Starting phenix.real_space_refine
on Thu Sep 18 03:12:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xjz_38411/09_2025/8xjz_38411.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xjz_38411/09_2025/8xjz_38411.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xjz_38411/09_2025/8xjz_38411.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xjz_38411/09_2025/8xjz_38411.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xjz_38411/09_2025/8xjz_38411.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xjz_38411/09_2025/8xjz_38411.cif"
  }
  resolution = 3.67
  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=   0.006
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      54      5.16       5
     C    8635      2.51       5
     N    2379      2.21       5
     O    2583      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 78 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: 13651
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6508
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 859, 6508
          Classifications: {'peptide': 859}
          Link IDs: {'PTRANS': 41, 'TRANS': 817}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 6576
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 867, 6576
          Classifications: {'peptide': 867}
          Link IDs: {'PTRANS': 42, 'TRANS': 824}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 437
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 437
          Classifications: {'peptide': 54}
          Link IDs: {'TRANS': 53}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 130
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 130
          Classifications: {'peptide': 26}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'TRANS': 25}
          Unresolved non-hydrogen bonds: 52
          Unresolved non-hydrogen angles: 78
          Unresolved non-hydrogen dihedrals: 26
          Planarities with less than four sites: {'UNK:plan-1': 26}
          Unresolved non-hydrogen planarities: 26
  Time building chain proxies: 3.26, per 1000 atoms: 0.24
  Number of scatterers: 13651
  At special positions: 0
  Unit cell: (98.118, 99.2082, 209.318, 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      54     16.00
     O    2583      8.00
     N    2379      7.00
     C    8635      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: 0.98
  Conformation dependent library (CDL) restraints added in 591.5 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3346

