Starting phenix.real_space_refine
on Thu Sep 18 01:13:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xju_38406/09_2025/8xju_38406.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xju_38406/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xju_38406/09_2025/8xju_38406.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xju_38406/09_2025/8xju_38406.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xju_38406/09_2025/8xju_38406.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xju_38406/09_2025/8xju_38406.map"
  }
  resolution = 2.91
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.28, per 1000 atoms: 0.25
  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: 1.05
  Conformation dependent library (CDL) restraints added in 570.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.53
  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: 2.54

  Time building geometry restraints manager: 1.34 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:             1.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     13.130
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.020
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.014   0.001   ARG B 489 
 TYR   0.031   0.004   TYR B 554 
 PHE   0.045   0.004   PHE A 232 
 TRP   0.023   0.003   TRP B 876 
 HIS   0.013   0.002   HIS B 228 

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

*********************** 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  : 0.470 
Fit side-chains
REVERT: A  134 MET cc_start: 0.4979 (tmm) cc_final: 0.4603 (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: 0.5308
  time to fit residues: 85.5550
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  : 0.420 
-------------------------------------------------------------------------------
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 98 optimal weight:    3.9990
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    0.3980
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:    0.1980
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9980
   chunk 149 optimal weight:   10.0000
   overall best weight:    0.6782

-------------------------------------------------------------------------------
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 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 = 0.4100 r_free = 0.4100 target = 0.186715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.150930 restraints weight = 12779.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3796 rms_B_bonded: 1.06
r_work: 0.3448 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3298 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.1255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  13244  Z= 0.132
  Angle     :  0.621   8.688  18046  Z= 0.323
  Chirality :  0.043   0.174   2063
  Planarity :  0.006   0.055   2363
  Dihedral  :  5.941  32.713   1837
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  :  9.44 %
    Favored  : 88.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.88 (0.19), residues: 1703
  helix: -0.96 (0.19), residues: 651
  sheet: -1.15 (0.34), residues: 211
  loop : -1.43 (0.21), residues: 841

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 874 
 TYR   0.011   0.001   TYR A 690 
 PHE   0.017   0.002   PHE A  26 
 TRP   0.010   0.001   TRP B 876 
 HIS   0.005   0.001   HIS B 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (13244)
  covalent geometry    : angle       0.62094 (18046)
  hydrogen bonds       : bond        0.04231 (  526)
  hydrogen bonds       : angle       5.98973 ( 1497)

*********************** 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
  137 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 0.507 
Fit side-chains
   revert: symmetry clash
REVERT: A  134 MET cc_start: 0.5379 (tmm) cc_final: 0.5020 (tmm)
REVERT: A  374 ILE cc_start: 0.8321 (mp) cc_final: 0.7974 (mt)
REVERT: A  526 GLN cc_start: 0.7499 (mp10) cc_final: 0.7277 (mp10)
REVERT: A  662 MET cc_start: 0.6775 (OUTLIER) cc_final: 0.6493 (mmm)
REVERT: A  668 PRO cc_start: 0.5942 (Cg_exo) cc_final: 0.5693 (Cg_endo)
REVERT: A  727 MET cc_start: 0.5873 (ttt) cc_final: 0.5504 (mpt)
REVERT: B  125 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7494 (ttt)
REVERT: B  526 GLN cc_start: 0.7012 (OUTLIER) cc_final: 0.5925 (mp10)
REVERT: B  575 HIS cc_start: 0.6398 (t-90) cc_final: 0.6197 (t-90)
REVERT: B  817 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.5867 (mpt180)
  outliers start: 23
  outliers final: 6
  residues processed: 130
  average time/residue: 0.5460
  time to fit residues: 78.1166
Evaluate side-chains
  115 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
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  829 SER
Chi-restraints excluded: chain B residue  125 MET
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  356 THR
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 104 optimal weight:    0.5980
   chunk 59 optimal weight:    7.9990
   chunk 64 optimal weight:    0.2980
   chunk 41 optimal weight:   10.0000
   chunk 34 optimal weight:    5.9990
   chunk 60 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 72 optimal weight:    5.9990
   chunk 65 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    2.1786

