
    Processing helix  chain 'B' and resid 337 through 357
      removed outlier: 3.799A  pdb=" N   THR B 343 " --> pdb=" O   THR B 339 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LYS B 351 " --> pdb=" O   ASN B 347 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   LEU B 352 " --> pdb=" O   ASN B 348 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ALA B 355 " --> pdb=" O   LYS B 351 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   SER B 357 " --> pdb=" O   LEU B 353 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 375 through 383
      removed outlier: 3.789A  pdb=" N   VAL B 379 " --> pdb=" O   THR B 375 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 425 through 449
      removed outlier: 3.634A  pdb=" N   THR B 429 " --> pdb=" O   PRO B 425 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ALA B 449 " --> pdb=" O   GLY B 445 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 472
      removed outlier: 3.826A  pdb=" N   SER B 456 " --> pdb=" O   ASN B 452 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 477 through 480
    Processing helix  chain 'B' and resid 481 through 492
      removed outlier: 3.597A  pdb=" N   MET B 485 " --> pdb=" O   HIS B 481 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   SER B 486 " --> pdb=" O   SER B 482 " (cutoff:3.500A)
      removed outlier: 4.855A  pdb=" N   VAL B 487 " --> pdb=" O   PRO B 483 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 495 through 501
      removed outlier: 3.949A  pdb=" N   GLY B 499 " --> pdb=" O   THR B 495 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 511 through 540
      removed outlier: 3.700A  pdb=" N   SER B 525 " --> pdb=" O   THR B 521 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   VAL B 526 " --> pdb=" O   PHE B 522 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   ASN B 527 " --> pdb=" O   ILE B 523 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   ILE B 528 " --> pdb=" O   SER B 524 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 541 through 543
      No H-bonds generated for 'chain 'B' and resid 541 through 543'
    Processing helix  chain 'B' and resid 551 through 554
    Processing helix  chain 'B' and resid 555 through 563
      removed outlier: 4.442A  pdb=" N   ALA B 559 " --> pdb=" O   TYR B 555 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   THR B 561 " --> pdb=" O   LEU B 557 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 563 through 572
      removed outlier: 3.801A  pdb=" N   ALA B 568 " --> pdb=" O   GLY B 564 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   SER B 569 " --> pdb=" O   GLY B 565 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 577 through 595
    Processing helix  chain 'B' and resid 600 through 622
    Processing helix  chain 'B' and resid 626 through 650
      removed outlier: 3.560A  pdb=" N   ALA B 648 " --> pdb=" O   GLY B 644 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   ARG B 650 " --> pdb=" O   THR B 646 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 655 through 663
      removed outlier: 3.600A  pdb=" N   VAL B 660 " --> pdb=" O   LEU B 656 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   ALA B 661 " --> pdb=" O   PRO B 657 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   ALA B 662 " --> pdb=" O   GLN B 658 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 664 through 682
      removed outlier: 4.041A  pdb=" N   GLY B 668 " --> pdb=" O   HIS B 664 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   LEU B 669 " --> pdb=" O   SER B 665 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 693 through 721
      removed outlier: 4.895A  pdb=" N   ALA B 699 " --> pdb=" O   THR B 695 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 735 through 747
    Processing helix  chain 'B' and resid 748 through 753
      Proline residue:  B 751  - end of helix
      No H-bonds generated for 'chain 'B' and resid 748 through 753'
    Processing helix  chain 'B' and resid 757 through 782
      removed outlier: 3.759A  pdb=" N   GLY B 761 " --> pdb=" O   SER B 757 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   ALA B 782 " --> pdb=" O   THR B 778 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 787 through 811
      removed outlier: 3.827A  pdb=" N   THR B 793 " --> pdb=" O   PRO B 789 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   GLY B 800 " --> pdb=" O   ASN B 796 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   TRP B 801 " --> pdb=" O   SER B 797 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 812 through 837
      removed outlier: 3.753A  pdb=" N   MET B 837 " --> pdb=" O   MET B 833 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 841 through 846
    Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 18
      removed outlier: 6.310A  pdb=" N   VAL A  16 " --> pdb=" O   VAL A  47 " (cutoff:3.500A)
      removed outlier: 7.969A  pdb=" N   GLU A  49 " --> pdb=" O   VAL A  16 " (cutoff:3.500A)
      removed outlier: 7.402A  pdb=" N   VAL A  18 " --> pdb=" O   GLU A  49 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   VAL A  46 " --> pdb=" O   GLN A  69 " (cutoff:3.500A)
      removed outlier: 7.375A  pdb=" N   GLN A  71 " --> pdb=" O   VAL A  46 " (cutoff:3.500A)
      removed outlier: 6.020A  pdb=" N   VAL A  48 " --> pdb=" O   GLN A  71 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 83
      removed outlier: 3.761A  pdb=" N   SER A 110 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91
      removed outlier: 3.822A  pdb=" N   ILE A  96 " --> pdb=" O   ASN A  91 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 177
    Processing sheet with id=AA5, first strand: chain 'A' and resid 209 through 210
      removed outlier: 6.007A  pdb=" N   LEU A 271 " --> pdb=" O   VAL A 301 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 386 through 387
    Processing sheet with id=AA7, first strand: chain 'A' and resid 867 through 868
      removed outlier: 7.046A  pdb=" N   THR A 867 " --> pdb=" O   MET A1021 " (cutoff:3.500A)
      removed outlier: 6.121A  pdb=" N   VAL A 995 " --> pdb=" O   ALA A1020 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   SER A 883 " --> pdb=" O   LEU A 959 " (cutoff:3.500A)
      removed outlier: 7.655A  pdb=" N   LEU A 961 " --> pdb=" O   SER A 883 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   ILE A 885 " --> pdb=" O   LEU A 961 " (cutoff:3.500A)
      removed outlier: 7.707A  pdb=" N   ILE A 963 " --> pdb=" O   ILE A 885 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   THR A 887 " --> pdb=" O   ILE A 963 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   ILE A 884 " --> pdb=" O   ARG A 916 " (cutoff:3.500A)
      removed outlier: 7.572A  pdb=" N   GLY A 918 " --> pdb=" O   ILE A 884 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   ILE A 886 " --> pdb=" O   GLY A 918 " (cutoff:3.500A)
      removed outlier: 8.620A  pdb=" N   LEU A 945 " --> pdb=" O   VAL A 915 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   PHE A 917 " --> pdb=" O   LEU A 945 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 69 through 71
      removed outlier: 7.185A  pdb=" N   VAL B  46 " --> pdb=" O   GLN B  69 " (cutoff:3.500A)
      removed outlier: 7.623A  pdb=" N   GLN B  71 " --> pdb=" O   VAL B  46 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   VAL B  48 " --> pdb=" O   GLN B  71 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   VAL B  16 " --> pdb=" O   VAL B  47 " (cutoff:3.500A)
      removed outlier: 7.774A  pdb=" N   GLU B  49 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
      removed outlier: 7.336A  pdb=" N   VAL B  18 " --> pdb=" O   GLU B  49 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   LEU B 108 " --> pdb=" O   LEU B 132 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   ALA B 133 " --> pdb=" O   VAL B 384 " (cutoff:3.500A)
      removed outlier: 5.934A  pdb=" N   VAL B 384 " --> pdb=" O   ALA B 133 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 176 through 177
      removed outlier: 3.883A  pdb=" N   THR B 177 " --> pdb=" O   GLY B 180 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   GLY B 180 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 209 through 210
      removed outlier: 3.695A  pdb=" N   ILE B 270 " --> pdb=" O   LYS B 186 " (cutoff:3.500A)
      removed outlier: 6.090A  pdb=" N   LEU B 271 " --> pdb=" O   VAL B 301 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ILE B 325 " --> pdb=" O   HIS B 322 " (cutoff:3.500A)

    702 hydrogen bonds defined for protein.
    2058 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: 9.63

