Starting phenix.real_space_refine
on Wed Jul 30 23:26:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xju_38406/07_2025/8xju_38406.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xju_38406/07_2025/8xju_38406.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.91
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xju_38406/07_2025/8xju_38406.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xju_38406/07_2025/8xju_38406.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xju_38406/07_2025/8xju_38406.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xju_38406/07_2025/8xju_38406.cif"
  }
  resolution = 2.91
  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=   0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    8199      2.51       5
     N    2254      2.21       5
     O    2455      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 82 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12960
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6469
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 854, 6469
          Classifications: {'peptide': 854}
          Link IDs: {'PTRANS': 40, 'TRANS': 813}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 6491
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 857, 6491
          Classifications: {'peptide': 857}
          Link IDs: {'PTRANS': 40, 'TRANS': 816}
          Chain breaks: 1
  Time building chain proxies: 8.31, per 1000 atoms: 0.64
  Number of scatterers: 12960
  At special positions: 0
  Unit cell: (98.175, 95.7, 198.825, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      52     16.00
     O    2455      8.00
     N    2254      7.00
     C    8199      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

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

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3166

  Finding SS restraints...
    Secondary structure from input PDB file:
      69 helices and 13 sheets defined
      41.5% alpha, 12.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 32
      removed outlier: 3.558A  pdb=" N   ASN A  29 " --> pdb=" O   ALA A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 49
    Processing helix  chain 'A' and resid 51 through 56
    Processing helix  chain 'A' and resid 81 through 87
    Processing helix  chain 'A' and resid 89 through 107
    Processing helix  chain 'A' and resid 109 through 113
      removed outlier: 3.692A  pdb=" N   TYR A 113 " --> pdb=" O   ALA A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 134
    Processing helix  chain 'A' and resid 156 through 165
    Processing helix  chain 'A' and resid 179 through 194
    Processing helix  chain 'A' and resid 253 through 259
    Processing helix  chain 'A' and resid 286 through 301
    Processing helix  chain 'A' and resid 304 through 306
      No H-bonds generated for 'chain 'A' and resid 304 through 306'
    Processing helix  chain 'A' and resid 321 through 333
    Processing helix  chain 'A' and resid 359 through 373
    Processing helix  chain 'A' and resid 436 through 440
      removed outlier: 4.099A  pdb=" N   ARG A 440 " --> pdb=" O   LEU A 437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 471
    Processing helix  chain 'A' and resid 477 through 487
    Processing helix  chain 'A' and resid 502 through 512
      removed outlier: 3.776A  pdb=" N   GLN A 512 " --> pdb=" O   THR A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 551
      removed outlier: 3.636A  pdb=" N   GLN A 549 " --> pdb=" O   HIS A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 568
    Processing helix  chain 'A' and resid 572 through 579
      removed outlier: 3.590A  pdb=" N   LEU A 577 " --> pdb=" O   ILE A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 583 through 590
    Processing helix  chain 'A' and resid 592 through 595
    Processing helix  chain 'A' and resid 596 through 612
    Processing helix  chain 'A' and resid 613 through 615
      No H-bonds generated for 'chain 'A' and resid 613 through 615'
    Processing helix  chain 'A' and resid 626 through 636
      removed outlier: 4.090A  pdb=" N   VAL A 630 " --> pdb=" O   LEU A 626 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 639 through 657
      removed outlier: 3.837A  pdb=" N   LEU A 646 " --> pdb=" O   ASP A 642 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   ALA A 648 " --> pdb=" O   LEU A 644 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   ARG A 649 " --> pdb=" O   ARG A 645 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 668 through 673
    Processing helix  chain 'A' and resid 696 through 707
    Processing helix  chain 'A' and resid 728 through 738
      removed outlier: 4.010A  pdb=" N   ALA A 734 " --> pdb=" O   ASP A 730 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   LEU A 735 " --> pdb=" O   ALA A 731 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ARG A 736 " --> pdb=" O   ALA A 732 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLN A 737 " --> pdb=" O   GLN A 733 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 771 through 777
    Processing helix  chain 'A' and resid 780 through 792
      removed outlier: 3.510A  pdb=" N   GLN A 786 " --> pdb=" O   SER A 782 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 803 through 808
      removed outlier: 3.532A  pdb=" N   GLN A 807 " --> pdb=" O   ALA A 803 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   LEU A 808 " --> pdb=" O   THR A 804 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 803 through 808'
    Processing helix  chain 'A' and resid 828 through 830
      No H-bonds generated for 'chain 'A' and resid 828 through 830'
    Processing helix  chain 'A' and resid 831 through 847
      removed outlier: 3.526A  pdb=" N   LEU A 837 " --> pdb=" O   HIS A 833 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 851 through 855
      removed outlier: 3.937A  pdb=" N   ALA A 854 " --> pdb=" O   ASP A 851 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 31
    Processing helix  chain 'B' and resid 41 through 46
      removed outlier: 4.068A  pdb=" N   LEU B  45 " --> pdb=" O   SER B  41 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   LEU B  46 " --> pdb=" O   ASP B  42 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 41 through 46'
    Processing helix  chain 'B' and resid 74 through 79
      removed outlier: 3.983A  pdb=" N   PHE B  78 " --> pdb=" O   ASP B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 89 through 107
    Processing helix  chain 'B' and resid 109 through 113
      removed outlier: 3.621A  pdb=" N   TYR B 113 " --> pdb=" O   ALA B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 128 through 134
    Processing helix  chain 'B' and resid 156 through 165
    Processing helix  chain 'B' and resid 179 through 194
    Processing helix  chain 'B' and resid 253 through 259
    Processing helix  chain 'B' and resid 286 through 301
    Processing helix  chain 'B' and resid 321 through 333
    Processing helix  chain 'B' and resid 346 through 350
      removed outlier: 3.666A  pdb=" N   THR B 349 " --> pdb=" O   SER B 346 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 354 through 356
      No H-bonds generated for 'chain 'B' and resid 354 through 356'
    Processing helix  chain 'B' and resid 357 through 373
    Processing helix  chain 'B' and resid 455 through 471
    Processing helix  chain 'B' and resid 482 through 488
    Processing helix  chain 'B' and resid 502 through 511
    Processing helix  chain 'B' and resid 544 through 551
      removed outlier: 3.583A  pdb=" N   GLN B 549 " --> pdb=" O   HIS B 545 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   VAL B 550 " --> pdb=" O   GLN B 546 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 551 through 569
      removed outlier: 3.798A  pdb=" N   LEU B 564 " --> pdb=" O   ARG B 560 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 583 through 588
    Processing helix  chain 'B' and resid 592 through 614
      Proline residue:  B 598  - end of helix
    Processing helix  chain 'B' and resid 626 through 636