-------------------------------------------------------------------------------
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 431 GLN
B 541 GLN
B 774 GLN
B 786 GLN
B 789 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.186005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.156832 restraints weight = 12715.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.3811 rms_B_bonded: 1.21
r_work: 0.3440 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.1431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  13244  Z= 0.218
  Angle     :  0.658   9.545  18046  Z= 0.342
  Chirality :  0.046   0.162   2063
  Planarity :  0.005   0.050   2363
  Dihedral  :  5.773  29.109   1837
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 14.08 %
    Favored  : 82.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.62 (0.20), residues: 1703
  helix: -0.62 (0.19), residues: 654
  sheet: -1.23 (0.33), residues: 231
  loop : -1.31 (0.22), residues: 818

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 478 
 TYR   0.015   0.002   TYR B 554 
 PHE   0.020   0.002   PHE A  26 
 TRP   0.011   0.001   TRP A 100 
 HIS   0.006   0.001   HIS B 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 (13244)
  covalent geometry    : angle       0.65828 (18046)
  hydrogen bonds       : bond        0.04307 (  526)
  hydrogen bonds       : angle       5.83527 ( 1497)

*********************** 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
  154 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 112
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 MET cc_start: 0.4134 (OUTLIER) cc_final: 0.3833 (mpm)
REVERT: A  134 MET cc_start: 0.5230 (tmm) cc_final: 0.4919 (tmm)
REVERT: A  235 ASN cc_start: 0.7265 (t0) cc_final: 0.6965 (t160)
REVERT: A  374 ILE cc_start: 0.8290 (mp) cc_final: 0.7972 (mt)
REVERT: A  662 MET cc_start: 0.6870 (OUTLIER) cc_final: 0.6561 (mmm)
REVERT: A  874 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7804 (tpt90)
REVERT: B  501 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.6539 (ptp90)
REVERT: B  526 GLN cc_start: 0.6936 (OUTLIER) cc_final: 0.5615 (mp10)
REVERT: B  789 GLN cc_start: 0.6833 (pt0) cc_final: 0.6606 (tt0)
REVERT: B  817 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.6075 (mpt180)
  outliers start: 42
  outliers final: 15
  residues processed: 138
  average time/residue: 0.5471
  time to fit residues: 83.6305
Evaluate side-chains
  127 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 106
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
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  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 73 optimal weight:    9.9990
   chunk 118 optimal weight:    4.9990
   chunk 124 optimal weight:    4.9990
   chunk 71 optimal weight:    0.0570
   chunk 84 optimal weight:    1.9990
   chunk 132 optimal weight:    0.8980
   chunk 106 optimal weight:    0.9980
   chunk 79 optimal weight:    9.9990
   chunk 23 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 141 optimal weight:    0.2980
   overall best weight:    0.6298

-------------------------------------------------------------------------------
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 541 GLN
B 724 HIS
B 786 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.190306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.165090 restraints weight = 12667.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.3900 rms_B_bonded: 0.98
r_work: 0.3547 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3399 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.1749

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= 0.118
  Angle     :  0.575   9.794  18046  Z= 0.294
  Chirality :  0.042   0.149   2063
  Planarity :  0.005   0.047   2363
  Dihedral  :  5.182  21.651   1835
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 16.10 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.12 (0.20), residues: 1703
  helix: -0.10 (0.20), residues: 657
  sheet: -1.03 (0.33), residues: 235
  loop : -1.11 (0.22), residues: 811

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 589 
 TYR   0.015   0.001   TYR B 548 
 PHE   0.016   0.001   PHE A  26 
 TRP   0.006   0.001   TRP A 614 
 HIS   0.004   0.001   HIS A  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (13244)
  covalent geometry    : angle       0.57465 (18046)
  hydrogen bonds       : bond        0.03647 (  526)
  hydrogen bonds       : angle       5.45588 ( 1497)