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 16 sheets defined
      35.3% alpha, 9.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 32
      removed outlier: 3.660A  pdb=" N   ALA A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 56
      removed outlier: 3.571A  pdb=" N   VAL A  55 " --> pdb=" O   SER A  51 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLN A  56 " --> pdb=" O   PRO A  52 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 51 through 56'
    Processing helix  chain 'A' and resid 74 through 79
      removed outlier: 4.282A  pdb=" N   PHE A  78 " --> pdb=" O   ASP A  74 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLY A  79 " --> pdb=" O   ALA A  75 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 74 through 79'
    Processing helix  chain 'A' and resid 94 through 104
      removed outlier: 3.627A  pdb=" N   PHE A 103 " --> pdb=" O   ALA A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 113
      removed outlier: 3.935A  pdb=" N   ASP A 112 " --> pdb=" O   VAL A 109 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   TYR A 113 " --> pdb=" O   ALA A 110 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 109 through 113'
    Processing helix  chain 'A' and resid 128 through 134
      removed outlier: 3.987A  pdb=" N   MET A 134 " --> pdb=" O   MET A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 155
      No H-bonds generated for 'chain 'A' and resid 153 through 155'
    Processing helix  chain 'A' and resid 156 through 164
      removed outlier: 4.011A  pdb=" N   THR A 160 " --> pdb=" O   SER A 156 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ILE A 161 " --> pdb=" O   ILE A 157 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   ALA A 162 " --> pdb=" O   THR A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 194
      removed outlier: 3.513A  pdb=" N   VAL A 185 " --> pdb=" O   SER A 181 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   GLN A 190 " --> pdb=" O   CYS A 186 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LEU A 193 " --> pdb=" O   CYS A 189 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   THR A 194 " --> pdb=" O   GLN A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 260
    Processing helix  chain 'A' and resid 288 through 301
      removed outlier: 3.791A  pdb=" N   ALA A 293 " --> pdb=" O   ALA A 289 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   ILE A 294 " --> pdb=" O   GLN A 290 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   GLN A 298 " --> pdb=" O   ILE A 294 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ALA A 301 " --> pdb=" O   ALA A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 308
    Processing helix  chain 'A' and resid 320 through 333
      removed outlier: 3.958A  pdb=" N   VAL A 324 " --> pdb=" O   LEU A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 350
      removed outlier: 3.665A  pdb=" N   THR A 349 " --> pdb=" O   SER A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 373
      removed outlier: 3.850A  pdb=" N   THR A 366 " --> pdb=" O   GLY A 362 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLN A 371 " --> pdb=" O   ALA A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 440
      removed outlier: 4.001A  pdb=" N   ALA A 439 " --> pdb=" O   ASP A 436 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ARG A 440 " --> pdb=" O   LEU A 437 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 436 through 440'
    Processing helix  chain 'A' and resid 456 through 461
    Processing helix  chain 'A' and resid 464 through 469
    Processing helix  chain 'A' and resid 478 through 483
      removed outlier: 3.695A  pdb=" N   ALA A 482 " --> pdb=" O   ARG A 478 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   TRP A 483 " --> pdb=" O   ARG A 479 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 478 through 483'
    Processing helix  chain 'A' and resid 502 through 512
      removed outlier: 3.676A  pdb=" N   THR A 508 " --> pdb=" O   HIS A 504 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   GLN A 512 " --> pdb=" O   THR A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 545 through 551
      removed outlier: 4.130A  pdb=" N   GLN A 549 " --> pdb=" O   HIS A 545 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   VAL A 550 " --> pdb=" O   GLN A 546 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   TRP A 551 " --> pdb=" O   LEU A 547 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 545 through 551'
    Processing helix  chain 'A' and resid 551 through 558
      removed outlier: 3.943A  pdb=" N   ALA A 555 " --> pdb=" O   TRP A 551 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 566
      removed outlier: 3.684A  pdb=" N   LEU A 565 " --> pdb=" O   CYS A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 574 through 579
      removed outlier: 3.607A  pdb=" N   PHE A 578 " --> pdb=" O   ARG A 574 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 596 through 611
    Processing helix  chain 'A' and resid 626 through 636
      removed outlier: 3.609A  pdb=" N   VAL A 630 " --> pdb=" O   LEU A 626 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   THR A 633 " --> pdb=" O   TRP A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 639 through 646
      removed outlier: 4.304A  pdb=" N   LEU A 646 " --> pdb=" O   ASP A 642 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 646 through 656
      removed outlier: 3.685A  pdb=" N   GLN A 656 " --> pdb=" O   GLU A 652 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 671 through 675
      removed outlier: 3.603A  pdb=" N   ALA A 674 " --> pdb=" O   GLN A 671 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   LEU A 675 " --> pdb=" O   ILE A 672 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 671 through 675'
    Processing helix  chain 'A' and resid 696 through 707
    Processing helix  chain 'A' and resid 732 through 738
    Processing helix  chain 'A' and resid 767 through 777
      removed outlier: 4.305A  pdb=" N   TRP A 771 " --> pdb=" O   THR A 767 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ILE A 772 " --> pdb=" O   PRO A 768 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   LEU A 776 " --> pdb=" O   ILE A 772 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 781 through 792
    Processing helix  chain 'A' and resid 806 through 811
    Processing helix  chain 'A' and resid 831 through 847
      removed outlier: 4.177A  pdb=" N   LEU A 837 " --> pdb=" O   HIS A 833 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ALA A 841 " --> pdb=" O   LEU A 837 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ALA A 842 " --> pdb=" O   ASP A 838 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   VAL A 845 " --> pdb=" O   ALA A 841 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   ARG A 846 " --> pdb=" O   ALA A 842 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   GLY A 847 " --> pdb=" O   LEU A 843 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 851 through 855
      removed outlier: 3.919A  pdb=" N   ALA A 854 " --> pdb=" O   ASP A 851 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   PHE A 855 " --> pdb=" O   LEU A 852 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 851 through 855'
    Processing helix  chain 'B' and resid 74 through 78
      removed outlier: 3.513A  pdb=" N   PHE B  77 " --> pdb=" O   ASP B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 89 through 105
      removed outlier: 3.689A  pdb=" N   ARG B  93 " --> pdb=" O   ASP B  89 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   VAL B  94 " --> pdb=" O   PRO B  90 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   LEU B  95 " --> pdb=" O   GLN B  91 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   ALA B 101 " --> pdb=" O   GLU B  97 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   PHE B 103 " --> pdb=" O   ALA B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 164
      removed outlier: 3.635A  pdb=" N   THR B 160 " --> pdb=" O   SER B 156 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   HIS B 164 " --> pdb=" O   THR B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 192
      removed outlier: 4.073A  pdb=" N   VAL B 185 " --> pdb=" O   SER B 181 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   CYS B 186 " --> pdb=" O   LEU B 182 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   GLN B 190 " --> pdb=" O   CYS B 186 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LEU B 192 " --> pdb=" O   ALA B 188 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 289 through 302
      removed outlier: 3.671A  pdb=" N   ILE B 294 " --> pdb=" O   GLN B 290 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ALA B 295 " --> pdb=" O   ALA B 291 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   ARG B 299 " --> pdb=" O   ALA B 295 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   GLY B 302 " --> pdb=" O   GLN B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 320 through 333
      removed outlier: 3.602A  pdb=" N   VAL B 324 " --> pdb=" O   LEU B 320 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   GLU B 325 " --> pdb=" O   GLY B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 359 through 373
      removed outlier: 3.946A  pdb=" N   LYS B 365 " --> pdb=" O   ALA B 361 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   GLN B 371 " --> pdb=" O   ALA B 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 458
    Processing helix  chain 'B' and resid 459 through 464
    Processing helix  chain 'B' and resid 465 through 471
      removed outlier: 3.634A  pdb=" N   PHE B 469 " --> pdb=" O   ARG B 465 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   GLN B 471 " --> pdb=" O   ALA B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 502 through 510
      removed outlier: 3.721A  pdb=" N   ALA B 506 " --> pdb=" O   ASP B 502 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 551 through 569
      removed outlier: 3.735A  pdb=" N   ALA B 555 " --> pdb=" O   TRP B 551 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   CYS B 561 " --> pdb=" O   ALA B 557 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU B 565 " --> pdb=" O   CYS B 561 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 583 through 591
      removed outlier: 3.801A  pdb=" N   GLY B 587 " --> pdb=" O   SER B 583 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   GLU B 588 " --> pdb=" O   LEU B 584 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   LEU B 590 " --> pdb=" O   GLN B 586 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ALA B 591 " --> pdb=" O   GLY B 587 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 592 through 614
      removed outlier: 4.215A  pdb=" N   GLN B 597 " --> pdb=" O   THR B 593 " (cutoff:3.500A)
      Proline residue:  B 598  - end of helix
      removed outlier: 3.781A  pdb=" N   SER B 613 " --> pdb=" O   GLN B 609 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   TRP B 614 " --> pdb=" O   LEU B 610 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 627 through 632
    Processing helix  chain 'B' and resid 639 through 654
      removed outlier: 3.728A  pdb=" N   ARG B 649 " --> pdb=" O   ARG B 645 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 668 through 675
    Processing helix  chain 'B' and resid 698 through 710
      removed outlier: 3.570A  pdb=" N   ARG B 706 " --> pdb=" O   ALA B 702 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLN B 710 " --> pdb=" O   ARG B 706 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 729 through 740
      removed outlier: 3.595A  pdb=" N   GLU B 740 " --> pdb=" O   ARG B 736 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 768 through 777
      removed outlier: 3.770A  pdb=" N   ILE B 772 " --> pdb=" O   PRO B 768 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   MET B 775 " --> pdb=" O   TRP B 771 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   LEU B 776 " --> pdb=" O   ILE B 772 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 782 through 785
    Processing helix  chain 'B' and resid 787 through 792
    Processing helix  chain 'B' and resid 803 through 810
      removed outlier: 3.894A  pdb=" N   ASN B 810 " --> pdb=" O   THR B 806 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 834 through 845
      removed outlier: 3.584A  pdb=" N   ALA B 841 " --> pdb=" O   LEU B 837 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   VAL B 845 " --> pdb=" O   ALA B 841 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 879 through 884
    Processing helix  chain 'C' and resid 1495 through 1503
    Processing helix  chain 'C' and resid 1525 through 1538
      removed outlier: 3.987A  pdb=" N   GLN C1529 " --> pdb=" O   LEU C1525 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ILE C1534 " --> pdb=" O   MET C1530 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   GLY C1535 " --> pdb=" O   GLN C1531 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   GLN C1536 " --> pdb=" O   GLN C1532 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   GLN C1537 " --> pdb=" O   TYR C1533 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1553 through 1562
    Processing helix  chain 'D' and resid 4 through 13
    Processing helix  chain 'D' and resid 18 through 23
    Processing sheet with id=AA1, first strand: chain 'A' and resid 171 through 172
      removed outlier: 6.543A  pdb=" N   ILE A 119 " --> pdb=" O   ILE A 172 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLY A 203 " --> pdb=" O   PHE A 120 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   VAL A 248 " --> pdb=" O   ALA A 202 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   VAL A 249 " --> pdb=" O   ILE A  11 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   ALA A 265 " --> pdb=" O   ILE A  10 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   VAL A 428 " --> pdb=" O   LYS A 268 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   PHE A 270 " --> pdb=" O   HIS A 426 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   HIS A 426 " --> pdb=" O   PHE A 270 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   VAL A 272 " --> pdb=" O   ASN A 424 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   ASN A 424 " --> pdb=" O   VAL A 272 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39
      removed outlier: 3.538A  pdb=" N   LYS A  64 " --> pdb=" O   SER A  38 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73
    Processing sheet with id=AA4, first strand: chain 'A' and resid 447 through 453
      removed outlier: 3.562A  pdb=" N   SER A 447 " --> pdb=" O   THR A 500 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ALA A 519 " --> pdb=" O   ALA A 497 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 661 through 665
      removed outlier: 8.189A  pdb=" N   TYR A 690 " --> pdb=" O   VAL A 685 " (cutoff:3.500A)
      removed outlier: 5.564A  pdb=" N   VAL A 685 " --> pdb=" O   TYR A 690 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   VAL A 692 " --> pdb=" O   ALA A 683 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ALA A 694 " --> pdb=" O   ALA A 681 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ALA A 681 " --> pdb=" O   ALA A 694 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   VAL A 779 " --> pdb=" O   ALA A 683 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 796 through 797
      removed outlier: 6.590A  pdb=" N   PHE A 796 " --> pdb=" O   PHE A 820 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 171 through 173
      removed outlier: 3.786A  pdb=" N   ALA B 121 " --> pdb=" O   ILE B 172 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 171 through 173
      removed outlier: 3.786A  pdb=" N   ALA B 121 " --> pdb=" O   ILE B 172 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   LEU B 247 " --> pdb=" O   MET B  13 " (cutoff:3.500A)
      removed outlier: 4.808A  pdb=" N   MET B  13 " --> pdb=" O   LEU B 247 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   VAL B 249 " --> pdb=" O   ILE B  11 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   ALA B 265 " --> pdb=" O   ILE B  10 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   VAL B 428 " --> pdb=" O   LYS B 268 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   PHE B 270 " --> pdb=" O   HIS B 426 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   HIS B 426 " --> pdb=" O   PHE B 270 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   LEU B 429 " --> pdb=" O   ALA B 413 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ALA B 413 " --> pdb=" O   LEU B 429 " (cutoff:3.500A)
      removed outlier: 7.363A  pdb=" N   VAL B 311 " --> pdb=" O   GLY B 345 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   CYS B 342 " --> pdb=" O   TYR B 396 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 38 through 39
      removed outlier: 3.888A  pdb=" N   LYS B  64 " --> pdb=" O   SER B  38 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 60 through 61
    Processing sheet with id=AB2, first strand: chain 'B' and resid 72 through 73
    Processing sheet with id=AB3, first strand: chain 'B' and resid 374 through 375
    Processing sheet with id=AB4, first strand: chain 'B' and resid 447 through 448
      removed outlier: 3.623A  pdb=" N   SER B 447 " --> pdb=" O   THR B 500 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 451 through 453
    Processing sheet with id=AB6, first strand: chain 'B' and resid 750 through 751
      removed outlier: 4.036A  pdb=" N   THR B 750 " --> pdb=" O   THR B 619 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   MET B 621 " --> pdb=" O   THR B 750 " (cutoff:3.500A)
      removed outlier: 5.965A  pdb=" N   LEU B 529 " --> pdb=" O   PRO B 618 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   VAL B 620 " --> pdb=" O   LEU B 529 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   GLY B 530 " --> pdb=" O   LEU B 797 " (cutoff:3.500A)
      removed outlier: 7.274A  pdb=" N   ILE B 799 " --> pdb=" O   GLY B 530 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   LEU B 532 " --> pdb=" O   ILE B 799 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 663 through 665
      removed outlier: 8.309A  pdb=" N   TYR B 690 " --> pdb=" O   VAL B 685 " (cutoff:3.500A)
      removed outlier: 5.538A  pdb=" N   VAL B 685 " --> pdb=" O   TYR B 690 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   VAL B 692 " --> pdb=" O   ALA B 683 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ALA B 681 " --> pdb=" O   ALA B 694 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   VAL B 779 " --> pdb=" O   ALA B 683 " (cutoff:3.500A)