      removed outlier: 3.663A  pdb=" N   VAL B 630 " --> pdb=" O   LEU B 626 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   THR B 633 " --> pdb=" O   TRP B 629 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 639 through 654
      removed outlier: 3.895A  pdb=" N   ARG B 650 " --> pdb=" O   LEU B 646 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 668 through 675
    Processing helix  chain 'B' and resid 696 through 702
    Processing helix  chain 'B' and resid 705 through 711
      removed outlier: 3.513A  pdb=" N   GLU B 709 " --> pdb=" O   GLN B 705 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 728 through 740
      removed outlier: 3.795A  pdb=" N   ALA B 732 " --> pdb=" O   MET B 728 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   LEU B 735 " --> pdb=" O   ALA B 731 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   GLN B 737 " --> pdb=" O   GLN B 733 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   ALA B 738 " --> pdb=" O   ALA B 734 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   GLU B 740 " --> pdb=" O   ARG B 736 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 761 through 767
      removed outlier: 4.063A  pdb=" N   LEU B 765 " --> pdb=" O   SER B 761 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   THR B 766 " --> pdb=" O   ALA B 762 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   THR B 767 " --> pdb=" O   ASP B 763 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 761 through 767'
    Processing helix  chain 'B' and resid 767 through 775
      removed outlier: 4.181A  pdb=" N   TRP B 771 " --> pdb=" O   THR B 767 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   MET B 775 " --> pdb=" O   TRP B 771 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 785 through 792
    Processing helix  chain 'B' and resid 803 through 812
      removed outlier: 3.585A  pdb=" N   GLN B 807 " --> pdb=" O   ALA B 803 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   LEU B 808 " --> pdb=" O   THR B 804 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 831 through 847
      removed outlier: 4.141A  pdb=" N   LEU B 837 " --> pdb=" O   HIS B 833 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 851 through 856
      removed outlier: 4.079A  pdb=" N   ALA B 856 " --> pdb=" O   SER B 853 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 171 through 173
      removed outlier: 8.480A  pdb=" N   ILE A 172 " --> pdb=" O   VAL A 117 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   ILE A 119 " --> pdb=" O   ILE A 172 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   GLY A 118 " --> pdb=" O   ILE A 201 " (cutoff:3.500A)
      removed outlier: 8.206A  pdb=" N   GLY A 203 " --> pdb=" O   GLY A 118 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   PHE A 120 " --> pdb=" O   GLY A 203 " (cutoff:3.500A)
      removed outlier: 8.558A  pdb=" N   VAL A 205 " --> pdb=" O   PHE A 120 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLY A  12 " --> pdb=" O   VAL A 249 " (cutoff:3.500A)
      removed outlier: 7.073A  pdb=" N   LYS A 251 " --> pdb=" O   ILE A  10 " (cutoff:3.500A)
      removed outlier: 5.037A  pdb=" N   ILE A  10 " --> pdb=" O   LYS A 251 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   ALA A 265 " --> pdb=" O   ILE A  10 " (cutoff:3.500A)
      removed outlier: 5.455A  pdb=" N   ILE A 267 " --> pdb=" O   GLU A 430 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   GLU A 430 " --> pdb=" O   ILE A 267 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLY A 269 " --> pdb=" O   VAL A 428 " (cutoff:3.500A)
      removed outlier: 7.135A  pdb=" N   ARG A 412 " --> pdb=" O   ILE A 308 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   TYR A 310 " --> pdb=" O   ARG A 412 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   THR A 309 " --> pdb=" O   ALA A 343 " (cutoff:3.500A)
      removed outlier: 8.048A  pdb=" N   GLY A 345 " --> pdb=" O   THR A 309 " (cutoff:3.500A)
      removed outlier: 6.276A  pdb=" N   VAL A 311 " --> pdb=" O   GLY A 345 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39
    Processing sheet with id=AA3, first strand: chain 'A' and resid 374 through 375
    Processing sheet with id=AA4, first strand: chain 'A' and resid 447 through 448
    Processing sheet with id=AA5, first strand: chain 'A' and resid 451 through 453
    Processing sheet with id=AA6, first strand: chain 'A' and resid 620 through 622
      removed outlier: 3.743A  pdb=" N   VAL A 620 " --> pdb=" O   LEU A 529 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 681 through 687
      removed outlier: 6.615A  pdb=" N   VAL A 692 " --> pdb=" O   ALA A 683 " (cutoff:3.500A)
      removed outlier: 5.234A  pdb=" N   VAL A 685 " --> pdb=" O   TYR A 690 " (cutoff:3.500A)
      removed outlier: 7.760A  pdb=" N   TYR A 690 " --> pdb=" O   VAL A 685 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   LYS A 715 " --> pdb=" O   MET A 664 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 171 through 173
      removed outlier: 8.554A  pdb=" N   ILE B 172 " --> pdb=" O   VAL B 117 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   ILE B 119 " --> pdb=" O   ILE B 172 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   GLY B 118 " --> pdb=" O   ILE B 201 " (cutoff:3.500A)
      removed outlier: 8.218A  pdb=" N   GLY B 203 " --> pdb=" O   GLY B 118 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   PHE B 120 " --> pdb=" O   GLY B 203 " (cutoff:3.500A)
      removed outlier: 8.541A  pdb=" N   VAL B 205 " --> pdb=" O   PHE B 120 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   GLY B 122 " --> pdb=" O   VAL B 205 " (cutoff:3.500A)
      removed outlier: 7.049A  pdb=" N   LYS B 251 " --> pdb=" O   ILE B  10 " (cutoff:3.500A)
      removed outlier: 5.074A  pdb=" N   ILE B  10 " --> pdb=" O   LYS B 251 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   ALA B 265 " --> pdb=" O   ILE B  10 " (cutoff:3.500A)
      removed outlier: 5.233A  pdb=" N   ILE B 267 " --> pdb=" O   GLU B 430 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   GLU B 430 " --> pdb=" O   ILE B 267 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   GLY B 269 " --> pdb=" O   VAL B 428 " (cutoff:3.500A)
      removed outlier: 7.295A  pdb=" N   ARG B 412 " --> pdb=" O   ILE B 308 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   TYR B 310 " --> pdb=" O   ARG B 412 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   THR B 309 " --> pdb=" O   ALA B 343 " (cutoff:3.500A)
      removed outlier: 8.108A  pdb=" N   GLY B 345 " --> pdb=" O   THR B 309 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   VAL B 311 " --> pdb=" O   GLY B 345 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 38 through 39
    Processing sheet with id=AB1, first strand: chain 'B' and resid 374 through 375
    Processing sheet with id=AB2, first strand: chain 'B' and resid 447 through 453
    Processing sheet with id=AB3, first strand: chain 'B' and resid 758 through 759
      removed outlier: 6.310A  pdb=" N   THR B 619 " --> pdb=" O   THR B 750 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   ILE B 752 " --> pdb=" O   THR B 619 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   MET B 621 " --> pdb=" O   ILE B 752 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   LEU B 529 " --> pdb=" O   PRO B 618 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   VAL B 620 " --> pdb=" O   LEU B 529 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 714 through 715
      removed outlier: 8.144A  pdb=" N   TYR B 690 " --> pdb=" O   VAL B 685 " (cutoff:3.500A)
      removed outlier: 5.583A  pdb=" N   VAL B 685 " --> pdb=" O   TYR B 690 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   VAL B 692 " --> pdb=" O   ALA B 683 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ALA B 694 " --> pdb=" O   ALA B 681 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   ALA B 681 " --> pdb=" O   ALA B 694 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   VAL B 779 " --> pdb=" O   ALA B 683 " (cutoff:3.500A)

    526 hydrogen bonds defined for protein.
    1497 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: 6.83