*********************** 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
  155 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 120
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 MET cc_start: 0.4167 (OUTLIER) cc_final: 0.3839 (mpm)
REVERT: A  134 MET cc_start: 0.5263 (tmm) cc_final: 0.4946 (tmm)
REVERT: A  235 ASN cc_start: 0.7327 (t0) cc_final: 0.7007 (t160)
REVERT: A  374 ILE cc_start: 0.8218 (mp) cc_final: 0.7872 (mt)
REVERT: A  590 LEU cc_start: 0.5737 (OUTLIER) cc_final: 0.5330 (pt)
REVERT: A  662 MET cc_start: 0.6883 (OUTLIER) cc_final: 0.6542 (mmm)
REVERT: A  668 PRO cc_start: 0.6261 (Cg_exo) cc_final: 0.6007 (Cg_endo)
REVERT: B  125 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7467 (ttt)
REVERT: B  526 GLN cc_start: 0.7039 (OUTLIER) cc_final: 0.5661 (mp10)
REVERT: B  645 ARG cc_start: 0.6885 (ttp-110) cc_final: 0.6497 (ttm110)
REVERT: B  789 GLN cc_start: 0.6948 (pt0) cc_final: 0.6629 (tt0)
REVERT: B  817 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.5981 (mpt180)
  outliers start: 35
  outliers final: 10
  residues processed: 143
  average time/residue: 0.5219
  time to fit residues: 82.9428
Evaluate side-chains
  121 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
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  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 B residue  125 MET
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  443 VAL
Chi-restraints excluded: chain B residue  526 GLN
Chi-restraints excluded: chain B residue  728 MET
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 91 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 99 optimal weight:    0.6980
   chunk 150 optimal weight:   10.0000
   chunk 136 optimal weight:    2.9990
   chunk 115 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 128 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 158 optimal weight:    0.7980
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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
** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.189302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.164910 restraints weight = 12713.852|
|-----------------------------------------------------------------------------|
r_work (start): 0.3901 rms_B_bonded: 0.98
r_work: 0.3696 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3644 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.1866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13244  Z= 0.137
  Angle     :  0.571   9.688  18046  Z= 0.293
  Chirality :  0.043   0.170   2063
  Planarity :  0.005   0.045   2363
  Dihedral  :  5.040  20.680   1835
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 17.15 %
    Favored  : 79.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.93 (0.20), residues: 1703
  helix:  0.14 (0.20), residues: 655
  sheet: -0.93 (0.33), residues: 232
  loop : -1.08 (0.22), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 874 
 TYR   0.014   0.001   TYR B 690 
 PHE   0.017   0.001   PHE A  26 
 TRP   0.006   0.001   TRP A 876 
 HIS   0.004   0.001   HIS B 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (13244)
  covalent geometry    : angle       0.57082 (18046)
  hydrogen bonds       : bond        0.03673 (  526)
  hydrogen bonds       : angle       5.32076 ( 1497)

*********************** 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
  149 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 110
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
REVERT: A  119 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7946 (tp)
REVERT: A  130 MET cc_start: 0.4190 (OUTLIER) cc_final: 0.3918 (mpm)
REVERT: A  235 ASN cc_start: 0.7373 (t0) cc_final: 0.7084 (t160)
REVERT: A  374 ILE cc_start: 0.8182 (mp) cc_final: 0.7838 (mt)
REVERT: A  590 LEU cc_start: 0.5985 (OUTLIER) cc_final: 0.5474 (pt)
REVERT: A  662 MET cc_start: 0.6758 (OUTLIER) cc_final: 0.6521 (mmm)
REVERT: B  501 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6500 (ptp90)
REVERT: B  526 GLN cc_start: 0.6985 (OUTLIER) cc_final: 0.5669 (mp10)
REVERT: B  645 ARG cc_start: 0.6810 (ttp-110) cc_final: 0.6592 (ttm110)
REVERT: B  817 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.6163 (mpt180)
  outliers start: 39
  outliers final: 20
  residues processed: 138
  average time/residue: 0.4833
  time to fit residues: 74.3927
Evaluate side-chains
  130 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 103
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
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  818 LEU
Chi-restraints excluded: chain A residue  829 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  728 MET
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 57 optimal weight:    2.9990
   chunk 111 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 92 optimal weight:    1.9990
   chunk 87 optimal weight:    0.0570
   chunk 53 optimal weight:    9.9990
   chunk 32 optimal weight:    4.9990
   chunk 66 optimal weight:   20.0000
   chunk 68 optimal weight:    5.9990
   chunk 39 optimal weight:    4.9990
   chunk 80 optimal weight:    0.5980
   overall best weight:    1.5304