  Time building geometry restraints manager: 5.31 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4230
        1.34 -     1.46: 2730
        1.46 -     1.58: 6938
        1.58 -     1.70: 13
        1.70 -     1.82: 142
  Bond restraints: 14053
  Sorted by residual:
  bond pdb=" O2B NAP A1101 "
       pdb=" P2B NAP A1101 "
    ideal  model  delta    sigma   weight residual
    1.736  1.580  0.156 2.00e-02 2.50e+03 6.11e+01
  bond pdb=" O3  NAD A1102 "
       pdb=" PA  NAD A1102 "
    ideal  model  delta    sigma   weight residual
    1.653  1.589  0.064 2.00e-02 2.50e+03 1.02e+01
  bond pdb=" O3  NAD B1101 "
       pdb=" PA  NAD B1101 "
    ideal  model  delta    sigma   weight residual
    1.653  1.589  0.064 2.00e-02 2.50e+03 1.01e+01
  bond pdb=" C   THR B 546 "
       pdb=" N   ASP B 547 "
    ideal  model  delta    sigma   weight residual
    1.331  1.265  0.066 2.07e-02 2.33e+03 1.00e+01
  bond pdb=" O5D NAP A1101 "
       pdb=" PN  NAP A1101 "
    ideal  model  delta    sigma   weight residual
    1.649  1.590  0.059 2.00e-02 2.50e+03 8.72e+00
  ... (remaining 14048 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.36: 18267
        2.36 -     4.72: 699
        4.72 -     7.09: 112
        7.09 -     9.45: 29
        9.45 -    11.81: 3
  Bond angle restraints: 19110
  Sorted by residual:
  angle pdb=" N   ALA A 518 "
        pdb=" CA  ALA A 518 "
        pdb=" C   ALA A 518 "
      ideal   model   delta    sigma   weight residual
     113.18  103.98    9.20 1.33e+00 5.65e-01 4.78e+01
  angle pdb=" C   GLN B  24 "
        pdb=" N   ASN B  25 "
        pdb=" CA  ASN B  25 "
      ideal   model   delta    sigma   weight residual
     122.46  131.85   -9.39 1.41e+00 5.03e-01 4.43e+01
  angle pdb=" C   PHE B 371 "
        pdb=" N   ASP B 372 "
        pdb=" CA  ASP B 372 "
      ideal   model   delta    sigma   weight residual
     122.44  114.57    7.87 1.19e+00 7.06e-01 4.38e+01
  angle pdb=" C   ALA A  38 "
        pdb=" N   LEU A  39 "
        pdb=" CA  LEU A  39 "
      ideal   model   delta    sigma   weight residual
     121.54  130.90   -9.36 1.91e+00 2.74e-01 2.40e+01
  angle pdb=" C   ALA B  38 "
        pdb=" N   LEU B  39 "
        pdb=" CA  LEU B  39 "
      ideal   model   delta    sigma   weight residual
     121.54  130.56   -9.02 1.91e+00 2.74e-01 2.23e+01
  ... (remaining 19105 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.23: 7937
       16.23 -    32.46: 382
       32.46 -    48.69: 87
       48.69 -    64.92: 35
       64.92 -    81.16: 23
  Dihedral angle restraints: 8464
    sinusoidal: 3233
      harmonic: 5231
  Sorted by residual:
  dihedral pdb=" CA  LYS B 399 "
           pdb=" C   LYS B 399 "
           pdb=" N   ASN B 400 "
           pdb=" CA  ASN B 400 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -138.96  -41.04     0      5.00e+00 4.00e-02 6.74e+01
  dihedral pdb=" CA  THR B 424 "
           pdb=" C   THR B 424 "
           pdb=" N   PRO B 425 "
           pdb=" CA  PRO B 425 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -149.47  -30.53     0      5.00e+00 4.00e-02 3.73e+01
  dihedral pdb=" CA  GLN A  37 "
           pdb=" C   GLN A  37 "
           pdb=" N   ALA A  38 "
           pdb=" CA  ALA A  38 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.64   29.36     0      5.00e+00 4.00e-02 3.45e+01
  ... (remaining 8461 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1647
       0.059 -    0.119: 507
       0.119 -    0.178: 102
       0.178 -    0.238: 16
       0.238 -    0.297: 3
  Chirality restraints: 2275
  Sorted by residual:
  chirality pdb=" CA  TRP B 474 "
            pdb=" N   TRP B 474 "
            pdb=" C   TRP B 474 "
            pdb=" CB  TRP B 474 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.21e+00
  chirality pdb=" CA  PHE B 365 "
            pdb=" N   PHE B 365 "
            pdb=" C   PHE B 365 "
            pdb=" CB  PHE B 365 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.58e+00
  chirality pdb=" CA  PHE B 752 "
            pdb=" N   PHE B 752 "
            pdb=" C   PHE B 752 "
            pdb=" CB  PHE B 752 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.48e+00
  ... (remaining 2272 not shown)

  Planarity restraints: 2416
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B  18 "   -0.048 5.00e-02 4.00e+02   7.29e-02 8.50e+00
        pdb=" N   PRO B  19 "    0.126 5.00e-02 4.00e+02
        pdb=" CA  PRO B  19 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO B  19 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 752 "   -0.025 2.00e-02 2.50e+03   2.19e-02 8.38e+00
        pdb=" CG  PHE B 752 "    0.051 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 752 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 752 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 752 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 752 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 752 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 673 "   -0.014 2.00e-02 2.50e+03   2.87e-02 8.25e+00
        pdb=" C   LEU B 673 "    0.050 2.00e-02 2.50e+03
        pdb=" O   LEU B 673 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   THR B 674 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 2413 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 2709
        2.76 -     3.30: 13362
        3.30 -     3.83: 22780
        3.83 -     4.37: 26115
        4.37 -     4.90: 44550
  Nonbonded interactions: 109516
  Sorted by model distance:
  nonbonded pdb=" O   TYR B 566 "
            pdb=" OG  SER B 569 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" O   GLN B 340 "
            pdb=" OG1 THR B 343 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" O   PHE A 954 "
            pdb=" OG  SER A 992 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" O   MET B 485 "
            pdb=" OG1 THR B 488 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" O   GLY A 776 "
            pdb=" OG1 THR A 780 "
     model   vdw
     2.287 3.040
  ... (remaining 109511 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             19.280
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.030
  Extract box with map and model:          55.320
  Check model and map are aligned:         0.160
  Set scattering table:                    0.200
  Process input model:                     42.060
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  121.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
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      :  0.009   0.156  14053  Z= 0.392
  Angle     :  1.104  11.811  19110  Z= 0.599
  Chirality :  0.059   0.297   2275
  Planarity :  0.008   0.073   2416
  Dihedral  : 12.099  81.155   5156
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  7.58 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.28 %
    Favored  : 96.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.11 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.49 (0.16), residues: 1859
  helix: -1.83 (0.13), residues: 985
  sheet: -1.62 (0.41), residues: 147
  loop : -3.04 (0.20), residues: 727

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.004   TRP B 474 
 HIS   0.011   0.003   HIS A 664 
 PHE   0.051   0.004   PHE B 752 
 TYR   0.027   0.003   TYR B 330 
 ARG   0.008   0.001   ARG B 734 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18092 (  702)
  hydrogen bonds       : angle       7.27392 ( 2058)
  covalent geometry    : bond        0.00871 (14053)
  covalent geometry    : angle       1.10439 (19110)