  Time building geometry restraints manager: 3.74 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2828
        1.33 -     1.45: 3075
        1.45 -     1.57: 7254
        1.57 -     1.69: 1
        1.69 -     1.82: 86
  Bond restraints: 13244
  Sorted by residual:
  bond pdb=" CA  GLU A 568 "
       pdb=" CB  GLU A 568 "
    ideal  model  delta    sigma   weight residual
    1.530  1.621 -0.091 2.20e-02 2.07e+03 1.70e+01
  bond pdb=" CA  SER A 181 "
       pdb=" CB  SER A 181 "
    ideal  model  delta    sigma   weight residual
    1.530  1.481  0.049 1.56e-02 4.11e+03 9.84e+00
  bond pdb=" N   GLN B 539 "
       pdb=" CA  GLN B 539 "
    ideal  model  delta    sigma   weight residual
    1.455  1.494 -0.039 1.27e-02 6.20e+03 9.30e+00
  bond pdb=" CB  THR B 158 "
       pdb=" CG2 THR B 158 "
    ideal  model  delta    sigma   weight residual
    1.521  1.421  0.100 3.30e-02 9.18e+02 9.13e+00
  bond pdb=" N   GLY B 352 "
       pdb=" CA  GLY B 352 "
    ideal  model  delta    sigma   weight residual
    1.446  1.476 -0.030 1.02e-02 9.61e+03 8.49e+00
  ... (remaining 13239 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.24: 16996
        2.24 -     4.47: 879
        4.47 -     6.71: 119
        6.71 -     8.95: 47
        8.95 -    11.18: 5
  Bond angle restraints: 18046
  Sorted by residual:
  angle pdb=" N   PRO A 209 "
        pdb=" CA  PRO A 209 "
        pdb=" C   PRO A 209 "
      ideal   model   delta    sigma   weight residual
     110.70  121.88  -11.18 1.22e+00 6.72e-01 8.40e+01
  angle pdb=" N   PRO B 209 "
        pdb=" CA  PRO B 209 "
        pdb=" C   PRO B 209 "
      ideal   model   delta    sigma   weight residual
     110.70  118.61   -7.91 1.22e+00 6.72e-01 4.20e+01
  angle pdb=" N   ARG B 479 "
        pdb=" CA  ARG B 479 "
        pdb=" C   ARG B 479 "
      ideal   model   delta    sigma   weight residual
     113.41  105.96    7.45 1.22e+00 6.72e-01 3.73e+01
  angle pdb=" N   ARG B 501 "
        pdb=" CA  ARG B 501 "
        pdb=" C   ARG B 501 "
      ideal   model   delta    sigma   weight residual
     114.12  105.77    8.35 1.39e+00 5.18e-01 3.61e+01
  angle pdb=" CA  GLY B 352 "
        pdb=" C   GLY B 352 "
        pdb=" O   GLY B 352 "
      ideal   model   delta    sigma   weight residual
     122.23  118.12    4.11 6.90e-01 2.10e+00 3.55e+01
  ... (remaining 18041 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 7004
       17.88 -    35.75: 704
       35.75 -    53.63: 101
       53.63 -    71.50: 30
       71.50 -    89.38: 13
  Dihedral angle restraints: 7852
    sinusoidal: 2935
      harmonic: 4917
  Sorted by residual:
  dihedral pdb=" CA  PHE A 638 "
           pdb=" C   PHE A 638 "
           pdb=" N   SER A 639 "
           pdb=" CA  SER A 639 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.68   28.32     0      5.00e+00 4.00e-02 3.21e+01
  dihedral pdb=" CA  GLU A  66 "
           pdb=" C   GLU A  66 "
           pdb=" N   VAL A  67 "
           pdb=" CA  VAL A  67 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.26   27.74     0      5.00e+00 4.00e-02 3.08e+01
  dihedral pdb=" CA  VAL A 428 "
           pdb=" C   VAL A 428 "
           pdb=" N   LEU A 429 "
           pdb=" CA  LEU A 429 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.03  -24.97     0      5.00e+00 4.00e-02 2.49e+01
  ... (remaining 7849 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.187: 2023
       0.187 -    0.375: 36
       0.375 -    0.562: 2
       0.562 -    0.749: 1
       0.749 -    0.937: 1
  Chirality restraints: 2063
  Sorted by residual:
  chirality pdb=" CB  ILE B 119 "
            pdb=" CA  ILE B 119 "
            pdb=" CG1 ILE B 119 "
            pdb=" CG2 ILE B 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    1.71    0.94 2.00e-01 2.50e+01 2.19e+01
  chirality pdb=" CB  ILE A 119 "
            pdb=" CA  ILE A 119 "
            pdb=" CG1 ILE A 119 "
            pdb=" CG2 ILE A 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    1.94    0.70 2.00e-01 2.50e+01 1.24e+01
  chirality pdb=" CB  ILE A 410 "
            pdb=" CA  ILE A 410 "
            pdb=" CG1 ILE A 410 "
            pdb=" CG2 ILE A 410 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.13    0.52 2.00e-01 2.50e+01 6.65e+00
  ... (remaining 2060 not shown)

  Planarity restraints: 2363
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 405 "    0.050 5.00e-02 4.00e+02   7.50e-02 9.00e+00
        pdb=" N   PRO B 406 "   -0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO B 406 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO B 406 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 687 "    0.047 5.00e-02 4.00e+02   7.18e-02 8.26e+00
        pdb=" N   PRO B 688 "   -0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO B 688 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO B 688 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 678 "    0.044 5.00e-02 4.00e+02   6.74e-02 7.26e+00
        pdb=" N   PRO B 679 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO B 679 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B 679 "    0.038 5.00e-02 4.00e+02
  ... (remaining 2360 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1616
        2.75 -     3.29: 12131
        3.29 -     3.82: 23425
        3.82 -     4.36: 28698
        4.36 -     4.90: 47906
  Nonbonded interactions: 113776
  Sorted by model distance:
  nonbonded pdb=" O   THR B 176 "
            pdb=" OG1 THR B 180 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" OG1 THR A 206 "
            pdb=" O   LEU A 354 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" OE1 GLU B 798 "
            pdb=" OG1 THR B 806 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" OG  SER A 753 "
            pdb=" OH  TYR A 770 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" OG  SER B 217 "
            pdb=" O   THR B 223 "
     model   vdw
     2.283 3.040
  ... (remaining 113771 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 6 through 134 or resid 154 through 878))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.520
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     35.150
  Find NCS groups from input model:        1.040
  Set up NCS constraints:                  0.100
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:22.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   60.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
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      :  0.010   0.100  13244  Z= 0.442
  Angle     :  1.146  11.184  18046  Z= 0.645
  Chirality :  0.074   0.937   2063
  Planarity :  0.008   0.075   2363
  Dihedral  : 15.133  89.376   4686
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.52 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  1.20 %
    Favored  : 97.90 %
  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: -2.92 (0.18), residues: 1703
  helix: -2.18 (0.16), residues: 654
  sheet: -1.51 (0.32), residues: 239
  loop : -1.73 (0.21), residues: 810

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP B 876 
 HIS   0.013   0.002   HIS B 228 
 PHE   0.045   0.004   PHE A 232 
 TYR   0.031   0.004   TYR B 554 
 ARG   0.014   0.001   ARG B 489 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17298 (  526)
  hydrogen bonds       : angle       8.07528 ( 1497)
  covalent geometry    : bond        0.00996 (13244)
  covalent geometry    : angle       1.14636 (18046)