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.187814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 94)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.147297 restraints weight = 12528.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 2.00
r_work: 0.3324 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3202 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.1884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  13244  Z= 0.168
  Angle     :  0.592  10.113  18046  Z= 0.304
  Chirality :  0.044   0.248   2063
  Planarity :  0.005   0.048   2363
  Dihedral  :  5.093  20.770   1835
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 18.13 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.95 (0.20), residues: 1703
  helix:  0.12 (0.20), residues: 660
  sheet: -1.09 (0.31), residues: 255
  loop : -1.04 (0.23), residues: 788

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 645 
 TYR   0.013   0.002   TYR B 548 
 PHE   0.019   0.002   PHE A  26 
 TRP   0.008   0.001   TRP A 100 
 HIS   0.005   0.001   HIS B 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (13244)
  covalent geometry    : angle       0.59165 (18046)
  hydrogen bonds       : bond        0.03796 (  526)
  hydrogen bonds       : angle       5.34016 ( 1497)

*********************** 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
  157 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 113
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 MET cc_start: 0.4284 (OUTLIER) cc_final: 0.3871 (mpm)
REVERT: A  235 ASN cc_start: 0.7297 (t0) cc_final: 0.6933 (t160)
REVERT: A  374 ILE cc_start: 0.8461 (mp) cc_final: 0.8141 (mt)
REVERT: A  590 LEU cc_start: 0.5123 (OUTLIER) cc_final: 0.4714 (pt)
REVERT: A  662 MET cc_start: 0.6590 (OUTLIER) cc_final: 0.6371 (mmm)
REVERT: A  871 ASP cc_start: 0.7757 (p0) cc_final: 0.7534 (p0)
REVERT: B  501 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.6518 (ptp90)
REVERT: B  526 GLN cc_start: 0.6915 (OUTLIER) cc_final: 0.5285 (mp10)
REVERT: B  645 ARG cc_start: 0.6557 (ttp-110) cc_final: 0.6134 (ttm110)
REVERT: B  817 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.5913 (mpt180)
  outliers start: 44
  outliers final: 25
  residues processed: 143
  average time/residue: 0.4985
  time to fit residues: 79.4085
Evaluate side-chains
  137 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 106
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
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  410 ILE
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 B residue  116 ASP
Chi-restraints excluded: chain B residue  125 MET
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  347 VAL
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  728 MET
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 71 optimal weight:   10.0000
   chunk 6 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9990
   chunk 29 optimal weight:    6.9990
   chunk 91 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9980
   chunk 96 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   chunk 148 optimal weight:    0.9990
   chunk 127 optimal weight:    0.8980
   chunk 161 optimal weight:    0.7980
   overall best weight:    0.8782

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.189529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.163227 restraints weight = 12576.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.3884 rms_B_bonded: 1.02
r_work: 0.3650 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3600 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.2041

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= 0.127
  Angle     :  0.565  10.590  18046  Z= 0.289
  Chirality :  0.043   0.222   2063
  Planarity :  0.004   0.047   2363
  Dihedral  :  4.908  21.464   1835
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 18.95 %
    Favored  : 77.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.85 (0.20), residues: 1703
  helix:  0.25 (0.20), residues: 661
  sheet: -1.01 (0.32), residues: 250
  loop : -1.04 (0.23), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 645 
 TYR   0.012   0.001   TYR B 554 
 PHE   0.016   0.001   PHE A  26 
 TRP   0.005   0.001   TRP A 100 
 HIS   0.004   0.001   HIS B 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (13244)
  covalent geometry    : angle       0.56513 (18046)
  hydrogen bonds       : bond        0.03557 (  526)
  hydrogen bonds       : angle       5.26985 ( 1497)