    358 hydrogen bonds defined for protein.
    999 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: 2.19

  Time building geometry restraints manager: 1.31 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3933
        1.33 -     1.46: 2826
        1.46 -     1.58: 7096
        1.58 -     1.70: 0
        1.70 -     1.82: 89
  Bond restraints: 13944
  Sorted by residual:
  bond pdb=" C   GLN B 597 "
       pdb=" N   PRO B 598 "
    ideal  model  delta    sigma   weight residual
    1.336  1.383 -0.047 1.23e-02 6.61e+03 1.46e+01
  bond pdb=" N   MET B 134 "
       pdb=" CA  MET B 134 "
    ideal  model  delta    sigma   weight residual
    1.462  1.489 -0.027 7.70e-03 1.69e+04 1.21e+01
  bond pdb=" N   VAL B 427 "
       pdb=" CA  VAL B 427 "
    ideal  model  delta    sigma   weight residual
    1.456  1.495 -0.039 1.15e-02 7.56e+03 1.16e+01
  bond pdb=" N   VAL B 863 "
       pdb=" CA  VAL B 863 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.038 1.11e-02 8.12e+03 1.15e+01
  bond pdb=" N   SER A 179 "
       pdb=" CA  SER A 179 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 9.00e-03 1.23e+04 1.14e+01
  ... (remaining 13939 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 17852
        2.38 -     4.77: 998
        4.77 -     7.15: 106
        7.15 -     9.54: 34
        9.54 -    11.92: 5
  Bond angle restraints: 18995
  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  119.74   -9.04 1.22e+00 6.72e-01 5.49e+01
  angle pdb=" N   THR A 484 "
        pdb=" CA  THR A 484 "
        pdb=" C   THR A 484 "
      ideal   model   delta    sigma   weight residual
     114.56  106.16    8.40 1.27e+00 6.20e-01 4.37e+01
  angle pdb=" N   PHE A 558 "
        pdb=" CA  PHE A 558 "
        pdb=" C   PHE A 558 "
      ideal   model   delta    sigma   weight residual
     111.82  104.93    6.89 1.16e+00 7.43e-01 3.53e+01
  angle pdb=" N   SER A 486 "
        pdb=" CA  SER A 486 "
        pdb=" C   SER A 486 "
      ideal   model   delta    sigma   weight residual
     113.38  106.09    7.29 1.23e+00 6.61e-01 3.51e+01
  angle pdb=" N   ILE C1553 "
        pdb=" CA  ILE C1553 "
        pdb=" C   ILE C1553 "
      ideal   model   delta    sigma   weight residual
     112.12  107.54    4.58 8.40e-01 1.42e+00 2.97e+01
  ... (remaining 18990 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 7297
       17.99 -    35.98: 751
       35.98 -    53.97: 174
       53.97 -    71.95: 41
       71.95 -    89.94: 9
  Dihedral angle restraints: 8272
    sinusoidal: 3082
      harmonic: 5190
  Sorted by residual:
  dihedral pdb=" CA  GLN B  24 "
           pdb=" C   GLN B  24 "
           pdb=" N   ALA B  25 "
           pdb=" CA  ALA B  25 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.02   25.98     0      5.00e+00 4.00e-02 2.70e+01
  dihedral pdb=" CA  ALA B 482 "
           pdb=" C   ALA B 482 "
           pdb=" N   TRP B 483 "
           pdb=" CA  TRP B 483 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.96   25.04     0      5.00e+00 4.00e-02 2.51e+01
  dihedral pdb=" CA  UNK D  15 "
           pdb=" C   UNK D  15 "
           pdb=" N   UNK D  16 "
           pdb=" CA  UNK D  16 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.13   24.87     0      5.00e+00 4.00e-02 2.47e+01
  ... (remaining 8269 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.095: 1812
       0.095 -    0.189: 323
       0.189 -    0.284: 30
       0.284 -    0.378: 5
       0.378 -    0.473: 4
  Chirality restraints: 2174
  Sorted by residual:
  chirality pdb=" CB  ILE B 157 "
            pdb=" CA  ILE B 157 "
            pdb=" CG1 ILE B 157 "
            pdb=" CG2 ILE B 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.17    0.47 2.00e-01 2.50e+01 5.59e+00
  chirality pdb=" CB  ILE B 201 "
            pdb=" CA  ILE B 201 "
            pdb=" CG1 ILE B 201 "
            pdb=" CG2 ILE B 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.23    0.42 2.00e-01 2.50e+01 4.37e+00
  chirality pdb=" CB  ILE A 201 "
            pdb=" CA  ILE A 201 "
            pdb=" CG1 ILE A 201 "
            pdb=" CG2 ILE A 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.24    0.41 2.00e-01 2.50e+01 4.12e+00
  ... (remaining 2171 not shown)