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

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

  3718 Ramachandran restraints generated.
    1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3718 Ramachandran restraints generated.
    1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  335 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 333
  time to evaluate  : 1.932 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 GLU cc_start: 0.8585 (tp30) cc_final: 0.8272 (tm-30)
REVERT: A   60 ASP cc_start: 0.9161 (m-30) cc_final: 0.8822 (t70)
REVERT: A   77 LEU cc_start: 0.9391 (mt) cc_final: 0.9079 (tp)
REVERT: A  172 PHE cc_start: 0.9237 (m-10) cc_final: 0.8879 (m-10)
REVERT: A  249 MET cc_start: 0.7611 (mmp) cc_final: 0.7355 (mmm)
REVERT: A  286 PHE cc_start: 0.8659 (m-80) cc_final: 0.8230 (m-10)
REVERT: A  288 LYS cc_start: 0.9299 (ptmm) cc_final: 0.9052 (ptpt)
REVERT: A  296 GLU cc_start: 0.7620 (mm-30) cc_final: 0.6704 (tm-30)
REVERT: A  337 MET cc_start: 0.8594 (mtp) cc_final: 0.8386 (mtp)
REVERT: A  345 TYR cc_start: 0.9065 (t80) cc_final: 0.8861 (t80)
REVERT: A  414 GLU cc_start: 0.8046 (tt0) cc_final: 0.7824 (mt-10)
REVERT: A  430 MET cc_start: 0.8947 (tpt) cc_final: 0.8674 (tpt)
REVERT: A  458 MET cc_start: 0.9234 (tpp) cc_final: 0.8981 (tpp)
REVERT: A  507 LEU cc_start: 0.8938 (mm) cc_final: 0.8694 (tt)
REVERT: A  754 MET cc_start: 0.7578 (mpt) cc_final: 0.7048 (mmp)
REVERT: A  764 CYS cc_start: 0.8918 (m) cc_final: 0.8631 (t)
REVERT: A  869 ILE cc_start: 0.8925 (pt) cc_final: 0.8546 (pt)
REVERT: A  873 ASN cc_start: 0.8463 (m110) cc_final: 0.7916 (t0)
REVERT: A  877 MET cc_start: 0.9124 (ttp) cc_final: 0.8761 (ptm)
REVERT: A  903 ASP cc_start: 0.8636 (t70) cc_final: 0.8237 (t0)
REVERT: A  907 MET cc_start: 0.8713 (mtt) cc_final: 0.8294 (mmm)
REVERT: A  947 MET cc_start: 0.9091 (ttp) cc_final: 0.8645 (tmm)
REVERT: A 1021 MET cc_start: 0.8833 (mmm) cc_final: 0.8504 (mmm)
REVERT: B  109 ILE cc_start: 0.8759 (mm) cc_final: 0.8323 (mm)
REVERT: B  286 PHE cc_start: 0.8791 (m-80) cc_final: 0.8521 (m-80)
REVERT: B  366 GLU cc_start: 0.8606 (tt0) cc_final: 0.8382 (tm-30)
REVERT: B  458 MET cc_start: 0.8999 (tpp) cc_final: 0.8446 (tpp)
REVERT: B  477 THR cc_start: 0.9384 (m) cc_final: 0.9174 (p)
REVERT: B  538 MET cc_start: 0.8887 (mtp) cc_final: 0.8592 (mtp)
REVERT: B  663 PHE cc_start: 0.8920 (m-10) cc_final: 0.8693 (m-10)
  outliers start: 2
  outliers final: 0
  residues processed: 335
  average time/residue: 0.3658
  time to fit residues: 186.2905
Evaluate side-chains
  182 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 1.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 156 optimal weight:    8.9990
   chunk 140 optimal weight:   30.0000
   chunk 77 optimal weight:   20.0000
   chunk 47 optimal weight:    0.0060
   chunk 94 optimal weight:   10.0000
   chunk 74 optimal weight:    7.9990
   chunk 145 optimal weight:   10.0000
   chunk 56 optimal weight:    8.9990
   chunk 88 optimal weight:    6.9990
   chunk 107 optimal weight:    7.9990
   chunk 168 optimal weight:    5.9990
   overall best weight:    5.8004

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

Flipped N/Q/H residues before XYZ refinement:
A 287 ASN
A 310 ASN
A 873 ASN
A 931 ASN
** B  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  62 HIS
B 166 ASN
** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 327 HIS
** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 489 ASN
B 527 ASN
B 735 HIS
B 796 ASN
** B 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 813 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.088579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.074659 restraints weight = 49592.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.076536 restraints weight = 24439.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.077776 restraints weight = 15174.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.2223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  14053  Z= 0.186
  Angle     :  0.696  10.627  19110  Z= 0.352
  Chirality :  0.044   0.224   2275
  Planarity :  0.005   0.050   2416
  Dihedral  :  8.612  51.553   2139
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 10.47 %
    Favored  : 86.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.19), residues: 1859
  helix:  0.29 (0.16), residues: 1002
  sheet: -1.33 (0.44), residues: 140
  loop : -2.57 (0.22), residues: 717

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 801 
 HIS   0.007   0.001   HIS A 664 
 PHE   0.035   0.002   PHE B 365 
 TYR   0.017   0.002   TYR B 330 
 ARG   0.004   0.000   ARG A 925 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04918 (  702)
  hydrogen bonds       : angle       4.52637 ( 2058)
  covalent geometry    : bond        0.00417 (14053)
  covalent geometry    : angle       0.69570 (19110)

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

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

  3718 Ramachandran restraints generated.
    1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3718 Ramachandran restraints generated.
    1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 210
  time to evaluate  : 1.419 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 GLU cc_start: 0.8363 (tp30) cc_final: 0.8099 (tm-30)
REVERT: A  288 LYS cc_start: 0.8859 (ptmm) cc_final: 0.8641 (mttp)
REVERT: A  296 GLU cc_start: 0.6674 (mm-30) cc_final: 0.6264 (tm-30)
REVERT: A  325 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8794 (mp)
REVERT: A  430 MET cc_start: 0.8267 (tpt) cc_final: 0.7735 (tpt)
REVERT: A  754 MET cc_start: 0.7064 (mpt) cc_final: 0.6526 (mmp)
REVERT: A  962 VAL cc_start: 0.9590 (t) cc_final: 0.9346 (p)
REVERT: B  430 MET cc_start: 0.7730 (tmm) cc_final: 0.7527 (tmm)
REVERT: B  458 MET cc_start: 0.8623 (tpp) cc_final: 0.8298 (tpp)
REVERT: B  524 SER cc_start: 0.8306 (p) cc_final: 0.7998 (m)
REVERT: B  829 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8661 (tt)
  outliers start: 44
  outliers final: 25
  residues processed: 244
  average time/residue: 0.1952
  time to fit residues: 75.9383
Evaluate side-chains
  178 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 151
  time to evaluate  : 1.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  325 ILE
Chi-restraints excluded: chain A residue  491 ILE
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  629 LEU
Chi-restraints excluded: chain A residue  674 THR
Chi-restraints excluded: chain A residue  742 LEU
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue  867 THR
Chi-restraints excluded: chain A residue  872 ASP
Chi-restraints excluded: chain A residue 1010 ASP
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  110 SER
Chi-restraints excluded: chain B residue  155 ILE
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  435 VAL
Chi-restraints excluded: chain B residue  482 SER
Chi-restraints excluded: chain B residue  494 LEU
Chi-restraints excluded: chain B residue  527 ASN
Chi-restraints excluded: chain B residue  626 CYS
Chi-restraints excluded: chain B residue  665 SER
Chi-restraints excluded: chain B residue  709 THR
Chi-restraints excluded: chain B residue  829 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 56 optimal weight:    7.9990
   chunk 108 optimal weight:   30.0000
   chunk 43 optimal weight:    5.9990
   chunk 72 optimal weight:    0.5980
   chunk 166 optimal weight:    0.2980
   chunk 178 optimal weight:    9.9990
   chunk 141 optimal weight:    1.9990
   chunk 151 optimal weight:    7.9990
   chunk 145 optimal weight:    8.9990
   chunk 181 optimal weight:    0.7980
   chunk 20 optimal weight:    7.9990
   overall best weight:    1.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 340 GLN
A 348 ASN
A 362 ASN
A 632 GLN
B  24 GLN
B 166 ASN
B 310 ASN
B 340 GLN
B 527 ASN
B 796 ASN
** B 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.090338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.076539 restraints weight = 49490.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.078490 restraints weight = 24203.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.079740 restraints weight = 14905.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.2818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  14053  Z= 0.123
  Angle     :  0.626   7.746  19110  Z= 0.312
  Chirality :  0.042   0.208   2275
  Planarity :  0.005   0.045   2416
  Dihedral  :  7.356  58.106   2139
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  6.62 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 13.41 %
    Favored  : 83.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.20), residues: 1859
  helix:  1.11 (0.17), residues: 995
  sheet: -1.13 (0.46), residues: 140
  loop : -2.33 (0.23), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 801 
 HIS   0.007   0.001   HIS A 664 
 PHE   0.032   0.001   PHE A 365 
 TYR   0.019   0.001   TYR B 551 
 ARG   0.003   0.000   ARG A1038 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04150 (  702)
  hydrogen bonds       : angle       4.11548 ( 2058)
  covalent geometry    : bond        0.00270 (14053)
  covalent geometry    : angle       0.62588 (19110)