*********************** 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
  151 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 110
  time to evaluate  : 0.543 
Fit side-chains
   revert: symmetry clash
REVERT: A  235 ASN cc_start: 0.7366 (t0) cc_final: 0.7071 (t160)
REVERT: A  374 ILE cc_start: 0.8209 (mp) cc_final: 0.7852 (mt)
REVERT: A  590 LEU cc_start: 0.5940 (OUTLIER) cc_final: 0.5320 (pt)
REVERT: A  592 GLN cc_start: 0.6624 (OUTLIER) cc_final: 0.5689 (mp10)
REVERT: A  599 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7407 (mp)
REVERT: A  662 MET cc_start: 0.6732 (OUTLIER) cc_final: 0.6493 (mmm)
REVERT: A  775 MET cc_start: 0.7475 (ttt) cc_final: 0.7218 (ttm)
REVERT: A  871 ASP cc_start: 0.7451 (p0) cc_final: 0.7233 (p0)
REVERT: B  501 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.6567 (ptp90)
REVERT: B  526 GLN cc_start: 0.6967 (OUTLIER) cc_final: 0.5632 (mp10)
REVERT: B  645 ARG cc_start: 0.6888 (ttp-110) cc_final: 0.6655 (ttm110)
REVERT: B  817 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.6076 (mpt180)
  outliers start: 41
  outliers final: 21
  residues processed: 140
  average time/residue: 0.5460
  time to fit residues: 84.7758
Evaluate side-chains
  132 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 104
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
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  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  805 LEU
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  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  728 MET
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 46 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 62 optimal weight:   10.0000
   chunk 109 optimal weight:    3.9990
   chunk 52 optimal weight:    7.9990
   chunk 154 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 56 optimal weight:    5.9990
   chunk 44 optimal weight:    0.8980
   chunk 152 optimal weight:    9.9990
   chunk 18 optimal weight:    5.9990
   overall best weight:    2.3386

-------------------------------------------------------------------------------
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 487 GLN
B 541 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.183437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.141509 restraints weight = 12578.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.3681 rms_B_bonded: 1.18
r_work: 0.3359 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3236 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.1948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  13244  Z= 0.223
  Angle     :  0.641  10.854  18046  Z= 0.330
  Chirality :  0.046   0.253   2063
  Planarity :  0.005   0.049   2363
  Dihedral  :  5.220  21.114   1835
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 19.33 %
    Favored  : 77.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.04 (0.20), residues: 1703
  helix: -0.01 (0.20), residues: 659
  sheet: -1.12 (0.31), residues: 258
  loop : -1.02 (0.23), residues: 786

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 645 
 TYR   0.013   0.002   TYR A 215 
 PHE   0.019   0.002   PHE A  26 
 TRP   0.011   0.002   TRP A 100 
 HIS   0.005   0.001   HIS B 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00519 (13244)
  covalent geometry    : angle       0.64101 (18046)
  hydrogen bonds       : bond        0.04017 (  526)
  hydrogen bonds       : angle       5.42392 ( 1497)

*********************** 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
  159 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 117
  time to evaluate  : 0.523 
Fit side-chains
   revert: symmetry clash
REVERT: A  235 ASN cc_start: 0.7308 (t0) cc_final: 0.6952 (t160)
REVERT: A  374 ILE cc_start: 0.8456 (mp) cc_final: 0.8127 (mt)
REVERT: A  420 MET cc_start: 0.7236 (mmm) cc_final: 0.6936 (mmt)
REVERT: A  526 GLN cc_start: 0.7608 (mp10) cc_final: 0.7408 (mp10)
REVERT: A  590 LEU cc_start: 0.5140 (OUTLIER) cc_final: 0.4647 (pt)
REVERT: A  592 GLN cc_start: 0.6363 (OUTLIER) cc_final: 0.5232 (mp10)
REVERT: A  599 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7795 (mp)
REVERT: A  662 MET cc_start: 0.6700 (OUTLIER) cc_final: 0.6477 (mmm)
REVERT: A  871 ASP cc_start: 0.7749 (p0) cc_final: 0.7531 (p0)
REVERT: B  501 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.6499 (ptp90)
REVERT: B  526 GLN cc_start: 0.6918 (OUTLIER) cc_final: 0.5254 (mp10)
REVERT: B  645 ARG cc_start: 0.6690 (ttp-110) cc_final: 0.6320 (ttm110)
REVERT: B  817 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.5924 (mpt180)
REVERT: B  851 ASP cc_start: 0.7382 (t0) cc_final: 0.7120 (t0)
  outliers start: 42
  outliers final: 23
  residues processed: 145
  average time/residue: 0.5180
  time to fit residues: 83.7784
Evaluate side-chains
  143 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 113
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
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  283 THR
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  410 ILE
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  829 SER
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  288 ASP
Chi-restraints excluded: chain B residue  347 VAL
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  728 MET
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 56 optimal weight:   10.0000
   chunk 145 optimal weight:    7.9990
   chunk 130 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 17 optimal weight:    5.9990
   chunk 79 optimal weight:    6.9990
   chunk 86 optimal weight:    0.6980
   chunk 98 optimal weight:    0.6980
   chunk 111 optimal weight:    0.7980
   chunk 55 optimal weight:    6.9990
   chunk 69 optimal weight:   10.0000
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
A 511 GLN
A 745 ASN
B 541 GLN
B 721 HIS
B 786 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.184886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.144184 restraints weight = 12733.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.3723 rms_B_bonded: 1.15
r_work: 0.3410 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3276 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13244  Z= 0.151
  Angle     :  0.595  11.376  18046  Z= 0.305
  Chirality :  0.044   0.310   2063
  Planarity :  0.005   0.050   2363
  Dihedral  :  5.033  20.828   1835
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 19.70 %
    Favored  : 77.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.91 (0.20), residues: 1703
  helix:  0.13 (0.20), residues: 660
  sheet: -1.01 (0.32), residues: 249
  loop : -1.00 (0.23), residues: 794