  Planarity restraints: 2489
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 767 "   -0.103 5.00e-02 4.00e+02   1.52e-01 3.68e+01
        pdb=" N   PRO A 768 "    0.262 5.00e-02 4.00e+02
        pdb=" CA  PRO A 768 "   -0.083 5.00e-02 4.00e+02
        pdb=" CD  PRO A 768 "   -0.077 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A  81 "   -0.049 5.00e-02 4.00e+02   7.37e-02 8.68e+00
        pdb=" N   PRO A  82 "    0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO A  82 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A  82 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 767 "    0.043 5.00e-02 4.00e+02   6.64e-02 7.05e+00
        pdb=" N   PRO B 768 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO B 768 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B 768 "    0.037 5.00e-02 4.00e+02
  ... (remaining 2486 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 2522
        2.77 -     3.30: 11510
        3.30 -     3.83: 21000
        3.83 -     4.37: 24460
        4.37 -     4.90: 43520
  Nonbonded interactions: 103012
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 181 "
            pdb=" O   THR B 356 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" O   PRO B 305 "
            pdb=" OH  TYR B 341 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" O   SER B 233 "
            pdb=" OG  SER B 236 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" OH  TYR A 215 "
            pdb=" O   ALA A 224 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" OH  TYR A 310 "
            pdb=" NZ  LYS A 365 "
     model   vdw
     2.297 3.120
  ... (remaining 103007 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 153 through 882))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.060
  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:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.010
  Find NCS groups from input model:        0.220
  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:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
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      :  0.011   0.103  13944  Z= 0.515
  Angle     :  1.212  11.922  18995  Z= 0.704
  Chirality :  0.074   0.473   2174
  Planarity :  0.009   0.152   2489
  Dihedral  : 16.051  89.942   4926
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  : 10.63 %
    Favored  : 89.31 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  :  2.94 %
    Favored  : 92.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -4.68 (0.16), residues: 1768
  helix: -3.40 (0.15), residues: 622
  sheet: -2.56 (0.37), residues: 192
  loop : -3.06 (0.16), residues: 954

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG B 489 
 TYR   0.022   0.004   TYR B 868 
 PHE   0.045   0.004   PHE B  26 
 TRP   0.034   0.004   TRP A 629 
 HIS   0.009   0.002   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.01079 (13944)
  covalent geometry    : angle       1.21199 (18995)
  hydrogen bonds       : bond        0.21072 (  353)
  hydrogen bonds       : angle       8.15678 (  999)

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

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

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 144
  time to evaluate  : 0.373 
Fit side-chains
REVERT: A  275 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7259 (p0)
REVERT: A  637 VAL cc_start: 0.7641 (OUTLIER) cc_final: 0.7429 (p)
REVERT: A  663 LEU cc_start: 0.8094 (tp) cc_final: 0.7687 (tp)
REVERT: B  423 THR cc_start: 0.6381 (OUTLIER) cc_final: 0.6139 (p)
REVERT: B  542 ARG cc_start: 0.6192 (OUTLIER) cc_final: 0.3197 (ttm110)
REVERT: B  728 MET cc_start: 0.4270 (mtt) cc_final: 0.3935 (mtt)
REVERT: C 1538 CYS cc_start: 0.3309 (OUTLIER) cc_final: 0.2643 (t)
  outliers start: 60
  outliers final: 7
  residues processed: 181
  average time/residue: 0.1141
  time to fit residues: 30.8314
Evaluate side-chains
  118 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  275 ASP
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  424 ASN
Chi-restraints excluded: chain A residue  637 VAL
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  128 TYR
Chi-restraints excluded: chain B residue  423 THR
Chi-restraints excluded: chain B residue  424 ASN
Chi-restraints excluded: chain B residue  542 ARG
Chi-restraints excluded: chain C residue 1538 CYS
Chi-restraints excluded: chain C residue 1548 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:   20.0000
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    0.1980
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    7.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 175 GLN
A 274 ASN
A 314 HIS
A 786 GLN
B  56 GLN
B 686 ASN
B 883 GLN
C1531 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.181633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.139831 restraints weight = 14589.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.138659 restraints weight = 32906.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.141245 restraints weight = 23936.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.140933 restraints weight = 14160.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.144142 restraints weight = 11877.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.1465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13944  Z= 0.133
  Angle     :  0.601   7.017  18995  Z= 0.314
  Chirality :  0.044   0.154   2174
  Planarity :  0.006   0.084   2489
  Dihedral  :  6.597  55.842   1954
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 10.68 %
    Favored  : 87.74 %
  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: -3.78 (0.17), residues: 1768
  helix: -2.49 (0.18), residues: 630
  sheet: -1.70 (0.39), residues: 187
  loop : -2.73 (0.17), residues: 951

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 489 
 TYR   0.013   0.001   TYR A 128 
 PHE   0.019   0.001   PHE A 518 
 TRP   0.016   0.001   TRP C1502 
 HIS   0.009   0.001   HIS C1541 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (13944)
  covalent geometry    : angle       0.60122 (18995)
  hydrogen bonds       : bond        0.03694 (  353)
  hydrogen bonds       : angle       5.53190 (  999)