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

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

  3718 Ramachandran restraints generated.
    1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3718 Ramachandran restraints generated.
    1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 193
  time to evaluate  : 1.748 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 GLU cc_start: 0.8349 (tp30) cc_final: 0.8015 (tm-30)
REVERT: A  288 LYS cc_start: 0.8901 (ptmm) cc_final: 0.8602 (ptpp)
REVERT: A  296 GLU cc_start: 0.6635 (mm-30) cc_final: 0.6087 (tm-30)
REVERT: A  430 MET cc_start: 0.8232 (tpt) cc_final: 0.7866 (ptt)
REVERT: A  754 MET cc_start: 0.7096 (mpt) cc_final: 0.6503 (mmp)
REVERT: A  947 MET cc_start: 0.8340 (tpp) cc_final: 0.7984 (tpp)
REVERT: B   63 TYR cc_start: 0.8779 (m-80) cc_final: 0.8544 (m-80)
REVERT: B  101 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8671 (tt)
REVERT: B  249 MET cc_start: 0.8143 (mmm) cc_final: 0.7884 (mmm)
REVERT: B  274 THR cc_start: 0.9425 (OUTLIER) cc_final: 0.8941 (p)
REVERT: B  337 MET cc_start: 0.8541 (mtp) cc_final: 0.8265 (mtm)
REVERT: B  458 MET cc_start: 0.8596 (tpp) cc_final: 0.8161 (tpp)
REVERT: B  737 LEU cc_start: 0.8318 (tp) cc_final: 0.8111 (tp)
REVERT: B  829 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8714 (tt)
  outliers start: 39
  outliers final: 24
  residues processed: 223
  average time/residue: 0.2419
  time to fit residues: 90.3589
Evaluate side-chains
  192 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 165
  time to evaluate  : 1.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  222 GLN
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain A residue  482 SER
Chi-restraints excluded: chain A residue  742 LEU
Chi-restraints excluded: chain A residue  867 THR
Chi-restraints excluded: chain A residue  872 ASP
Chi-restraints excluded: chain A residue  884 ILE
Chi-restraints excluded: chain A residue  915 VAL
Chi-restraints excluded: chain A residue  939 VAL
Chi-restraints excluded: chain B residue   56 SER
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  110 SER
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  482 SER
Chi-restraints excluded: chain B residue  484 LEU
Chi-restraints excluded: chain B residue  526 VAL
Chi-restraints excluded: chain B residue  626 CYS
Chi-restraints excluded: chain B residue  665 SER
Chi-restraints excluded: chain B residue  829 LEU
Chi-restraints excluded: chain B residue  833 MET
Chi-restraints excluded: chain B residue  841 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 102 optimal weight:    0.9980
   chunk 24 optimal weight:   20.0000
   chunk 145 optimal weight:    5.9990
   chunk 110 optimal weight:    8.9990
   chunk 100 optimal weight:   20.0000
   chunk 60 optimal weight:    0.9980
   chunk 15 optimal weight:    8.9990
   chunk 11 optimal weight:    9.9990
   chunk 160 optimal weight:    6.9990
   chunk 81 optimal weight:    7.9990
   chunk 116 optimal weight:    7.9990
   overall best weight:    4.5986

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

Flipped N/Q/H residues before XYZ refinement:
A 866 HIS
A 931 ASN
B 166 ASN
B 527 ASN
B 812 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.088015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.073610 restraints weight = 49723.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.075518 restraints weight = 23964.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.076764 restraints weight = 14708.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.3142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  14053  Z= 0.153
  Angle     :  0.636  11.513  19110  Z= 0.315
  Chirality :  0.043   0.217   2275
  Planarity :  0.004   0.041   2416
  Dihedral  :  6.871  56.372   2139
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 14.46 %
    Favored  : 82.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.21), residues: 1859
  helix:  1.56 (0.17), residues: 998
  sheet: -0.91 (0.47), residues: 136
  loop : -2.26 (0.23), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 801 
 HIS   0.006   0.001   HIS B 378 
 PHE   0.030   0.002   PHE A 365 
 TYR   0.021   0.001   TYR B 551 
 ARG   0.002   0.000   ARG A 427 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04141 (  702)
  hydrogen bonds       : angle       4.00089 ( 2058)
  covalent geometry    : bond        0.00351 (14053)
  covalent geometry    : angle       0.63649 (19110)

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

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

  3718 Ramachandran restraints generated.
    1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3718 Ramachandran restraints generated.
    1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 170
  time to evaluate  : 1.588 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 GLU cc_start: 0.8448 (tp30) cc_final: 0.8062 (tm-30)
REVERT: A  258 MET cc_start: 0.8905 (tpp) cc_final: 0.8642 (tmm)
REVERT: A  288 LYS cc_start: 0.9024 (ptmm) cc_final: 0.8711 (ptpp)
REVERT: A  296 GLU cc_start: 0.6595 (mm-30) cc_final: 0.6308 (tm-30)
REVERT: A  337 MET cc_start: 0.8547 (mmm) cc_final: 0.8215 (mmm)
REVERT: A  393 PHE cc_start: 0.7641 (t80) cc_final: 0.7423 (t80)
REVERT: A  430 MET cc_start: 0.8289 (tpt) cc_final: 0.7822 (ptt)
REVERT: A  633 MET cc_start: 0.8486 (mtm) cc_final: 0.8163 (mtm)
REVERT: A  754 MET cc_start: 0.7039 (mpt) cc_final: 0.6509 (mmp)
REVERT: B   28 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8332 (ptt90)
REVERT: B   63 TYR cc_start: 0.8832 (m-80) cc_final: 0.8584 (m-80)
REVERT: B  124 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9056 (mm)
REVERT: B  249 MET cc_start: 0.7977 (mmm) cc_final: 0.7677 (mmm)
REVERT: B  337 MET cc_start: 0.8695 (mtp) cc_final: 0.8388 (mtm)
REVERT: B  458 MET cc_start: 0.8742 (tpp) cc_final: 0.8204 (tpp)
REVERT: B  829 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8610 (tt)
  outliers start: 48
  outliers final: 24
  residues processed: 207
  average time/residue: 0.2882
  time to fit residues: 96.5041
Evaluate side-chains
  178 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 151
  time to evaluate  : 2.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 ASN
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain A residue  482 SER
Chi-restraints excluded: chain A residue  629 LEU
Chi-restraints excluded: chain A residue  742 LEU
Chi-restraints excluded: chain A residue  884 ILE
Chi-restraints excluded: chain A residue  915 VAL
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain A residue  939 VAL
Chi-restraints excluded: chain B residue   28 ARG
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  110 SER
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  482 SER
Chi-restraints excluded: chain B residue  484 LEU
Chi-restraints excluded: chain B residue  526 VAL
Chi-restraints excluded: chain B residue  626 CYS
Chi-restraints excluded: chain B residue  665 SER
Chi-restraints excluded: chain B residue  829 LEU
Chi-restraints excluded: chain B residue  833 MET
Chi-restraints excluded: chain B residue  835 VAL
Chi-restraints excluded: chain B residue  841 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 14 optimal weight:    9.9990
   chunk 38 optimal weight:    6.9990
   chunk 152 optimal weight:   20.0000
   chunk 111 optimal weight:   30.0000
   chunk 104 optimal weight:    9.9990
   chunk 32 optimal weight:   20.0000
   chunk 180 optimal weight:    5.9990
   chunk 15 optimal weight:    9.9990
   chunk 105 optimal weight:    6.9990
   chunk 7 optimal weight:   20.0000
   chunk 81 optimal weight:    8.9990
   overall best weight:    7.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  97 HIS
B 481 HIS
B 527 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.085974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.071462 restraints weight = 50694.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.073350 restraints weight = 24422.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.074558 restraints weight = 15067.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.3363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  14053  Z= 0.217
  Angle     :  0.698  11.860  19110  Z= 0.346
  Chirality :  0.045   0.180   2275
  Planarity :  0.004   0.041   2416
  Dihedral  :  6.868  58.946   2139
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  7.37 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 14.94 %
    Favored  : 81.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.21), residues: 1859
  helix:  1.66 (0.17), residues: 1004
  sheet: -0.87 (0.48), residues: 136
  loop : -2.19 (0.23), residues: 719