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

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

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 137
  time to evaluate  : 1.284 
Fit side-chains
REVERT: A  134 MET cc_start: 0.4979 (tmm) cc_final: 0.4602 (tmm)
REVERT: B  641 GLU cc_start: 0.6436 (mp0) cc_final: 0.6186 (mp0)
  outliers start: 12
  outliers final: 1
  residues processed: 146
  average time/residue: 1.1053
  time to fit residues: 178.8739
Evaluate side-chains
  102 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 101
  time to evaluate  : 1.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  354 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 143 optimal weight:    0.9990
   chunk 128 optimal weight:    0.9980
   chunk 71 optimal weight:    0.0060
   chunk 44 optimal weight:    0.7980
   chunk 86 optimal weight:    0.6980
   chunk 68 optimal weight:   10.0000
   chunk 133 optimal weight:    3.9990
   chunk 51 optimal weight:    8.9990
   chunk 81 optimal weight:    0.9990
   chunk 99 optimal weight:    0.6980
   chunk 154 optimal weight:    6.9990
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
A 511 GLN
A 512 GLN
A 526 GLN
A 536 GLN
A 745 ASN
** B  92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 314 HIS
B 609 GLN
B 745 ASN
B 786 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.186871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.151103 restraints weight = 12623.099|
|-----------------------------------------------------------------------------|
r_work (start): 0.3793 rms_B_bonded: 1.76
r_work: 0.3363 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3232 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.1240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  13244  Z= 0.137
  Angle     :  0.629   7.985  18046  Z= 0.329
  Chirality :  0.043   0.191   2063
  Planarity :  0.006   0.056   2363
  Dihedral  :  5.942  32.404   1837
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  :  9.44 %
    Favored  : 88.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.92 (0.19), residues: 1703
  helix: -0.99 (0.19), residues: 651
  sheet: -1.19 (0.33), residues: 214
  loop : -1.44 (0.21), residues: 838

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 876 
 HIS   0.005   0.001   HIS B 228 
 PHE   0.018   0.002   PHE A  26 
 TYR   0.010   0.001   TYR B 690 
 ARG   0.007   0.000   ARG B 874 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04522 (  526)
  hydrogen bonds       : angle       6.01442 ( 1497)
  covalent geometry    : bond        0.00297 (13244)
  covalent geometry    : angle       0.62921 (18046)

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

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

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 1.518 
Fit side-chains
REVERT: A  134 MET cc_start: 0.5345 (tmm) cc_final: 0.4974 (tmm)
REVERT: A  374 ILE cc_start: 0.8389 (mp) cc_final: 0.8039 (mt)
REVERT: A  526 GLN cc_start: 0.7551 (mp10) cc_final: 0.7321 (mp10)
REVERT: A  662 MET cc_start: 0.6677 (OUTLIER) cc_final: 0.6406 (mmm)
REVERT: A  668 PRO cc_start: 0.5742 (Cg_exo) cc_final: 0.5502 (Cg_endo)
REVERT: A  727 MET cc_start: 0.5982 (OUTLIER) cc_final: 0.5539 (mpt)
REVERT: B  125 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7516 (ttt)
REVERT: B  526 GLN cc_start: 0.6986 (OUTLIER) cc_final: 0.5859 (mp10)
REVERT: B  575 HIS cc_start: 0.6339 (t-90) cc_final: 0.6112 (t-90)
REVERT: B  727 MET cc_start: 0.5655 (ppp) cc_final: 0.5328 (ppp)
REVERT: B  817 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.5855 (mpt180)
  outliers start: 24
  outliers final: 5
  residues processed: 131
  average time/residue: 1.1879
  time to fit residues: 171.5869
Evaluate side-chains
  116 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 1.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  662 MET
Chi-restraints excluded: chain A residue  727 MET
Chi-restraints excluded: chain A residue  829 SER
Chi-restraints excluded: chain B residue  125 MET
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  526 GLN
Chi-restraints excluded: chain B residue  547 LEU
Chi-restraints excluded: chain B residue  752 ILE
Chi-restraints excluded: chain B residue  817 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 116 optimal weight:    0.9990
   chunk 89 optimal weight:    4.9990
   chunk 37 optimal weight:    4.9990
   chunk 71 optimal weight:   20.0000
   chunk 33 optimal weight:    5.9990
   chunk 64 optimal weight:    0.3980
   chunk 99 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 85 optimal weight:    5.9990
   chunk 137 optimal weight:    6.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    2.4788

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

Flipped N/Q/H residues before XYZ refinement:
A 487 GLN
A 511 GLN
A 721 HIS
A 745 ASN
** B  92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 GLN
B 431 GLN
B 541 GLN
B 774 GLN
B 786 GLN
B 789 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.181825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.148157 restraints weight = 12772.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.3766 rms_B_bonded: 0.98
r_work: 0.3443 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3264 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.1420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062  13244  Z= 0.238
  Angle     :  0.672   9.540  18046  Z= 0.351
  Chirality :  0.047   0.174   2063
  Planarity :  0.005   0.051   2363
  Dihedral  :  5.859  30.606   1837
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 13.93 %
    Favored  : 83.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.65 (0.20), residues: 1703
  helix: -0.67 (0.19), residues: 652
  sheet: -1.23 (0.33), residues: 231
  loop : -1.32 (0.21), residues: 820

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 100 
 HIS   0.006   0.001   HIS B 228 
 PHE   0.021   0.002   PHE A  26 
 TYR   0.014   0.002   TYR A 215 
 ARG   0.006   0.001   ARG A 478 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04423 (  526)
  hydrogen bonds       : angle       5.88694 ( 1497)
  covalent geometry    : bond        0.00548 (13244)
  covalent geometry    : angle       0.67210 (18046)

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

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

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 112
  time to evaluate  : 1.445 
Fit side-chains
REVERT: A  130 MET cc_start: 0.4198 (OUTLIER) cc_final: 0.3820 (mpm)
REVERT: A  134 MET cc_start: 0.5316 (tmm) cc_final: 0.4963 (tmm)
REVERT: A  235 ASN cc_start: 0.7302 (t0) cc_final: 0.6943 (t160)
REVERT: A  374 ILE cc_start: 0.8442 (mp) cc_final: 0.8101 (mt)
REVERT: A  526 GLN cc_start: 0.7577 (mp10) cc_final: 0.7348 (mp10)
REVERT: A  662 MET cc_start: 0.6865 (OUTLIER) cc_final: 0.6535 (mmm)
REVERT: A  874 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.7920 (tpt90)
REVERT: B  501 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.6622 (ptp90)
REVERT: B  526 GLN cc_start: 0.7027 (OUTLIER) cc_final: 0.5555 (mp10)
REVERT: B  575 HIS cc_start: 0.6431 (t-90) cc_final: 0.6205 (t-90)
REVERT: B  789 GLN cc_start: 0.6872 (pt0) cc_final: 0.6533 (tt0)
REVERT: B  817 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.6075 (mpt180)
  outliers start: 40
  outliers final: 16
  residues processed: 136
  average time/residue: 1.1073
  time to fit residues: 167.2673
Evaluate side-chains
  136 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 114
  time to evaluate  : 1.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ASP
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  400 THR
Chi-restraints excluded: chain A residue  522 VAL
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  662 MET
Chi-restraints excluded: chain A residue  829 SER
Chi-restraints excluded: chain A residue  874 ARG
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  501 ARG
Chi-restraints excluded: chain B residue  526 GLN
Chi-restraints excluded: chain B residue  547 LEU
Chi-restraints excluded: chain B residue  691 SER
Chi-restraints excluded: chain B residue  728 MET
Chi-restraints excluded: chain B residue  752 ILE
Chi-restraints excluded: chain B residue  817 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 78 optimal weight:    9.9990
   chunk 152 optimal weight:    6.9990
   chunk 50 optimal weight:    3.9990
   chunk 51 optimal weight:    8.9990
   chunk 65 optimal weight:   20.0000
   chunk 151 optimal weight:   20.0000
   chunk 86 optimal weight:    0.7980
   chunk 132 optimal weight:    0.6980
   chunk 17 optimal weight:    0.6980
   chunk 157 optimal weight:    0.8980
   chunk 112 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 511 GLN
A 512 GLN
A 745 ASN
B 340 GLN
B 541 GLN
B 786 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.189205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.165043 restraints weight = 12634.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.3902 rms_B_bonded: 0.94
r_work: 0.3564 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3391 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.1699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13244  Z= 0.128
  Angle     :  0.583  11.118  18046  Z= 0.299
  Chirality :  0.042   0.153   2063
  Planarity :  0.005   0.048   2363
  Dihedral  :  5.258  21.840   1835
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 14.98 %
    Favored  : 81.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.16 (0.20), residues: 1703
  helix: -0.18 (0.20), residues: 657
  sheet: -0.98 (0.33), residues: 231
  loop : -1.11 (0.22), residues: 815