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

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

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 130
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
REVERT: A  275 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7612 (p0)
REVERT: A  554 TYR cc_start: 0.8531 (t80) cc_final: 0.8308 (t80)
REVERT: A  637 VAL cc_start: 0.7786 (OUTLIER) cc_final: 0.7491 (p)
REVERT: B  423 THR cc_start: 0.6001 (OUTLIER) cc_final: 0.5649 (p)
REVERT: B  728 MET cc_start: 0.4302 (mtt) cc_final: 0.3886 (mtt)
REVERT: C 1538 CYS cc_start: 0.3626 (OUTLIER) cc_final: 0.3276 (p)
  outliers start: 22
  outliers final: 13
  residues processed: 144
  average time/residue: 0.0999
  time to fit residues: 22.0226
Evaluate side-chains
  131 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 114
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  275 ASP
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  356 THR
Chi-restraints excluded: chain A residue  424 ASN
Chi-restraints excluded: chain A residue  617 THR
Chi-restraints excluded: chain A residue  637 VAL
Chi-restraints excluded: chain A residue  786 GLN
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue  128 TYR
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  423 THR
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain C residue 1538 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 167 optimal weight:    2.9990
   chunk 164 optimal weight:   10.0000
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 84 optimal weight:    0.0870
   chunk 94 optimal weight:    3.9990
   chunk 111 optimal weight:    7.9990
   chunk 48 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   chunk 49 optimal weight:    5.9990
   overall best weight:    2.2166

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.175613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.132558 restraints weight = 14882.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.130876 restraints weight = 34797.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.133711 restraints weight = 23873.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.133550 restraints weight = 13679.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.136141 restraints weight = 11196.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.1654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  13944  Z= 0.187
  Angle     :  0.621   6.840  18995  Z= 0.325
  Chirality :  0.045   0.196   2174
  Planarity :  0.005   0.070   2489
  Dihedral  :  5.967  48.940   1941
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.54 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 13.76 %
    Favored  : 83.30 %
  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: -3.46 (0.18), residues: 1768
  helix: -2.09 (0.19), residues: 633
  sheet: -1.50 (0.39), residues: 195
  loop : -2.67 (0.18), residues: 940

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 319 
 TYR   0.016   0.002   TYR B 875 
 PHE   0.023   0.002   PHE A  26 
 TRP   0.014   0.001   TRP C1502 
 HIS   0.006   0.001   HIS C1541 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 (13944)
  covalent geometry    : angle       0.62110 (18995)
  hydrogen bonds       : bond        0.03989 (  353)
  hydrogen bonds       : angle       5.33177 (  999)

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

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

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 126
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 ASP cc_start: 0.8157 (t0) cc_final: 0.7952 (t0)
REVERT: A  255 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7077 (mp0)
REVERT: A  275 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7600 (p0)
REVERT: A  554 TYR cc_start: 0.8608 (t80) cc_final: 0.8348 (t80)
REVERT: A  637 VAL cc_start: 0.7872 (OUTLIER) cc_final: 0.7608 (p)
REVERT: B  728 MET cc_start: 0.4260 (mtt) cc_final: 0.3807 (mtt)
  outliers start: 41
  outliers final: 23
  residues processed: 150
  average time/residue: 0.1087
  time to fit residues: 25.2299
Evaluate side-chains
  138 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 112
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 THR
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  213 THR
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  275 ASP
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  424 ASN
Chi-restraints excluded: chain A residue  617 THR
Chi-restraints excluded: chain A residue  637 VAL
Chi-restraints excluded: chain A residue  786 GLN
Chi-restraints excluded: chain B residue   45 LEU
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain B residue  128 TYR
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  423 THR
Chi-restraints excluded: chain B residue  424 ASN
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  612 LEU
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  621 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 160 optimal weight:    0.8980
   chunk 3 optimal weight:    0.3980
   chunk 120 optimal weight:    0.9990
   chunk 171 optimal weight:    1.9990
   chunk 52 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   chunk 99 optimal weight:    4.9990
   chunk 14 optimal weight:    4.9990
   chunk 108 optimal weight:    0.9980
   chunk 77 optimal weight:    6.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 402 GLN
A 686 ASN
A 786 GLN
B 350 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.179600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.138686 restraints weight = 14586.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.136773 restraints weight = 27358.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.137846 restraints weight = 26521.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.139183 restraints weight = 13610.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.141204 restraints weight = 10624.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.1964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13944  Z= 0.114
  Angle     :  0.545   7.834  18995  Z= 0.282
  Chirality :  0.043   0.200   2174
  Planarity :  0.005   0.059   2489
  Dihedral  :  5.466  47.423   1940
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 16.20 %
    Favored  : 81.65 %
  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: -3.09 (0.18), residues: 1768
  helix: -1.71 (0.20), residues: 628
  sheet: -1.26 (0.39), residues: 193
  loop : -2.52 (0.18), residues: 947

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 645 
 TYR   0.010   0.001   TYR A 868 
 PHE   0.016   0.001   PHE A  26 
 TRP   0.012   0.001   TRP C1502 
 HIS   0.005   0.001   HIS B 848 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (13944)
  covalent geometry    : angle       0.54543 (18995)
  hydrogen bonds       : bond        0.03177 (  353)
  hydrogen bonds       : angle       4.97013 (  999)

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

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

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 129
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
REVERT: A   89 ASP cc_start: 0.8219 (t0) cc_final: 0.7761 (m-30)
REVERT: A  255 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.6972 (mp0)
REVERT: A  275 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7669 (p0)
REVERT: A  637 VAL cc_start: 0.7795 (OUTLIER) cc_final: 0.7544 (p)
REVERT: B  199 MET cc_start: 0.8735 (ttt) cc_final: 0.8514 (tmm)
REVERT: B  526 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.7114 (mp10)
REVERT: B  600 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7870 (tt)
REVERT: B  728 MET cc_start: 0.4264 (mtt) cc_final: 0.3801 (mtt)
  outliers start: 30
  outliers final: 18
  residues processed: 147
  average time/residue: 0.1073
  time to fit residues: 23.9513
Evaluate side-chains
  141 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  213 THR
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  275 ASP
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  637 VAL
Chi-restraints excluded: chain A residue  739 PHE
Chi-restraints excluded: chain A residue  786 GLN
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain B residue  128 TYR
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  423 THR
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  526 GLN
Chi-restraints excluded: chain B residue  593 THR
Chi-restraints excluded: chain B residue  600 LEU
Chi-restraints excluded: chain B residue  612 LEU
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  810 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 106 optimal weight:    9.9990
   chunk 1 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 172 optimal weight:    2.9990
   chunk 140 optimal weight:   10.0000
   chunk 75 optimal weight:    8.9990
   chunk 130 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0870
   overall best weight:    2.2166

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

Flipped N/Q/H residues before XYZ refinement:
A 402 GLN
A 786 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.176547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.134842 restraints weight = 14836.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.133979 restraints weight = 34189.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.136000 restraints weight = 24162.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.136010 restraints weight = 14018.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.137707 restraints weight = 11704.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.2009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  13944  Z= 0.182
  Angle     :  0.596   6.893  18995  Z= 0.308
  Chirality :  0.045   0.243   2174
  Planarity :  0.005   0.056   2489
  Dihedral  :  5.524  49.333   1938
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.48 %
    Favored  : 91.52 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 16.92 %
    Favored  : 79.78 %
  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: -3.04 (0.19), residues: 1768
  helix: -1.58 (0.21), residues: 623
  sheet: -1.44 (0.39), residues: 198
  loop : -2.50 (0.18), residues: 947