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B 801 
 HIS   0.006   0.001   HIS A 664 
 PHE   0.025   0.002   PHE B 752 
 TYR   0.022   0.002   TYR B 551 
 ARG   0.004   0.001   ARG A 734 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04641 (  702)
  hydrogen bonds       : angle       4.19189 ( 2058)
  covalent geometry    : bond        0.00493 (14053)
  covalent geometry    : angle       0.69825 (19110)

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

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

  3718 Ramachandran restraints generated.
    1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3718 Ramachandran restraints generated.
    1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 148
  time to evaluate  : 1.917 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 GLU cc_start: 0.8562 (tp30) cc_final: 0.8102 (tm-30)
REVERT: A   97 HIS cc_start: 0.8439 (OUTLIER) cc_final: 0.7486 (t70)
REVERT: A  258 MET cc_start: 0.8849 (tpp) cc_final: 0.8599 (tmm)
REVERT: A  288 LYS cc_start: 0.9062 (ptmm) cc_final: 0.8753 (ptpp)
REVERT: A  296 GLU cc_start: 0.6646 (mm-30) cc_final: 0.6247 (tm-30)
REVERT: A  319 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7742 (tp)
REVERT: A  337 MET cc_start: 0.8577 (mmm) cc_final: 0.8267 (mmm)
REVERT: A  430 MET cc_start: 0.8295 (tpt) cc_final: 0.7825 (ptt)
REVERT: A  633 MET cc_start: 0.8565 (mtm) cc_final: 0.8243 (mtm)
REVERT: A  742 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8163 (tt)
REVERT: A  754 MET cc_start: 0.6975 (mpt) cc_final: 0.6408 (mmp)
REVERT: A  947 MET cc_start: 0.8566 (tpp) cc_final: 0.8282 (tpp)
REVERT: B   28 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8327 (ptt90)
REVERT: B  274 THR cc_start: 0.9458 (OUTLIER) cc_final: 0.8979 (p)
REVERT: B  290 MET cc_start: 0.7959 (ptm) cc_final: 0.7711 (ptt)
REVERT: B  337 MET cc_start: 0.8743 (mtp) cc_final: 0.8418 (mtp)
REVERT: B  458 MET cc_start: 0.8788 (tpp) cc_final: 0.8328 (tpp)
REVERT: B  592 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.8983 (mm)
REVERT: B  616 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8874 (mm)
REVERT: B  663 PHE cc_start: 0.8413 (OUTLIER) cc_final: 0.8119 (m-80)
  outliers start: 57
  outliers final: 31
  residues processed: 195
  average time/residue: 0.2617
  time to fit residues: 82.6883
Evaluate side-chains
  180 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 141
  time to evaluate  : 1.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 ASN
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   89 MET
Chi-restraints excluded: chain A residue   97 HIS
Chi-restraints excluded: chain A residue  222 GLN
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain A residue  482 SER
Chi-restraints excluded: chain A residue  629 LEU
Chi-restraints excluded: chain A residue  742 LEU
Chi-restraints excluded: chain A residue  749 ILE
Chi-restraints excluded: chain A residue  884 ILE
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   28 ARG
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  110 SER
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  155 ILE
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  435 VAL
Chi-restraints excluded: chain B residue  474 TRP
Chi-restraints excluded: chain B residue  484 LEU
Chi-restraints excluded: chain B residue  494 LEU
Chi-restraints excluded: chain B residue  526 VAL
Chi-restraints excluded: chain B residue  592 LEU
Chi-restraints excluded: chain B residue  616 LEU
Chi-restraints excluded: chain B residue  626 CYS
Chi-restraints excluded: chain B residue  663 PHE
Chi-restraints excluded: chain B residue  665 SER
Chi-restraints excluded: chain B residue  780 THR
Chi-restraints excluded: chain B residue  833 MET
Chi-restraints excluded: chain B residue  835 VAL
Chi-restraints excluded: chain B residue  841 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 149 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 29 optimal weight:   30.0000
   chunk 58 optimal weight:    9.9990
   chunk 113 optimal weight:   10.0000
   chunk 180 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 129 optimal weight:    6.9990
   chunk 132 optimal weight:    6.9990
   chunk 150 optimal weight:    9.9990
   chunk 128 optimal weight:    5.9990
   overall best weight:    4.1388

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

Flipped N/Q/H residues before XYZ refinement:
A  97 HIS
A 489 ASN
B 287 ASN
B 527 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.087327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.073010 restraints weight = 50019.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.074910 restraints weight = 23385.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.076149 restraints weight = 14298.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.3557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14053  Z= 0.146
  Angle     :  0.648  10.078  19110  Z= 0.316
  Chirality :  0.043   0.287   2275
  Planarity :  0.004   0.042   2416
  Dihedral  :  6.557  56.553   2139
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 15.71 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.21), residues: 1859
  helix:  1.92 (0.17), residues: 1001
  sheet: -0.80 (0.48), residues: 136
  loop : -2.07 (0.24), residues: 722

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 801 
 HIS   0.009   0.001   HIS A  97 
 PHE   0.024   0.002   PHE A 393 
 TYR   0.014   0.001   TYR B 551 
 ARG   0.002   0.000   ARG A 427 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04139 (  702)
  hydrogen bonds       : angle       3.97306 ( 2058)
  covalent geometry    : bond        0.00335 (14053)
  covalent geometry    : angle       0.64831 (19110)