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 614 
 HIS   0.004   0.001   HIS B 228 
 PHE   0.017   0.001   PHE A  26 
 TYR   0.017   0.001   TYR B 548 
 ARG   0.007   0.000   ARG A 645 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03734 (  526)
  hydrogen bonds       : angle       5.51205 ( 1497)
  covalent geometry    : bond        0.00291 (13244)
  covalent geometry    : angle       0.58253 (18046)

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

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

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 121
  time to evaluate  : 1.330 
Fit side-chains
REVERT: A  130 MET cc_start: 0.4378 (OUTLIER) cc_final: 0.4016 (mpm)
REVERT: A  235 ASN cc_start: 0.7411 (t0) cc_final: 0.7099 (t160)
REVERT: A  374 ILE cc_start: 0.8270 (mp) cc_final: 0.7920 (mt)
REVERT: A  526 GLN cc_start: 0.7593 (mp10) cc_final: 0.7382 (mp10)
REVERT: A  590 LEU cc_start: 0.5769 (OUTLIER) cc_final: 0.5362 (pt)
REVERT: A  662 MET cc_start: 0.6883 (OUTLIER) cc_final: 0.6576 (mmm)
REVERT: A  668 PRO cc_start: 0.6297 (Cg_exo) cc_final: 0.6027 (Cg_endo)
REVERT: B  501 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.6653 (ptp90)
REVERT: B  526 GLN cc_start: 0.7075 (OUTLIER) cc_final: 0.5723 (mp10)
REVERT: B  645 ARG cc_start: 0.6910 (ttp-110) cc_final: 0.6553 (ttm110)
REVERT: B  789 GLN cc_start: 0.6990 (pt0) cc_final: 0.6705 (tt0)
REVERT: B  817 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.6093 (mpt180)
  outliers start: 46
  outliers final: 15
  residues processed: 150
  average time/residue: 0.9867
  time to fit residues: 165.5073
Evaluate side-chains
  133 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 1.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  522 VAL
Chi-restraints excluded: chain A residue  590 LEU
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  662 MET
Chi-restraints excluded: chain A residue  818 LEU
Chi-restraints excluded: chain A residue  829 SER
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  423 THR
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  501 ARG
Chi-restraints excluded: chain B residue  526 GLN
Chi-restraints excluded: chain B residue  575 HIS
Chi-restraints excluded: chain B residue  691 SER
Chi-restraints excluded: chain B residue  817 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 54 optimal weight:    9.9990
   chunk 125 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 87 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 169 optimal weight:    4.9990
   chunk 38 optimal weight:    0.0970
   chunk 1 optimal weight:    0.9980
   chunk 70 optimal weight:   30.0000
   chunk 73 optimal weight:    0.0970
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.8378

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

Flipped N/Q/H residues before XYZ refinement:
A 745 ASN
B 541 GLN
** B 724 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 786 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.186187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.144087 restraints weight = 12783.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.3723 rms_B_bonded: 1.17
r_work: 0.3426 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3320 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.1863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13244  Z= 0.127
  Angle     :  0.570  10.266  18046  Z= 0.291
  Chirality :  0.042   0.139   2063
  Planarity :  0.005   0.048   2363
  Dihedral  :  5.015  20.742   1835
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 17.30 %
    Favored  : 79.63 %
  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: -0.92 (0.20), residues: 1703
  helix:  0.13 (0.20), residues: 653
  sheet: -0.96 (0.33), residues: 235
  loop : -1.05 (0.22), residues: 815

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 876 
 HIS   0.004   0.001   HIS A  92 
 PHE   0.017   0.001   PHE A  26 
 TYR   0.014   0.001   TYR B 554 
 ARG   0.009   0.000   ARG A 874 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03623 (  526)
  hydrogen bonds       : angle       5.33248 ( 1497)
  covalent geometry    : bond        0.00288 (13244)
  covalent geometry    : angle       0.56981 (18046)

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

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

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 117
  time to evaluate  : 1.302 
Fit side-chains
REVERT: A  119 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7939 (tp)
REVERT: A  235 ASN cc_start: 0.7276 (t0) cc_final: 0.6931 (t160)
REVERT: A  374 ILE cc_start: 0.8337 (mp) cc_final: 0.7989 (mt)
REVERT: A  590 LEU cc_start: 0.5324 (OUTLIER) cc_final: 0.4872 (pt)
REVERT: A  662 MET cc_start: 0.6710 (OUTLIER) cc_final: 0.6413 (mmm)
REVERT: A  668 PRO cc_start: 0.5760 (Cg_exo) cc_final: 0.5534 (Cg_endo)
REVERT: A  871 ASP cc_start: 0.7601 (p0) cc_final: 0.7392 (p0)
REVERT: B  119 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.8000 (tp)
REVERT: B  501 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6497 (ptp90)
REVERT: B  526 GLN cc_start: 0.6879 (OUTLIER) cc_final: 0.5336 (mp10)
REVERT: B  645 ARG cc_start: 0.6721 (ttp-110) cc_final: 0.6303 (ttm110)
REVERT: B  789 GLN cc_start: 0.6870 (pt0) cc_final: 0.6482 (tt0)
REVERT: B  817 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.5975 (mpt180)
  outliers start: 41
  outliers final: 20
  residues processed: 146
  average time/residue: 1.0303
  time to fit residues: 168.3206
Evaluate side-chains
  134 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 107
  time to evaluate  : 1.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  590 LEU
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  662 MET
Chi-restraints excluded: chain A residue  818 LEU
Chi-restraints excluded: chain A residue  829 SER
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  423 THR
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  457 SER
Chi-restraints excluded: chain B residue  501 ARG
Chi-restraints excluded: chain B residue  526 GLN
Chi-restraints excluded: chain B residue  626 LEU
Chi-restraints excluded: chain B residue  637 VAL
Chi-restraints excluded: chain B residue  691 SER
Chi-restraints excluded: chain B residue  752 ILE
Chi-restraints excluded: chain B residue  817 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 89 optimal weight:    7.9990
   chunk 56 optimal weight:    9.9990
   chunk 1 optimal weight:    2.9990
   chunk 114 optimal weight:    6.9990
   chunk 43 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 125 optimal weight:    1.9990
   chunk 134 optimal weight:    0.9980
   chunk 73 optimal weight:   10.0000
   chunk 6 optimal weight:    0.5980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
B 541 GLN
B 786 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.185189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.145258 restraints weight = 12829.738|
|-----------------------------------------------------------------------------|
r_work (start): 0.3733 rms_B_bonded: 1.19
r_work: 0.3404 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3271 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.1897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13244  Z= 0.154
  Angle     :  0.585   9.534  18046  Z= 0.300
  Chirality :  0.043   0.162   2063
  Planarity :  0.005   0.046   2363
  Dihedral  :  5.044  20.774   1835
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 18.20 %
    Favored  : 78.58 %
  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: -0.92 (0.20), residues: 1703
  helix:  0.11 (0.20), residues: 666
  sheet: -1.00 (0.33), residues: 245
  loop : -1.02 (0.23), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 100 
 HIS   0.004   0.001   HIS B 228 
 PHE   0.018   0.002   PHE A  26 
 TYR   0.012   0.002   TYR B 548 
 ARG   0.008   0.000   ARG A 645 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03728 (  526)
  hydrogen bonds       : angle       5.36149 ( 1497)
  covalent geometry    : bond        0.00354 (13244)
  covalent geometry    : angle       0.58538 (18046)