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 645 
 TYR   0.015   0.002   TYR A 868 
 PHE   0.023   0.002   PHE A  26 
 TRP   0.013   0.001   TRP C1502 
 HIS   0.004   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 (13944)
  covalent geometry    : angle       0.59560 (18995)
  hydrogen bonds       : bond        0.03595 (  353)
  hydrogen bonds       : angle       5.04214 (  999)

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

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

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 119
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
REVERT: A  255 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7121 (mp0)
REVERT: A  275 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.7854 (p0)
REVERT: A  637 VAL cc_start: 0.7863 (OUTLIER) cc_final: 0.7562 (p)
REVERT: B  155 ASP cc_start: 0.6622 (t0) cc_final: 0.5961 (m-30)
REVERT: B  526 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.7245 (mp10)
REVERT: B  565 LEU cc_start: 0.5913 (OUTLIER) cc_final: 0.5644 (tt)
REVERT: B  600 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8016 (tt)
REVERT: B  649 ARG cc_start: 0.7578 (tpm170) cc_final: 0.7280 (tpm170)
  outliers start: 46
  outliers final: 24
  residues processed: 153
  average time/residue: 0.0994
  time to fit residues: 23.4462
Evaluate side-chains
  145 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 115
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  213 THR
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  275 ASP
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  424 ASN
Chi-restraints excluded: chain A residue  473 GLU
Chi-restraints excluded: chain A residue  617 THR
Chi-restraints excluded: chain A residue  637 VAL
Chi-restraints excluded: chain A residue  739 PHE
Chi-restraints excluded: chain A residue  786 GLN
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  128 TYR
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  526 GLN
Chi-restraints excluded: chain B residue  565 LEU
Chi-restraints excluded: chain B residue  600 LEU
Chi-restraints excluded: chain B residue  612 LEU
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  621 MET
Chi-restraints excluded: chain B residue  810 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 114 optimal weight:    4.9990
   chunk 94 optimal weight:    0.9990
   chunk 175 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 117 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 100 optimal weight:    3.9990
   chunk 60 optimal weight:   10.0000
   overall best weight:    1.3388

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

Flipped N/Q/H residues before XYZ refinement:
A 402 GLN
A 526 GLN
A 786 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.178059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.136932 restraints weight = 14636.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.136006 restraints weight = 34141.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.137802 restraints weight = 25145.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.137804 restraints weight = 14745.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.139087 restraints weight = 12597.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13944  Z= 0.128
  Angle     :  0.545   6.876  18995  Z= 0.282
  Chirality :  0.043   0.206   2174
  Planarity :  0.005   0.053   2489
  Dihedral  :  5.246  49.072   1937
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 17.85 %
    Favored  : 79.43 %
  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: -2.84 (0.19), residues: 1768
  helix: -1.42 (0.21), residues: 624
  sheet: -1.28 (0.39), residues: 194
  loop : -2.39 (0.18), residues: 950

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 645 
 TYR   0.010   0.001   TYR A 868 
 PHE   0.017   0.001   PHE A  26 
 TRP   0.015   0.001   TRP A 629 
 HIS   0.003   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (13944)
  covalent geometry    : angle       0.54520 (18995)
  hydrogen bonds       : bond        0.03127 (  353)
  hydrogen bonds       : angle       4.82810 (  999)

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

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

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 119
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
REVERT: A  255 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7140 (mp0)
REVERT: A  275 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.7845 (p0)
REVERT: A  637 VAL cc_start: 0.7894 (OUTLIER) cc_final: 0.7577 (p)
REVERT: A  662 MET cc_start: 0.7654 (mmt) cc_final: 0.7151 (mmt)
REVERT: B  199 MET cc_start: 0.8706 (ttt) cc_final: 0.8470 (tmm)
REVERT: B  526 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.7244 (mp10)
REVERT: B  565 LEU cc_start: 0.5853 (OUTLIER) cc_final: 0.5570 (tt)
REVERT: B  600 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7983 (tt)
REVERT: B  649 ARG cc_start: 0.7338 (tpm170) cc_final: 0.6994 (tpm170)
  outliers start: 38
  outliers final: 27
  residues processed: 146
  average time/residue: 0.1078
  time to fit residues: 23.8151
Evaluate side-chains
  151 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 118
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  213 THR
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  275 ASP
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  356 THR
Chi-restraints excluded: chain A residue  374 ILE
Chi-restraints excluded: chain A residue  424 ASN
Chi-restraints excluded: chain A residue  617 THR
Chi-restraints excluded: chain A residue  637 VAL
Chi-restraints excluded: chain A residue  739 PHE
Chi-restraints excluded: chain A residue  786 GLN
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  128 TYR
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  423 THR
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  526 GLN
Chi-restraints excluded: chain B residue  565 LEU
Chi-restraints excluded: chain B residue  593 THR
Chi-restraints excluded: chain B residue  600 LEU
Chi-restraints excluded: chain B residue  612 LEU
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  793 ASP
Chi-restraints excluded: chain B residue  810 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 146 optimal weight:    0.0050
   chunk 79 optimal weight:    7.9990
   chunk 131 optimal weight:    4.9990
   chunk 53 optimal weight:    9.9990
   chunk 95 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 161 optimal weight:    6.9990
   chunk 50 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   chunk 54 optimal weight:   10.0000
   chunk 97 optimal weight:    1.9990
   overall best weight:    2.1400

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

Flipped N/Q/H residues before XYZ refinement:
A 402 GLN
A 786 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.175271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.134907 restraints weight = 14713.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.135645 restraints weight = 35189.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.136805 restraints weight = 21146.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.136143 restraints weight = 14722.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.138530 restraints weight = 11408.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.2231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  13944  Z= 0.177
  Angle     :  0.586   6.950  18995  Z= 0.304
  Chirality :  0.045   0.214   2174
  Planarity :  0.005   0.055   2489
  Dihedral  :  5.405  53.934   1937
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.37 %
    Favored  : 91.63 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 17.28 %
    Favored  : 79.21 %
  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: -2.93 (0.19), residues: 1768
  helix: -1.43 (0.21), residues: 623
  sheet: -1.48 (0.39), residues: 186
  loop : -2.44 (0.18), residues: 959

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 645 
 TYR   0.014   0.002   TYR A 868 
 PHE   0.022   0.002   PHE A  26 
 TRP   0.016   0.001   TRP A 629 
 HIS   0.004   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 (13944)
  covalent geometry    : angle       0.58618 (18995)
  hydrogen bonds       : bond        0.03467 (  353)
  hydrogen bonds       : angle       4.94054 (  999)