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

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

  3718 Ramachandran restraints generated.
    1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3718 Ramachandran restraints generated.
    1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 165
  time to evaluate  : 1.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 GLU cc_start: 0.8556 (tp30) cc_final: 0.8100 (tm-30)
REVERT: A  258 MET cc_start: 0.8873 (tpp) cc_final: 0.8620 (tmm)
REVERT: A  288 LYS cc_start: 0.9107 (ptmm) cc_final: 0.8790 (ptpp)
REVERT: A  296 GLU cc_start: 0.6636 (mm-30) cc_final: 0.6338 (tm-30)
REVERT: A  319 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7204 (tp)
REVERT: A  337 MET cc_start: 0.8620 (mmm) cc_final: 0.8292 (mmt)
REVERT: A  430 MET cc_start: 0.8226 (tpt) cc_final: 0.7772 (ptt)
REVERT: A  633 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.7995 (mtt)
REVERT: A  742 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8123 (tt)
REVERT: A  754 MET cc_start: 0.6784 (mpt) cc_final: 0.6089 (mmp)
REVERT: A  947 MET cc_start: 0.8540 (tpp) cc_final: 0.8242 (tpp)
REVERT: B   28 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8313 (ptt90)
REVERT: B   63 TYR cc_start: 0.8729 (m-10) cc_final: 0.8404 (m-80)
REVERT: B  274 THR cc_start: 0.9446 (OUTLIER) cc_final: 0.8970 (p)
REVERT: B  337 MET cc_start: 0.8691 (mtp) cc_final: 0.8418 (mtp)
REVERT: B  458 MET cc_start: 0.8754 (tpp) cc_final: 0.8313 (tpp)
REVERT: B  592 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.8932 (mm)
  outliers start: 51
  outliers final: 29
  residues processed: 205
  average time/residue: 0.2109
  time to fit residues: 68.6756
Evaluate side-chains
  188 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 153
  time to evaluate  : 1.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   89 MET
Chi-restraints excluded: chain A residue  222 GLN
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain A residue  482 SER
Chi-restraints excluded: chain A residue  629 LEU
Chi-restraints excluded: chain A residue  633 MET
Chi-restraints excluded: chain A residue  742 LEU
Chi-restraints excluded: chain A residue  749 ILE
Chi-restraints excluded: chain A residue  867 THR
Chi-restraints excluded: chain A residue  884 ILE
Chi-restraints excluded: chain A residue  915 VAL
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain B residue   28 ARG
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  110 SER
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  161 VAL
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  474 TRP
Chi-restraints excluded: chain B residue  512 THR
Chi-restraints excluded: chain B residue  526 VAL
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  592 LEU
Chi-restraints excluded: chain B residue  626 CYS
Chi-restraints excluded: chain B residue  665 SER
Chi-restraints excluded: chain B residue  833 MET
Chi-restraints excluded: chain B residue  835 VAL
Chi-restraints excluded: chain B residue  841 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 2 optimal weight:    8.9990
   chunk 92 optimal weight:   10.0000
   chunk 18 optimal weight:   30.0000
   chunk 71 optimal weight:    7.9990
   chunk 93 optimal weight:   10.0000
   chunk 79 optimal weight:   10.0000
   chunk 103 optimal weight:   40.0000
   chunk 152 optimal weight:    5.9990
   chunk 27 optimal weight:   10.0000
   chunk 48 optimal weight:    6.9990
   chunk 176 optimal weight:    5.9990
   overall best weight:    7.1990

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

Flipped N/Q/H residues before XYZ refinement:
B 527 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.085677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.071328 restraints weight = 50117.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.073202 restraints weight = 23988.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.074421 restraints weight = 14660.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.3698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  14053  Z= 0.206
  Angle     :  0.697  11.660  19110  Z= 0.343
  Chirality :  0.045   0.339   2275
  Planarity :  0.004   0.038   2416
  Dihedral  :  6.560  56.880   2139
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.91 %
    Favored  : 92.09 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 17.18 %
    Favored  : 79.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.21), residues: 1859
  helix:  1.84 (0.17), residues: 1003
  sheet: -0.80 (0.47), residues: 138
  loop : -2.07 (0.24), residues: 718

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 801 
 HIS   0.005   0.001   HIS A 664 
 PHE   0.021   0.002   PHE B 752 
 TYR   0.016   0.001   TYR B 551 
 ARG   0.003   0.000   ARG B 734 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04474 (  702)
  hydrogen bonds       : angle       4.13208 ( 2058)
  covalent geometry    : bond        0.00473 (14053)
  covalent geometry    : angle       0.69737 (19110)

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

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

  3718 Ramachandran restraints generated.
    1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3718 Ramachandran restraints generated.
    1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 150
  time to evaluate  : 2.456 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  288 LYS cc_start: 0.9159 (ptmm) cc_final: 0.8888 (ptpp)
REVERT: A  296 GLU cc_start: 0.6639 (mm-30) cc_final: 0.6261 (tm-30)
REVERT: A  337 MET cc_start: 0.8660 (mmm) cc_final: 0.8336 (mmt)
REVERT: A  430 MET cc_start: 0.8253 (tpt) cc_final: 0.7784 (ptt)
REVERT: A  580 MET cc_start: 0.8700 (mmm) cc_final: 0.8490 (tpt)
REVERT: A  633 MET cc_start: 0.8554 (mtm) cc_final: 0.8322 (mtm)
REVERT: A  742 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8167 (tt)
REVERT: A  754 MET cc_start: 0.6558 (mpt) cc_final: 0.6033 (mmp)
REVERT: A  947 MET cc_start: 0.8560 (tpp) cc_final: 0.8225 (tpp)
REVERT: B   28 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8336 (ptt90)
REVERT: B  274 THR cc_start: 0.9465 (OUTLIER) cc_final: 0.8999 (p)
REVERT: B  337 MET cc_start: 0.8775 (mtp) cc_final: 0.8456 (mtp)
REVERT: B  458 MET cc_start: 0.8815 (tpp) cc_final: 0.8370 (tpp)
REVERT: B  592 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.8957 (mm)
  outliers start: 47
  outliers final: 34
  residues processed: 186
  average time/residue: 0.2409
  time to fit residues: 69.9732
Evaluate side-chains
  181 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 143
  time to evaluate  : 1.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   89 MET
Chi-restraints excluded: chain A residue  222 GLN
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain A residue  482 SER
Chi-restraints excluded: chain A residue  629 LEU
Chi-restraints excluded: chain A residue  674 THR
Chi-restraints excluded: chain A residue  742 LEU
Chi-restraints excluded: chain A residue  749 ILE
Chi-restraints excluded: chain A residue  867 THR
Chi-restraints excluded: chain A residue  884 ILE
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain B residue   28 ARG
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  110 SER
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  155 ILE
Chi-restraints excluded: chain B residue  161 VAL
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  474 TRP
Chi-restraints excluded: chain B residue  482 SER
Chi-restraints excluded: chain B residue  494 LEU
Chi-restraints excluded: chain B residue  512 THR
Chi-restraints excluded: chain B residue  526 VAL
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  592 LEU
Chi-restraints excluded: chain B residue  626 CYS
Chi-restraints excluded: chain B residue  665 SER
Chi-restraints excluded: chain B residue  780 THR
Chi-restraints excluded: chain B residue  833 MET
Chi-restraints excluded: chain B residue  835 VAL
Chi-restraints excluded: chain B residue  841 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 147 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   chunk 51 optimal weight:    6.9990
   chunk 20 optimal weight:   20.0000
   chunk 0 optimal weight:   30.0000
   chunk 133 optimal weight:    8.9990
   chunk 28 optimal weight:   10.0000
   chunk 38 optimal weight:    5.9990
   chunk 140 optimal weight:   30.0000
   chunk 27 optimal weight:    8.9990
   chunk 154 optimal weight:   10.0000
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 527 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.086624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.072321 restraints weight = 50104.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.074205 restraints weight = 23829.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.075359 restraints weight = 14501.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.3806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  14053  Z= 0.167
  Angle     :  0.681  10.709  19110  Z= 0.332
  Chirality :  0.045   0.352   2275
  Planarity :  0.004   0.038   2416
  Dihedral  :  6.445  56.900   2139
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.15 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 17.18 %
    Favored  : 79.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.21), residues: 1859
  helix:  1.97 (0.17), residues: 996
  sheet: -0.76 (0.47), residues: 138
  loop : -1.97 (0.24), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 801 
 HIS   0.005   0.001   HIS A 664 
 PHE   0.026   0.002   PHE A 393 
 TYR   0.013   0.001   TYR B 551 
 ARG   0.002   0.000   ARG B 734 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04248 (  702)
  hydrogen bonds       : angle       4.02813 ( 2058)
  covalent geometry    : bond        0.00387 (14053)
  covalent geometry    : angle       0.68068 (19110)