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 874 
 TYR   0.022   0.002   TYR B 540 
 PHE   0.018   0.001   PHE A  26 
 TRP   0.007   0.001   TRP A 100 
 HIS   0.004   0.001   HIS B 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (13244)
  covalent geometry    : angle       0.59504 (18046)
  hydrogen bonds       : bond        0.03687 (  526)
  hydrogen bonds       : angle       5.35170 ( 1497)

*********************** 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
  153 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 112
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  235 ASN cc_start: 0.7302 (t0) cc_final: 0.6950 (t160)
REVERT: A  374 ILE cc_start: 0.8396 (mp) cc_final: 0.8072 (mt)
REVERT: A  420 MET cc_start: 0.7239 (mmm) cc_final: 0.6951 (mmt)
REVERT: A  526 GLN cc_start: 0.7602 (mp10) cc_final: 0.7384 (mp10)
REVERT: A  590 LEU cc_start: 0.5170 (OUTLIER) cc_final: 0.4763 (pt)
REVERT: A  592 GLN cc_start: 0.6294 (OUTLIER) cc_final: 0.5195 (mp10)
REVERT: A  662 MET cc_start: 0.6685 (OUTLIER) cc_final: 0.6435 (mmm)
REVERT: A  871 ASP cc_start: 0.7695 (p0) cc_final: 0.7472 (p0)
REVERT: B  487 GLN cc_start: 0.7589 (mm110) cc_final: 0.7326 (mm-40)
REVERT: B  501 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6463 (ptp90)
REVERT: B  526 GLN cc_start: 0.6918 (OUTLIER) cc_final: 0.5277 (mp10)
REVERT: B  645 ARG cc_start: 0.6726 (ttp-110) cc_final: 0.6316 (ttm110)
REVERT: B  817 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.5853 (mpt180)
REVERT: B  851 ASP cc_start: 0.7422 (t0) cc_final: 0.7196 (t0)
  outliers start: 41
  outliers final: 21
  residues processed: 143
  average time/residue: 0.5240
  time to fit residues: 83.4912
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  : 0.561 
-------------------------------------------------------------------------------
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  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  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 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  728 MET
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 42 optimal weight:    1.9990
   chunk 67 optimal weight:    6.9990
   chunk 95 optimal weight:    1.9990
   chunk 118 optimal weight:    4.9990
   chunk 98 optimal weight:    0.4980
   chunk 162 optimal weight:    4.9990
   chunk 127 optimal weight:    0.7980
   chunk 89 optimal weight:    9.9990
   chunk 92 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 122 optimal weight:    0.4980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 511 GLN
B 431 GLN
B 541 GLN
B 721 HIS
B 786 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.186646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 118)---------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.143184 restraints weight = 12699.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.3708 rms_B_bonded: 1.13
r_work: 0.3432 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3316 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.2193

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= 0.124
  Angle     :  0.578  12.097  18046  Z= 0.294
  Chirality :  0.043   0.269   2063
  Planarity :  0.004   0.049   2363
  Dihedral  :  4.853  20.217   1835
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 20.45 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.83 (0.20), residues: 1703
  helix:  0.23 (0.20), residues: 666
  sheet: -0.95 (0.33), residues: 242
  loop : -1.01 (0.23), residues: 795