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

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

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 114
  time to evaluate  : 0.507 
Fit side-chains
   revert: symmetry clash
REVERT: A  255 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7203 (mp0)
REVERT: A  275 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.7806 (p0)
REVERT: A  662 MET cc_start: 0.7678 (mmt) cc_final: 0.7219 (mmt)
REVERT: B  155 ASP cc_start: 0.7058 (t0) cc_final: 0.6846 (t0)
REVERT: B  526 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.7170 (mp10)
REVERT: B  565 LEU cc_start: 0.5746 (OUTLIER) cc_final: 0.5460 (tt)
REVERT: B  600 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7973 (tt)
REVERT: B  649 ARG cc_start: 0.7523 (tpm170) cc_final: 0.7055 (tpm170)
  outliers start: 49
  outliers final: 35
  residues processed: 154
  average time/residue: 0.1057
  time to fit residues: 25.2699
Evaluate side-chains
  150 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 110
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  213 THR
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  275 ASP
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  356 THR
Chi-restraints excluded: chain A residue  374 ILE
Chi-restraints excluded: chain A residue  424 ASN
Chi-restraints excluded: chain A residue  617 THR
Chi-restraints excluded: chain A residue  637 VAL
Chi-restraints excluded: chain A residue  739 PHE
Chi-restraints excluded: chain A residue  786 GLN
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  126 ASP
Chi-restraints excluded: chain B residue  128 TYR
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  390 LEU
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  526 GLN
Chi-restraints excluded: chain B residue  565 LEU
Chi-restraints excluded: chain B residue  593 THR
Chi-restraints excluded: chain B residue  600 LEU
Chi-restraints excluded: chain B residue  612 LEU
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  621 MET
Chi-restraints excluded: chain B residue  752 ILE
Chi-restraints excluded: chain B residue  793 ASP
Chi-restraints excluded: chain B residue  797 LEU
Chi-restraints excluded: chain B residue  810 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 53 optimal weight:   10.0000
   chunk 81 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 175 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 77 optimal weight:    6.9990
   chunk 169 optimal weight:    0.5980
   chunk 166 optimal weight:    0.6980
   chunk 85 optimal weight:    3.9990
   chunk 13 optimal weight:    0.0980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 402 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.178527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.136567 restraints weight = 14476.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.134328 restraints weight = 26094.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.135687 restraints weight = 25030.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.136581 restraints weight = 12934.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.138105 restraints weight = 10561.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.2396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13944  Z= 0.110
  Angle     :  0.530   7.445  18995  Z= 0.273
  Chirality :  0.042   0.193   2174
  Planarity :  0.004   0.051   2489
  Dihedral  :  5.077  50.540   1937
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 18.28 %
    Favored  : 78.78 %
  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: -2.71 (0.19), residues: 1768
  helix: -1.27 (0.21), residues: 624
  sheet: -1.45 (0.38), residues: 194
  loop : -2.28 (0.18), residues: 950

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 645 
 TYR   0.009   0.001   TYR B 128 
 PHE   0.015   0.001   PHE A  26 
 TRP   0.016   0.001   TRP A 629 
 HIS   0.003   0.000   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (13944)
  covalent geometry    : angle       0.53030 (18995)
  hydrogen bonds       : bond        0.02927 (  353)
  hydrogen bonds       : angle       4.68471 (  999)

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

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

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 119
  time to evaluate  : 0.486 
Fit side-chains
   revert: symmetry clash
REVERT: A  255 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7144 (mp0)
REVERT: A  275 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.7797 (p0)
REVERT: A  662 MET cc_start: 0.7681 (mmt) cc_final: 0.7221 (mmt)
REVERT: A  663 LEU cc_start: 0.7773 (tp) cc_final: 0.7447 (tp)
REVERT: B  155 ASP cc_start: 0.7099 (t0) cc_final: 0.6868 (t0)
REVERT: B  199 MET cc_start: 0.8725 (ttt) cc_final: 0.8475 (tmm)
REVERT: B  282 TYR cc_start: 0.8046 (t80) cc_final: 0.7740 (t80)
REVERT: B  526 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.7083 (mp10)
REVERT: B  565 LEU cc_start: 0.5559 (OUTLIER) cc_final: 0.5233 (tt)
REVERT: B  600 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7943 (tt)
REVERT: B  649 ARG cc_start: 0.7530 (tpm170) cc_final: 0.7111 (tpm170)
  outliers start: 41
  outliers final: 28
  residues processed: 151
  average time/residue: 0.1092
  time to fit residues: 25.0737
Evaluate side-chains
  148 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 115
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  213 THR
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  275 ASP
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  356 THR
Chi-restraints excluded: chain A residue  424 ASN
Chi-restraints excluded: chain A residue  637 VAL
Chi-restraints excluded: chain A residue  739 PHE
Chi-restraints excluded: chain A residue  786 GLN
Chi-restraints excluded: chain A residue  831 ASP
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  128 TYR
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  526 GLN
Chi-restraints excluded: chain B residue  565 LEU
Chi-restraints excluded: chain B residue  593 THR
Chi-restraints excluded: chain B residue  600 LEU
Chi-restraints excluded: chain B residue  612 LEU
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  810 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   chunk 113 optimal weight:    0.9980
   chunk 107 optimal weight:    0.8980
   chunk 142 optimal weight:   10.0000
   chunk 75 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 160 optimal weight:    8.9990
   chunk 164 optimal weight:    0.5980
   chunk 65 optimal weight:   10.0000
   chunk 61 optimal weight:    2.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A 786 GLN
B 686 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.178134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.135021 restraints weight = 14537.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.132041 restraints weight = 30957.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.134634 restraints weight = 26230.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.134995 restraints weight = 14292.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.138025 restraints weight = 12290.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.2469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13944  Z= 0.115
  Angle     :  0.532   7.302  18995  Z= 0.274
  Chirality :  0.042   0.190   2174
  Planarity :  0.004   0.051   2489
  Dihedral  :  4.989  49.998   1937
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.62 %
    Favored  : 93.38 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 18.42 %
    Favored  : 78.78 %
  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: -2.60 (0.19), residues: 1768
  helix: -1.19 (0.21), residues: 623
  sheet: -1.22 (0.38), residues: 203
  loop : -2.25 (0.19), residues: 942

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 645 
 TYR   0.010   0.001   TYR B 128 
 PHE   0.017   0.001   PHE A  26 
 TRP   0.015   0.001   TRP A 629 
 HIS   0.003   0.000   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (13944)
  covalent geometry    : angle       0.53190 (18995)
  hydrogen bonds       : bond        0.02889 (  353)
  hydrogen bonds       : angle       4.62879 (  999)