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

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

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 116
  time to evaluate  : 1.401 
Fit side-chains
REVERT: A  119 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8097 (tp)
REVERT: A  130 MET cc_start: 0.4295 (OUTLIER) cc_final: 0.3863 (mpm)
REVERT: A  235 ASN cc_start: 0.7320 (t0) cc_final: 0.6964 (t160)
REVERT: A  374 ILE cc_start: 0.8409 (mp) cc_final: 0.8088 (mt)
REVERT: A  590 LEU cc_start: 0.5305 (OUTLIER) cc_final: 0.4888 (pt)
REVERT: A  662 MET cc_start: 0.6674 (OUTLIER) cc_final: 0.6419 (mmm)
REVERT: A  775 MET cc_start: 0.6811 (ttt) cc_final: 0.6523 (ttm)
REVERT: A  853 SER cc_start: 0.7193 (OUTLIER) cc_final: 0.6883 (p)
REVERT: A  871 ASP cc_start: 0.7679 (p0) cc_final: 0.7459 (p0)
REVERT: B  501 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.6618 (ptp90)
REVERT: B  526 GLN cc_start: 0.6942 (OUTLIER) cc_final: 0.5335 (mp10)
REVERT: B  645 ARG cc_start: 0.6741 (ttp-110) cc_final: 0.6328 (ttm110)
REVERT: B  727 MET cc_start: 0.5764 (ppp) cc_final: 0.5539 (ppp)
REVERT: B  789 GLN cc_start: 0.6896 (pt0) cc_final: 0.6419 (tt0)
REVERT: B  817 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.5939 (mpt180)
  outliers start: 43
  outliers final: 21
  residues processed: 150
  average time/residue: 1.0218
  time to fit residues: 171.2262
Evaluate side-chains
  137 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 108
  time to evaluate  : 1.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  590 LEU
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  662 MET
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  818 LEU
Chi-restraints excluded: chain A residue  829 SER
Chi-restraints excluded: chain A residue  853 SER
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  423 THR
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  457 SER
Chi-restraints excluded: chain B residue  501 ARG
Chi-restraints excluded: chain B residue  526 GLN
Chi-restraints excluded: chain B residue  626 LEU
Chi-restraints excluded: chain B residue  637 VAL
Chi-restraints excluded: chain B residue  691 SER
Chi-restraints excluded: chain B residue  752 ILE
Chi-restraints excluded: chain B residue  817 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9990
   chunk 92 optimal weight:    0.2980
   chunk 132 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 157 optimal weight:    5.9990
   chunk 78 optimal weight:    8.9990
   chunk 163 optimal weight:    4.9990
   chunk 60 optimal weight:    5.9990
   chunk 104 optimal weight:    0.0670
   chunk 127 optimal weight:    0.9980
   overall best weight:    0.6720

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

Flipped N/Q/H residues before XYZ refinement:
A 745 ASN
B 541 GLN
B 786 GLN
** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.187495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 91)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.147467 restraints weight = 12731.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.3758 rms_B_bonded: 1.13
r_work: 0.3456 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3328 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.2090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13244  Z= 0.117
  Angle     :  0.559   9.309  18046  Z= 0.286
  Chirality :  0.042   0.214   2063
  Planarity :  0.004   0.047   2363
  Dihedral  :  4.839  21.567   1835
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 18.95 %
    Favored  : 78.13 %
  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: -0.82 (0.21), residues: 1703
  helix:  0.23 (0.20), residues: 667
  sheet: -0.94 (0.32), residues: 247
  loop : -1.01 (0.23), residues: 789

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 100 
 HIS   0.004   0.001   HIS A  92 
 PHE   0.015   0.001   PHE A  26 
 TYR   0.013   0.001   TYR B 554 
 ARG   0.007   0.000   ARG A 645 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03499 (  526)
  hydrogen bonds       : angle       5.29308 ( 1497)
  covalent geometry    : bond        0.00265 (13244)
  covalent geometry    : angle       0.55905 (18046)

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

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

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 118
  time to evaluate  : 1.379 
Fit side-chains
REVERT: A  119 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7926 (tp)
REVERT: A  235 ASN cc_start: 0.7264 (t0) cc_final: 0.6920 (t160)
REVERT: A  374 ILE cc_start: 0.8327 (mp) cc_final: 0.7975 (mt)
REVERT: A  590 LEU cc_start: 0.5189 (OUTLIER) cc_final: 0.4661 (pt)
REVERT: A  592 GLN cc_start: 0.6332 (OUTLIER) cc_final: 0.5351 (mp10)
REVERT: A  599 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7780 (mp)
REVERT: A  662 MET cc_start: 0.6680 (OUTLIER) cc_final: 0.6427 (mmm)
REVERT: A  775 MET cc_start: 0.6732 (ttt) cc_final: 0.6496 (ttm)
REVERT: A  853 SER cc_start: 0.7041 (OUTLIER) cc_final: 0.6745 (p)
REVERT: A  871 ASP cc_start: 0.7575 (p0) cc_final: 0.7352 (p0)
REVERT: B  501 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.6523 (ptp90)
REVERT: B  526 GLN cc_start: 0.6846 (OUTLIER) cc_final: 0.5310 (mp10)
REVERT: B  645 ARG cc_start: 0.6760 (ttp-110) cc_final: 0.6359 (ttm110)
REVERT: B  727 MET cc_start: 0.5761 (ppp) cc_final: 0.5497 (ppp)
REVERT: B  789 GLN cc_start: 0.6851 (pt0) cc_final: 0.6615 (tt0)
REVERT: B  817 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.5983 (mpt180)
REVERT: B  831 ASP cc_start: 0.7593 (m-30) cc_final: 0.6992 (t0)
  outliers start: 39
  outliers final: 18
  residues processed: 147
  average time/residue: 1.0506
  time to fit residues: 171.8149
Evaluate side-chains
  139 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 112
  time to evaluate  : 1.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  501 ARG
Chi-restraints excluded: chain A residue  590 LEU
Chi-restraints excluded: chain A residue  592 GLN
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  662 MET
Chi-restraints excluded: chain A residue  818 LEU
Chi-restraints excluded: chain A residue  853 SER
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  423 THR
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  457 SER
Chi-restraints excluded: chain B residue  501 ARG
Chi-restraints excluded: chain B residue  526 GLN
Chi-restraints excluded: chain B residue  626 LEU
Chi-restraints excluded: chain B residue  637 VAL
Chi-restraints excluded: chain B residue  691 SER
Chi-restraints excluded: chain B residue  817 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 149 optimal weight:   10.0000
   chunk 167 optimal weight:    2.9990
   chunk 12 optimal weight:    0.1980
   chunk 128 optimal weight:    0.9980
   chunk 47 optimal weight:    0.6980
   chunk 79 optimal weight:    0.0470
   chunk 143 optimal weight:    6.9990
   chunk 157 optimal weight:   10.0000
   chunk 74 optimal weight:    0.9980
   chunk 99 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.5878