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

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

  3718 Ramachandran restraints generated.
    1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3718 Ramachandran restraints generated.
    1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 153
  time to evaluate  : 1.893 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 HIS cc_start: 0.8435 (OUTLIER) cc_final: 0.7383 (t70)
REVERT: A  288 LYS cc_start: 0.9156 (ptmm) cc_final: 0.8817 (ptpp)
REVERT: A  296 GLU cc_start: 0.6676 (mm-30) cc_final: 0.6153 (tm-30)
REVERT: A  319 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7149 (tp)
REVERT: A  337 MET cc_start: 0.8629 (mmm) cc_final: 0.8286 (mmt)
REVERT: A  430 MET cc_start: 0.8225 (tpt) cc_final: 0.7755 (ptt)
REVERT: A  742 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8123 (tt)
REVERT: A  754 MET cc_start: 0.6542 (mpt) cc_final: 0.5984 (mmp)
REVERT: A  947 MET cc_start: 0.8524 (tpp) cc_final: 0.8208 (tpp)
REVERT: B   28 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8306 (ptt90)
REVERT: B   63 TYR cc_start: 0.8702 (m-10) cc_final: 0.8389 (m-80)
REVERT: B  258 MET cc_start: 0.8641 (ttm) cc_final: 0.8436 (mtp)
REVERT: B  274 THR cc_start: 0.9433 (OUTLIER) cc_final: 0.8937 (p)
REVERT: B  337 MET cc_start: 0.8710 (mtp) cc_final: 0.8436 (mtp)
REVERT: B  458 MET cc_start: 0.8790 (tpp) cc_final: 0.8369 (tpp)
REVERT: B  592 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.8940 (mm)
  outliers start: 52
  outliers final: 37
  residues processed: 194
  average time/residue: 0.2250
  time to fit residues: 68.7209
Evaluate side-chains
  191 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 148
  time to evaluate  : 1.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   89 MET
Chi-restraints excluded: chain A residue   97 HIS
Chi-restraints excluded: chain A residue  222 GLN
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain A residue  482 SER
Chi-restraints excluded: chain A residue  597 THR
Chi-restraints excluded: chain A residue  629 LEU
Chi-restraints excluded: chain A residue  689 ASP
Chi-restraints excluded: chain A residue  742 LEU
Chi-restraints excluded: chain A residue  749 ILE
Chi-restraints excluded: chain A residue  867 THR
Chi-restraints excluded: chain A residue  884 ILE
Chi-restraints excluded: chain A residue  907 MET
Chi-restraints excluded: chain A residue  915 VAL
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   28 ARG
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  110 SER
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  161 VAL
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  401 ILE
Chi-restraints excluded: chain B residue  474 TRP
Chi-restraints excluded: chain B residue  494 LEU
Chi-restraints excluded: chain B residue  512 THR
Chi-restraints excluded: chain B residue  526 VAL
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  592 LEU
Chi-restraints excluded: chain B residue  626 CYS
Chi-restraints excluded: chain B residue  665 SER
Chi-restraints excluded: chain B residue  780 THR
Chi-restraints excluded: chain B residue  833 MET
Chi-restraints excluded: chain B residue  835 VAL
Chi-restraints excluded: chain B residue  841 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 97 optimal weight:    0.0170
   chunk 146 optimal weight:    7.9990
   chunk 151 optimal weight:   20.0000
   chunk 145 optimal weight:    0.0170
   chunk 51 optimal weight:    5.9990
   chunk 0 optimal weight:   30.0000
   chunk 171 optimal weight:   20.0000
   chunk 95 optimal weight:    9.9990
   chunk 103 optimal weight:   30.0000
   chunk 31 optimal weight:    0.6980
   chunk 162 optimal weight:   10.0000
   overall best weight:    2.9460

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

Flipped N/Q/H residues before XYZ refinement:
B 166 ASN
B 287 ASN
B 362 ASN
B 527 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.088406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.074062 restraints weight = 49425.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.075984 restraints weight = 23625.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.077222 restraints weight = 14410.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.3994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  14053  Z= 0.127
  Angle     :  0.653  11.996  19110  Z= 0.315
  Chirality :  0.044   0.361   2275
  Planarity :  0.004   0.038   2416
  Dihedral  :  6.233  58.693   2139
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 17.53 %
    Favored  : 79.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.21), residues: 1859
  helix:  2.12 (0.17), residues: 998
  sheet: -0.70 (0.46), residues: 138
  loop : -1.87 (0.24), residues: 723

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 801 
 HIS   0.005   0.001   HIS A 664 
 PHE   0.024   0.001   PHE B 365 
 TYR   0.010   0.001   TYR A 683 
 ARG   0.002   0.000   ARG A 427 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03899 (  702)
  hydrogen bonds       : angle       3.86475 ( 2058)
  covalent geometry    : bond        0.00291 (14053)
  covalent geometry    : angle       0.65270 (19110)

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

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

  3718 Ramachandran restraints generated.
    1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3718 Ramachandran restraints generated.
    1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 161
  time to evaluate  : 1.578 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 HIS cc_start: 0.8457 (OUTLIER) cc_final: 0.7412 (t70)
REVERT: A  288 LYS cc_start: 0.9130 (ptmm) cc_final: 0.8887 (ptpp)
REVERT: A  296 GLU cc_start: 0.6595 (mm-30) cc_final: 0.6098 (tm-30)
REVERT: A  319 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.6940 (tp)
REVERT: A  337 MET cc_start: 0.8613 (mmm) cc_final: 0.8276 (mmt)
REVERT: A  430 MET cc_start: 0.8098 (tpt) cc_final: 0.7695 (ptt)
REVERT: A  580 MET cc_start: 0.8585 (mmm) cc_final: 0.8374 (tpt)
REVERT: A  742 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8058 (tt)
REVERT: A  754 MET cc_start: 0.6530 (mpt) cc_final: 0.5917 (mmp)
REVERT: A  947 MET cc_start: 0.8521 (tpp) cc_final: 0.8173 (tpp)
REVERT: A  984 MET cc_start: 0.8013 (tpp) cc_final: 0.7597 (tpp)
REVERT: B   28 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8330 (ptt90)
REVERT: B   63 TYR cc_start: 0.8655 (m-10) cc_final: 0.8323 (m-80)
REVERT: B  274 THR cc_start: 0.9421 (OUTLIER) cc_final: 0.8956 (p)
REVERT: B  337 MET cc_start: 0.8655 (mtp) cc_final: 0.8386 (mtp)
REVERT: B  345 TYR cc_start: 0.8653 (t80) cc_final: 0.8349 (t80)
REVERT: B  458 MET cc_start: 0.8726 (tpp) cc_final: 0.8316 (tpp)
REVERT: B  503 MET cc_start: 0.6310 (mtm) cc_final: 0.5403 (ptp)
REVERT: B  538 MET cc_start: 0.8061 (ttp) cc_final: 0.7853 (ttp)
REVERT: B  592 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.8885 (mm)
REVERT: B  714 LEU cc_start: 0.7928 (tp) cc_final: 0.7548 (pp)
  outliers start: 45
  outliers final: 31
  residues processed: 195
  average time/residue: 0.2407
  time to fit residues: 75.5459
Evaluate side-chains
  190 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 153
  time to evaluate  : 1.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   89 MET
Chi-restraints excluded: chain A residue   97 HIS
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain A residue  482 SER
Chi-restraints excluded: chain A residue  597 THR
Chi-restraints excluded: chain A residue  629 LEU
Chi-restraints excluded: chain A residue  720 LEU
Chi-restraints excluded: chain A residue  742 LEU
Chi-restraints excluded: chain A residue  884 ILE
Chi-restraints excluded: chain A residue  907 MET
Chi-restraints excluded: chain A residue  915 VAL
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   28 ARG
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  110 SER
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  161 VAL
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  474 TRP
Chi-restraints excluded: chain B residue  494 LEU
Chi-restraints excluded: chain B residue  512 THR
Chi-restraints excluded: chain B residue  526 VAL
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  592 LEU
Chi-restraints excluded: chain B residue  616 LEU
Chi-restraints excluded: chain B residue  665 SER
Chi-restraints excluded: chain B residue  780 THR
Chi-restraints excluded: chain B residue  833 MET
Chi-restraints excluded: chain B residue  835 VAL
Chi-restraints excluded: chain B residue  841 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 120 optimal weight:    0.9990
   chunk 28 optimal weight:    9.9990
   chunk 19 optimal weight:   30.0000
   chunk 118 optimal weight:   10.0000
   chunk 132 optimal weight:   30.0000
   chunk 55 optimal weight:    9.9990
   chunk 74 optimal weight:    0.9980
   chunk 8 optimal weight:   20.0000
   chunk 59 optimal weight:   20.0000
   chunk 63 optimal weight:    9.9990
   chunk 43 optimal weight:    5.9990
   overall best weight:    5.5988