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

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

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 118
  time to evaluate  : 0.526 
Fit side-chains
   revert: symmetry clash
REVERT: A  255 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7161 (mp0)
REVERT: A  275 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.7785 (p0)
REVERT: A  662 MET cc_start: 0.7678 (mmt) cc_final: 0.7223 (mmt)
REVERT: A  663 LEU cc_start: 0.7780 (tp) cc_final: 0.7462 (tp)
REVERT: A  664 MET cc_start: 0.6963 (tmm) cc_final: 0.6721 (tmm)
REVERT: B  282 TYR cc_start: 0.8048 (t80) cc_final: 0.7758 (t80)
REVERT: B  526 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.7117 (mp10)
REVERT: B  565 LEU cc_start: 0.5551 (OUTLIER) cc_final: 0.5229 (tt)
REVERT: B  600 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7912 (tt)
REVERT: B  649 ARG cc_start: 0.7507 (tpm170) cc_final: 0.7097 (tpm170)
  outliers start: 39
  outliers final: 33
  residues processed: 147
  average time/residue: 0.1161
  time to fit residues: 25.8916
Evaluate side-chains
  154 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 116
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  213 THR
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  275 ASP
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  356 THR
Chi-restraints excluded: chain A residue  374 ILE
Chi-restraints excluded: chain A residue  424 ASN
Chi-restraints excluded: chain A residue  515 THR
Chi-restraints excluded: chain A residue  617 THR
Chi-restraints excluded: chain A residue  637 VAL
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  739 PHE
Chi-restraints excluded: chain A residue  786 GLN
Chi-restraints excluded: chain A residue  831 ASP
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  128 TYR
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  374 ILE
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  526 GLN
Chi-restraints excluded: chain B residue  565 LEU
Chi-restraints excluded: chain B residue  593 THR
Chi-restraints excluded: chain B residue  600 LEU
Chi-restraints excluded: chain B residue  612 LEU
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  793 ASP
Chi-restraints excluded: chain B residue  810 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 152 optimal weight:   10.0000
   chunk 126 optimal weight:    0.8980
   chunk 99 optimal weight:    0.9990
   chunk 176 optimal weight:    9.9990
   chunk 35 optimal weight:    2.9990
   chunk 118 optimal weight:    0.9990
   chunk 171 optimal weight:    0.9980
   chunk 150 optimal weight:    0.9990
   chunk 89 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 177 optimal weight:   10.0000
   overall best weight:    0.9786

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.179147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.136443 restraints weight = 14609.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.134014 restraints weight = 30944.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.136570 restraints weight = 25808.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.136770 restraints weight = 14260.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.140502 restraints weight = 12032.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.2546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13944  Z= 0.109
  Angle     :  0.531   7.091  18995  Z= 0.274
  Chirality :  0.042   0.184   2174
  Planarity :  0.004   0.050   2489
  Dihedral  :  4.901  49.445   1937
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 18.78 %
    Favored  : 78.28 %
  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: -2.51 (0.19), residues: 1768
  helix: -1.12 (0.21), residues: 623
  sheet: -1.14 (0.38), residues: 203
  loop : -2.21 (0.19), residues: 942

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 645 
 TYR   0.009   0.001   TYR B 128 
 PHE   0.016   0.001   PHE A  26 
 TRP   0.016   0.001   TRP A 629 
 HIS   0.002   0.000   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (13944)
  covalent geometry    : angle       0.53149 (18995)
  hydrogen bonds       : bond        0.02847 (  353)
  hydrogen bonds       : angle       4.53675 (  999)

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

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

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3536 Ramachandran restraints generated.
    1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 122
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
REVERT: A  255 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7142 (mp0)
REVERT: A  275 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.7772 (p0)
REVERT: A  662 MET cc_start: 0.7662 (mmt) cc_final: 0.7211 (mmt)
REVERT: A  663 LEU cc_start: 0.7805 (tp) cc_final: 0.7490 (tp)
REVERT: A  664 MET cc_start: 0.6944 (tmm) cc_final: 0.6715 (tmm)
REVERT: B  199 MET cc_start: 0.8731 (ttt) cc_final: 0.8523 (ttt)
REVERT: B  282 TYR cc_start: 0.8034 (t80) cc_final: 0.7742 (t80)
REVERT: B  565 LEU cc_start: 0.5603 (OUTLIER) cc_final: 0.5234 (tt)
REVERT: B  600 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7894 (tt)
REVERT: B  649 ARG cc_start: 0.7496 (tpm170) cc_final: 0.7135 (tpm170)
  outliers start: 41
  outliers final: 33
  residues processed: 150
  average time/residue: 0.1138
  time to fit residues: 26.0883
Evaluate side-chains
  157 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 120
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  201 ILE
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  213 THR
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  275 ASP
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  356 THR
Chi-restraints excluded: chain A residue  374 ILE
Chi-restraints excluded: chain A residue  424 ASN
Chi-restraints excluded: chain A residue  515 THR
Chi-restraints excluded: chain A residue  617 THR
Chi-restraints excluded: chain A residue  637 VAL
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  739 PHE
Chi-restraints excluded: chain A residue  786 GLN
Chi-restraints excluded: chain A residue  831 ASP
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  112 ASP
Chi-restraints excluded: chain B residue  119 ILE
Chi-restraints excluded: chain B residue  128 TYR
Chi-restraints excluded: chain B residue  130 MET
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  180 THR
Chi-restraints excluded: chain B residue  201 ILE
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  565 LEU
Chi-restraints excluded: chain B residue  593 THR
Chi-restraints excluded: chain B residue  600 LEU
Chi-restraints excluded: chain B residue  612 LEU
Chi-restraints excluded: chain B residue  620 VAL
Chi-restraints excluded: chain B residue  793 ASP
Chi-restraints excluded: chain B residue  810 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 160 optimal weight:    0.0010
   chunk 41 optimal weight:    0.9980
   chunk 44 optimal weight:    0.0770
   chunk 145 optimal weight:    9.9990
   chunk 18 optimal weight:    4.9990
   chunk 133 optimal weight:    6.9990
   chunk 49 optimal weight:    7.9990
   chunk 128 optimal weight:    4.9990
   chunk 20 optimal weight:    9.9990
   chunk 8 optimal weight:    0.0670
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.8284

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

Flipped N/Q/H residues before XYZ refinement:
A 686 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.179637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.141839 restraints weight = 14689.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.140267 restraints weight = 26643.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.141108 restraints weight = 23861.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.141112 restraints weight = 15749.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.142818 restraints weight = 12754.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.2605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  13944  Z= 0.103
  Angle     :  0.524   7.293  18995  Z= 0.270
  Chirality :  0.042   0.179   2174
  Planarity :  0.004   0.050   2489
  Dihedral  :  4.801  48.656   1937
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 19.00 %
    Favored  : 78.06 %
  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: -2.39 (0.19), residues: 1768
  helix: -0.95 (0.21), residues: 617
  sheet: -1.08 (0.38), residues: 198
  loop : -2.17 (0.19), residues: 953

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 645 
 TYR   0.009   0.001   TYR B 128 
 PHE   0.015   0.001   PHE A  26 
 TRP   0.014   0.001   TRP A 629 
 HIS   0.002   0.000   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 (13944)
  covalent geometry    : angle       0.52383 (18995)
  hydrogen bonds       : bond        0.02726 (  353)
  hydrogen bonds       : angle       4.46488 (  999)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1896.88 seconds
wall clock time: 33 minutes 39.52 seconds (2019.52 seconds total)