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

Flipped N/Q/H residues before XYZ refinement:
A 190 GLN
A 511 GLN
B 487 GLN
B 541 GLN
B 786 GLN
** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.188131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 104)---------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.144795 restraints weight = 12778.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.3727 rms_B_bonded: 1.16
r_work: 0.3454 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3341 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.2229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13244  Z= 0.112
  Angle     :  0.550   8.474  18046  Z= 0.280
  Chirality :  0.042   0.166   2063
  Planarity :  0.004   0.048   2363
  Dihedral  :  4.704  19.375   1835
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 19.78 %
    Favored  : 77.38 %
  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: -0.76 (0.20), residues: 1703
  helix:  0.38 (0.20), residues: 670
  sheet: -0.99 (0.32), residues: 250
  loop : -1.03 (0.23), residues: 783

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 614 
 HIS   0.003   0.001   HIS A  92 
 PHE   0.015   0.001   PHE A  26 
 TYR   0.011   0.001   TYR B 554 
 ARG   0.004   0.000   ARG A 874 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03438 (  526)
  hydrogen bonds       : angle       5.16141 ( 1497)
  covalent geometry    : bond        0.00256 (13244)
  covalent geometry    : angle       0.55039 (18046)

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

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

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 119
  time to evaluate  : 1.330 
Fit side-chains
REVERT: A  119 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7886 (tp)
REVERT: A  235 ASN cc_start: 0.7319 (t0) cc_final: 0.7014 (t160)
REVERT: A  374 ILE cc_start: 0.8319 (mp) cc_final: 0.7978 (mt)
REVERT: A  590 LEU cc_start: 0.5225 (OUTLIER) cc_final: 0.4729 (pt)
REVERT: A  592 GLN cc_start: 0.6287 (OUTLIER) cc_final: 0.5295 (mp10)
REVERT: A  599 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7783 (mp)
REVERT: A  662 MET cc_start: 0.6638 (OUTLIER) cc_final: 0.6387 (mmm)
REVERT: A  727 MET cc_start: 0.6265 (mpt) cc_final: 0.4590 (ttt)
REVERT: A  775 MET cc_start: 0.6630 (ttt) cc_final: 0.6298 (ttm)
REVERT: A  853 SER cc_start: 0.6976 (OUTLIER) cc_final: 0.6683 (p)
REVERT: A  871 ASP cc_start: 0.7571 (p0) cc_final: 0.7342 (p0)
REVERT: B  501 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6500 (ptp90)
REVERT: B  526 GLN cc_start: 0.6955 (OUTLIER) cc_final: 0.5373 (mp10)
REVERT: B  645 ARG cc_start: 0.6765 (ttp-110) cc_final: 0.6371 (ttm110)
REVERT: B  789 GLN cc_start: 0.6847 (pt0) cc_final: 0.6611 (tt0)
REVERT: B  817 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.5872 (mpt180)
REVERT: B  831 ASP cc_start: 0.7556 (m-30) cc_final: 0.7001 (t0)
  outliers start: 38
  outliers final: 17
  residues processed: 145
  average time/residue: 1.1343
  time to fit residues: 182.5482
Evaluate side-chains
  134 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 1.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  501 ARG
Chi-restraints excluded: chain A residue  590 LEU
Chi-restraints excluded: chain A residue  592 GLN
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  662 MET
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  818 LEU
Chi-restraints excluded: chain A residue  853 SER
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  288 ASP
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  405 GLN
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  457 SER
Chi-restraints excluded: chain B residue  501 ARG
Chi-restraints excluded: chain B residue  526 GLN
Chi-restraints excluded: chain B residue  637 VAL
Chi-restraints excluded: chain B residue  691 SER
Chi-restraints excluded: chain B residue  817 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 82 optimal weight:    0.0970
   chunk 69 optimal weight:    0.9990
   chunk 75 optimal weight:    9.9990
   chunk 41 optimal weight:    0.8980
   chunk 53 optimal weight:    9.9990
   chunk 157 optimal weight:   20.0000
   chunk 66 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 158 optimal weight:    1.9990
   chunk 99 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
A 402 GLN
A 511 GLN
B 541 GLN
B 786 GLN
** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.185444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.149579 restraints weight = 12662.591|
|-----------------------------------------------------------------------------|
r_work (start): 0.3779 rms_B_bonded: 1.09
r_work: 0.3430 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3287 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.2153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  13244  Z= 0.160
  Angle     :  0.592   8.369  18046  Z= 0.304
  Chirality :  0.044   0.188   2063
  Planarity :  0.005   0.048   2363
  Dihedral  :  4.872  19.615   1835
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 20.07 %
    Favored  : 77.08 %
  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: -0.79 (0.20), residues: 1703
  helix:  0.29 (0.20), residues: 661
  sheet: -1.02 (0.32), residues: 255
  loop : -0.98 (0.23), residues: 787

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 100 
 HIS   0.004   0.001   HIS B 228 
 PHE   0.018   0.002   PHE A  26 
 TYR   0.010   0.002   TYR A 282 
 ARG   0.011   0.000   ARG A 645 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03678 (  526)
  hydrogen bonds       : angle       5.35737 ( 1497)
  covalent geometry    : bond        0.00371 (13244)
  covalent geometry    : angle       0.59193 (18046)