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 645 
 TYR   0.018   0.001   TYR B 540 
 PHE   0.016   0.001   PHE A  26 
 TRP   0.006   0.001   TRP A 614 
 HIS   0.004   0.001   HIS A  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (13244)
  covalent geometry    : angle       0.57810 (18046)
  hydrogen bonds       : bond        0.03513 (  526)
  hydrogen bonds       : angle       5.26972 ( 1497)

********************** 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
  146 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 113
  time to evaluate  : 0.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  235 ASN cc_start: 0.7268 (t0) cc_final: 0.6921 (t160)
REVERT: A  374 ILE cc_start: 0.8332 (mp) cc_final: 0.7977 (mt)
REVERT: A  420 MET cc_start: 0.7253 (mmm) cc_final: 0.7000 (mmt)
REVERT: A  473 GLU cc_start: 0.6439 (pm20) cc_final: 0.6220 (mp0)
REVERT: A  526 GLN cc_start: 0.7606 (mp10) cc_final: 0.7399 (mp10)
REVERT: A  590 LEU cc_start: 0.5145 (OUTLIER) cc_final: 0.4723 (pt)
REVERT: A  592 GLN cc_start: 0.6285 (OUTLIER) cc_final: 0.5219 (mp10)
REVERT: A  662 MET cc_start: 0.6714 (OUTLIER) cc_final: 0.6427 (mmm)
REVERT: A  727 MET cc_start: 0.6197 (mpt) cc_final: 0.4629 (ttt)
REVERT: A  871 ASP cc_start: 0.7637 (p0) cc_final: 0.7411 (p0)
REVERT: B  501 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.6586 (ptp90)
REVERT: B  526 GLN cc_start: 0.6898 (OUTLIER) cc_final: 0.5285 (mp10)
REVERT: B  645 ARG cc_start: 0.6766 (ttp-110) cc_final: 0.6378 (ttm110)
REVERT: B  817 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.5862 (mpt180)
REVERT: B  831 ASP cc_start: 0.7588 (m-30) cc_final: 0.6964 (t0)
REVERT: B  851 ASP cc_start: 0.7444 (t0) cc_final: 0.7156 (t0)
  outliers start: 33
  outliers final: 20
  residues processed: 138
  average time/residue: 0.5277
  time to fit residues: 81.0638
Evaluate side-chains
  137 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 111
  time to evaluate  : 0.596 
-------------------------------------------------------------------------------
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  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 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  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  728 MET
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 81 optimal weight:    0.9980
   chunk 75 optimal weight:    9.9990
   chunk 160 optimal weight:    0.0970
   chunk 161 optimal weight:    3.9990
   chunk 137 optimal weight:    5.9990
   chunk 78 optimal weight:    9.9990
   chunk 15 optimal weight:    4.9990
   chunk 130 optimal weight:    0.9980
   chunk 5 optimal weight:    7.9990
   chunk 6 optimal weight:    0.5980
   chunk 140 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 511 GLN
B 431 GLN
B 487 GLN
B 541 GLN
B 786 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.187467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 96)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.145118 restraints weight = 12716.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.3729 rms_B_bonded: 1.13
r_work: 0.3444 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3326 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.2287

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= 0.123
  Angle     :  0.572  12.345  18046  Z= 0.292
  Chirality :  0.043   0.272   2063
  Planarity :  0.004   0.050   2363
  Dihedral  :  4.778  20.011   1835
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 20.22 %
    Favored  : 77.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.75 (0.20), residues: 1703
  helix:  0.30 (0.20), residues: 671
  sheet: -0.89 (0.32), residues: 242
  loop : -0.98 (0.23), residues: 790

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 645 
 TYR   0.017   0.001   TYR B 540 
 PHE   0.016   0.001   PHE A  26 
 TRP   0.007   0.001   TRP B 611 
 HIS   0.004   0.001   HIS A  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (13244)
  covalent geometry    : angle       0.57241 (18046)
  hydrogen bonds       : bond        0.03498 (  526)
  hydrogen bonds       : angle       5.14934 ( 1497)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4715.72 seconds
wall clock time: 81 minutes 15.19 seconds (4875.19 seconds total)