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

Flipped N/Q/H residues before XYZ refinement:
B 166 ASN
B 527 ASN
** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.087047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.072724 restraints weight = 49913.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.074623 restraints weight = 23875.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.075842 restraints weight = 14530.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.4053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  14053  Z= 0.171
  Angle     :  0.690  11.894  19110  Z= 0.335
  Chirality :  0.045   0.371   2275
  Planarity :  0.004   0.037   2416
  Dihedral  :  6.267  59.744   2139
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 18.02 %
    Favored  : 79.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.21), residues: 1859
  helix:  2.15 (0.17), residues: 991
  sheet: -0.74 (0.45), residues: 145
  loop : -1.88 (0.24), residues: 723

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 801 
 HIS   0.005   0.001   HIS A 664 
 PHE   0.026   0.002   PHE A 393 
 TYR   0.015   0.001   TYR B 551 
 ARG   0.003   0.000   ARG A 427 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04268 (  702)
  hydrogen bonds       : angle       4.00795 ( 2058)
  covalent geometry    : bond        0.00396 (14053)
  covalent geometry    : angle       0.68984 (19110)

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

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

  3718 Ramachandran restraints generated.
    1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3718 Ramachandran restraints generated.
    1859 Oldfield, 0 Emsley, 1859 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 152
  time to evaluate  : 1.594 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 HIS cc_start: 0.8485 (OUTLIER) cc_final: 0.7444 (t70)
REVERT: A  258 MET cc_start: 0.9053 (tpp) cc_final: 0.8689 (tpt)
REVERT: A  288 LYS cc_start: 0.9106 (ptmm) cc_final: 0.8817 (ptpp)
REVERT: A  296 GLU cc_start: 0.6743 (mm-30) cc_final: 0.6290 (tm-30)
REVERT: A  319 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.6994 (tp)
REVERT: A  337 MET cc_start: 0.8625 (mmm) cc_final: 0.8312 (mmt)
REVERT: A  430 MET cc_start: 0.8150 (tpt) cc_final: 0.7760 (ptt)
REVERT: A  580 MET cc_start: 0.8633 (mmm) cc_final: 0.8429 (tpt)
REVERT: A  742 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8103 (tt)
REVERT: A  754 MET cc_start: 0.6439 (mpt) cc_final: 0.5836 (mmp)
REVERT: A  947 MET cc_start: 0.8516 (tpp) cc_final: 0.8172 (tpp)
REVERT: B   28 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8319 (ptt90)
REVERT: B   63 TYR cc_start: 0.8676 (m-10) cc_final: 0.8373 (m-80)
REVERT: B  274 THR cc_start: 0.9440 (OUTLIER) cc_final: 0.8988 (p)
REVERT: B  458 MET cc_start: 0.8780 (tpp) cc_final: 0.8352 (tpp)
REVERT: B  485 MET cc_start: 0.8635 (mmm) cc_final: 0.8121 (mmt)
REVERT: B  538 MET cc_start: 0.8066 (ttp) cc_final: 0.7839 (ttp)
REVERT: B  592 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.8930 (mm)
REVERT: B  737 LEU cc_start: 0.8226 (tp) cc_final: 0.7991 (tp)
  outliers start: 41
  outliers final: 30
  residues processed: 182
  average time/residue: 0.2192
  time to fit residues: 63.2774
Evaluate side-chains
  183 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 147
  time to evaluate  : 1.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   89 MET
Chi-restraints excluded: chain A residue   97 HIS
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  422 THR
Chi-restraints excluded: chain A residue  482 SER
Chi-restraints excluded: chain A residue  597 THR
Chi-restraints excluded: chain A residue  629 LEU
Chi-restraints excluded: chain A residue  689 ASP
Chi-restraints excluded: chain A residue  720 LEU
Chi-restraints excluded: chain A residue  742 LEU
Chi-restraints excluded: chain A residue  884 ILE
Chi-restraints excluded: chain A residue  907 MET
Chi-restraints excluded: chain A residue  915 VAL
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain B residue   14 LEU
Chi-restraints excluded: chain B residue   28 ARG
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  161 VAL
Chi-restraints excluded: chain B residue  187 ILE
Chi-restraints excluded: chain B residue  274 THR
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  349 ILE
Chi-restraints excluded: chain B residue  367 VAL
Chi-restraints excluded: chain B residue  474 TRP
Chi-restraints excluded: chain B residue  494 LEU
Chi-restraints excluded: chain B residue  512 THR
Chi-restraints excluded: chain B residue  526 VAL
Chi-restraints excluded: chain B residue  579 ILE
Chi-restraints excluded: chain B residue  592 LEU
Chi-restraints excluded: chain B residue  665 SER
Chi-restraints excluded: chain B residue  780 THR
Chi-restraints excluded: chain B residue  835 VAL
Chi-restraints excluded: chain B residue  841 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 185
   random chunks:
   chunk 177 optimal weight:    9.9990
   chunk 162 optimal weight:   10.0000
   chunk 91 optimal weight:    9.9990
   chunk 73 optimal weight:    5.9990
   chunk 151 optimal weight:    6.9990
   chunk 57 optimal weight:    1.9990
   chunk 181 optimal weight:    0.0570
   chunk 61 optimal weight:    7.9990
   chunk 140 optimal weight:   40.0000
   chunk 87 optimal weight:    8.9990
   chunk 46 optimal weight:    7.9990
   overall best weight:    4.6106

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

Flipped N/Q/H residues before XYZ refinement:
B 527 ASN
** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.087470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.073141 restraints weight = 51082.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.075035 restraints weight = 24447.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.076275 restraints weight = 14921.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.4146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  14053  Z= 0.153
  Angle     :  0.682  11.563  19110  Z= 0.332
  Chirality :  0.045   0.353   2275
  Planarity :  0.004   0.038   2416
  Dihedral  :  6.211  58.693   2139
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 17.95 %
    Favored  : 78.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.21), residues: 1859
  helix:  2.19 (0.17), residues: 988
  sheet: -0.69 (0.45), residues: 145
  loop : -1.81 (0.24), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 801 
 HIS   0.005   0.001   HIS A 664 
 PHE   0.022   0.002   PHE A 365 
 TYR   0.024   0.001   TYR B 364 
 ARG   0.002   0.000   ARG B 734 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04179 (  702)
  hydrogen bonds       : angle       4.00745 ( 2058)
  covalent geometry    : bond        0.00354 (14053)
  covalent geometry    : angle       0.68216 (19110)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4923.40 seconds
wall clock time: 91 minutes 37.19 seconds (5497.19 seconds total)