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

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

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 113
  time to evaluate  : 1.469 
Fit side-chains
REVERT: A  119 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.8077 (tp)
REVERT: A  235 ASN cc_start: 0.7445 (t0) cc_final: 0.7156 (t160)
REVERT: A  374 ILE cc_start: 0.8413 (mp) cc_final: 0.8036 (mt)
REVERT: A  590 LEU cc_start: 0.5430 (OUTLIER) cc_final: 0.4921 (pt)
REVERT: A  592 GLN cc_start: 0.6501 (OUTLIER) cc_final: 0.5364 (mp10)
REVERT: A  601 PHE cc_start: 0.7309 (t80) cc_final: 0.7053 (t80)
REVERT: A  638 PHE cc_start: 0.7133 (OUTLIER) cc_final: 0.6698 (m-80)
REVERT: A  662 MET cc_start: 0.6801 (OUTLIER) cc_final: 0.6528 (mmm)
REVERT: A  727 MET cc_start: 0.6179 (mpt) cc_final: 0.4648 (ttt)
REVERT: A  775 MET cc_start: 0.6944 (ttt) cc_final: 0.6686 (ttm)
REVERT: A  853 SER cc_start: 0.7100 (OUTLIER) cc_final: 0.6804 (p)
REVERT: A  871 ASP cc_start: 0.7715 (p0) cc_final: 0.7492 (p0)
REVERT: B  501 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.6652 (ptp90)
REVERT: B  526 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.5534 (mp10)
REVERT: B  645 ARG cc_start: 0.6894 (ttp-110) cc_final: 0.6540 (ttm110)
REVERT: B  817 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.6018 (mpt180)
REVERT: B  831 ASP cc_start: 0.7701 (m-30) cc_final: 0.7145 (t0)
  outliers start: 38
  outliers final: 21
  residues processed: 140
  average time/residue: 1.0596
  time to fit residues: 165.2540
Evaluate side-chains
  139 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 109
  time to evaluate  : 1.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  501 ARG
Chi-restraints excluded: chain A residue  590 LEU
Chi-restraints excluded: chain A residue  592 GLN
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  638 PHE
Chi-restraints excluded: chain A residue  662 MET
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  818 LEU
Chi-restraints excluded: chain A residue  829 SER
Chi-restraints excluded: chain A residue  853 SER
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  288 ASP
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  423 THR
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  457 SER
Chi-restraints excluded: chain B residue  501 ARG
Chi-restraints excluded: chain B residue  526 GLN
Chi-restraints excluded: chain B residue  637 VAL
Chi-restraints excluded: chain B residue  691 SER
Chi-restraints excluded: chain B residue  817 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 36 optimal weight:    7.9990
   chunk 74 optimal weight:    0.9980
   chunk 85 optimal weight:    4.9990
   chunk 107 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 135 optimal weight:    1.9990
   chunk 56 optimal weight:    9.9990
   chunk 159 optimal weight:    0.9990
   chunk 134 optimal weight:    0.0060
   chunk 140 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   overall best weight:    1.2002

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

Flipped N/Q/H residues before XYZ refinement:
A 511 GLN
** B  92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 541 GLN
B 786 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.185893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.152640 restraints weight = 12601.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3812 rms_B_bonded: 0.96
r_work: 0.3496 rms_B_bonded: 1.79 restraints_weight: 0.5000
r_work: 0.3333 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.2190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13244  Z= 0.147
  Angle     :  0.583  10.621  18046  Z= 0.298
  Chirality :  0.044   0.255   2063
  Planarity :  0.005   0.054   2363
  Dihedral  :  4.858  19.566   1835
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 20.07 %
    Favored  : 77.15 %
  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: -0.77 (0.20), residues: 1703
  helix:  0.31 (0.20), residues: 659
  sheet: -1.01 (0.32), residues: 250
  loop : -0.95 (0.23), residues: 794

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 100 
 HIS   0.004   0.001   HIS B 228 
 PHE   0.017   0.001   PHE A  26 
 TYR   0.011   0.001   TYR A 282 
 ARG   0.014   0.000   ARG A 645 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03636 (  526)
  hydrogen bonds       : angle       5.28300 ( 1497)
  covalent geometry    : bond        0.00339 (13244)
  covalent geometry    : angle       0.58260 (18046)

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

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

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3406 Ramachandran restraints generated.
    1703 Oldfield, 0 Emsley, 1703 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 108
  time to evaluate  : 1.312 
Fit side-chains
REVERT: A  119 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.8056 (tp)
REVERT: A  235 ASN cc_start: 0.7320 (t0) cc_final: 0.7019 (t160)
REVERT: A  374 ILE cc_start: 0.8340 (mp) cc_final: 0.8010 (mt)
REVERT: A  590 LEU cc_start: 0.5396 (OUTLIER) cc_final: 0.4896 (pt)
REVERT: A  592 GLN cc_start: 0.6446 (OUTLIER) cc_final: 0.5309 (mp10)
REVERT: A  662 MET cc_start: 0.6730 (OUTLIER) cc_final: 0.6461 (mmm)
REVERT: A  727 MET cc_start: 0.6159 (mpt) cc_final: 0.4610 (ttt)
REVERT: A  853 SER cc_start: 0.6978 (OUTLIER) cc_final: 0.6700 (p)
REVERT: A  871 ASP cc_start: 0.7627 (p0) cc_final: 0.7401 (p0)
REVERT: B  501 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.6660 (ptp90)
REVERT: B  526 GLN cc_start: 0.7034 (OUTLIER) cc_final: 0.5416 (mp10)
REVERT: B  645 ARG cc_start: 0.6856 (ttp-110) cc_final: 0.6514 (ttm110)
REVERT: B  817 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.5955 (mpt180)
REVERT: B  831 ASP cc_start: 0.7632 (m-30) cc_final: 0.7084 (t0)
  outliers start: 37
  outliers final: 20
  residues processed: 135
  average time/residue: 1.1517
  time to fit residues: 173.2314
Evaluate side-chains
  135 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 107
  time to evaluate  : 1.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  501 ARG
Chi-restraints excluded: chain A residue  590 LEU
Chi-restraints excluded: chain A residue  592 GLN
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  662 MET
Chi-restraints excluded: chain A residue  805 LEU
Chi-restraints excluded: chain A residue  818 LEU
Chi-restraints excluded: chain A residue  829 SER
Chi-restraints excluded: chain A residue  853 SER
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  288 ASP
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  423 THR
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  457 SER
Chi-restraints excluded: chain B residue  501 ARG
Chi-restraints excluded: chain B residue  526 GLN
Chi-restraints excluded: chain B residue  637 VAL
Chi-restraints excluded: chain B residue  691 SER
Chi-restraints excluded: chain B residue  817 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 37 optimal weight:    0.6980
   chunk 105 optimal weight:   10.0000
   chunk 95 optimal weight:    0.9980
   chunk 145 optimal weight:    0.8980
   chunk 53 optimal weight:   10.0000
   chunk 48 optimal weight:    1.9990
   chunk 102 optimal weight:    0.9980
   chunk 165 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A 511 GLN
** B  92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 541 GLN
B 786 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.188906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.164217 restraints weight = 12516.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.3896 rms_B_bonded: 1.11
r_work: 0.3663 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3598 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.2239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13244  Z= 0.143
  Angle     :  0.580   7.981  18046  Z= 0.299
  Chirality :  0.044   0.355   2063
  Planarity :  0.004   0.048   2363
  Dihedral  :  4.846  19.383   1835
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 20.15 %
    Favored  : 77.08 %
  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: -0.74 (0.20), residues: 1703
  helix:  0.30 (0.20), residues: 664
  sheet: -0.98 (0.32), residues: 252
  loop : -0.93 (0.23), residues: 787

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 100 
 HIS   0.004   0.001   HIS B 228 
 PHE   0.017   0.001   PHE A  26 
 TYR   0.020   0.002   TYR B 540 
 ARG   0.011   0.000   ARG A 645 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03622 (  526)
  hydrogen bonds       : angle       5.30149 ( 1497)
  covalent geometry    : bond        0.00329 (13244)
  covalent geometry    : angle       0.57982 (18046)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9690.75 seconds
wall clock time: 166 minutes 34.56 seconds (9994.56 seconds total)