Starting phenix.real_space_refine
on Sat Aug 23 14:18:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ut8_64484/08_2025/9ut8_64484.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ut8_64484/08_2025/9ut8_64484.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.41
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ut8_64484/08_2025/9ut8_64484.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ut8_64484/08_2025/9ut8_64484.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ut8_64484/08_2025/9ut8_64484.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ut8_64484/08_2025/9ut8_64484.cif"
  }
  resolution = 3.41
  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=   0.001 sd=   0.018
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      95      5.16       5
     C    7890      2.51       5
     N    2059      2.21       5
     O    2170      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12214
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6157
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 770, 6157
          Classifications: {'peptide': 770}
          Link IDs: {'PTRANS': 39, 'TRANS': 730}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 6057
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 782, 6057
          Classifications: {'peptide': 782}
          Link IDs: {'PTRANS': 44, 'TRANS': 737}
          Chain breaks: 3
  Time building chain proxies: 3.75, per 1000 atoms: 0.31
  Number of scatterers: 12214
  At special positions: 0
  Unit cell: (95.04, 90.24, 190.08, 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      95     16.00
     O    2170      8.00
     N    2059      7.00
     C    7890      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=18, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  59 " - pdb=" SG  CYS A 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 233 " - pdb=" SG  CYS A 513 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 405 " - pdb=" SG  CYS A 410 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 495 " - pdb=" SG  CYS A 514 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 499 " - pdb=" SG  CYS A 517 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 520 " - pdb=" SG  CYS A 535 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 538 " - pdb=" SG  CYS A 551 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 630 " - pdb=" SG  CYS A 720 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  24 " - pdb=" SG  CYS B 351 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  62 " - pdb=" SG  CYS B 103 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 236 " - pdb=" SG  CYS B 517 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 370 " - pdb=" SG  CYS B 373 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 410 " - pdb=" SG  CYS B 415 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 499 " - pdb=" SG  CYS B 518 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 503 " - pdb=" SG  CYS B 521 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 524 " - pdb=" SG  CYS B 538 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 541 " - pdb=" SG  CYS B 554 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 633 " - pdb=" SG  CYS B 722 " distance=2.28

  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: 0.96
  Conformation dependent library (CDL) restraints added in 598.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2930

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 13 sheets defined
      51.3% alpha, 9.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 85
      removed outlier: 3.804A  pdb=" N   TYR A  69 " --> pdb=" O   LYS A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 115
    Processing helix  chain 'A' and resid 143 through 155
      removed outlier: 3.558A  pdb=" N   PHE A 153 " --> pdb=" O   THR A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 173
      removed outlier: 3.687A  pdb=" N   ASP A 173 " --> pdb=" O   GLU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 201
      removed outlier: 4.012A  pdb=" N   HIS A 190 " --> pdb=" O   SER A 186 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   PHE A 201 " --> pdb=" O   LEU A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 229
      removed outlier: 3.996A  pdb=" N   ARG A 229 " --> pdb=" O   GLU A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 265
    Processing helix  chain 'A' and resid 280 through 291
      removed outlier: 4.469A  pdb=" N   PHE A 284 " --> pdb=" O   THR A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
    Processing helix  chain 'A' and resid 313 through 320
      removed outlier: 3.681A  pdb=" N   HIS A 318 " --> pdb=" O   GLU A 315 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   LEU A 319 " --> pdb=" O   LEU A 316 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   GLY A 320 " --> pdb=" O   ARG A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 341
    Processing helix  chain 'A' and resid 368 through 373
    Processing helix  chain 'A' and resid 373 through 380
    Processing helix  chain 'A' and resid 384 through 404
      removed outlier: 3.747A  pdb=" N   VAL A 388 " --> pdb=" O   VAL A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 425
      removed outlier: 3.751A  pdb=" N   LEU A 420 " --> pdb=" O   TYR A 416 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   LEU A 421 " --> pdb=" O   PRO A 417 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   GLU A 422 " --> pdb=" O   TRP A 418 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   GLU A 423 " --> pdb=" O   GLN A 419 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 563 through 590
      removed outlier: 3.704A  pdb=" N   HIS A 590 " --> pdb=" O   ILE A 586 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 593 through 598
    Processing helix  chain 'A' and resid 601 through 617
      removed outlier: 4.167A  pdb=" N   PHE A 605 " --> pdb=" O   GLY A 601 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LEU A 610 " --> pdb=" O   LEU A 606 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   LEU A 611 " --> pdb=" O   MET A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 618 through 622
    Processing helix  chain 'A' and resid 626 through 665
      removed outlier: 4.169A  pdb=" N   CYS A 632 " --> pdb=" O   SER A 628 " (cutoff:3.500A)
      removed outlier: 4.871A  pdb=" N   PHE A 637 " --> pdb=" O   ARG A 633 " (cutoff:3.500A)
      Proline residue:  A 638  - end of helix
      removed outlier: 4.154A  pdb=" N   PHE A 641 " --> pdb=" O   PHE A 637 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   THR A 642 " --> pdb=" O   PRO A 638 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   ILE A 643 " --> pdb=" O   LEU A 639 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ILE A 648 " --> pdb=" O   CYS A 644 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   VAL A 656 " --> pdb=" O   SER A 652 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ALA A 658 " --> pdb=" O   GLN A 654 " (cutoff:3.500A)
      removed outlier: 5.150A  pdb=" N   PHE A 659 " --> pdb=" O   ILE A 655 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   ALA A 662 " --> pdb=" O   ALA A 658 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 668 through 676
      removed outlier: 3.749A  pdb=" N   ARG A 674 " --> pdb=" O   SER A 670 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   TYR A 675 " --> pdb=" O   TYR A 671 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   GLN A 676 " --> pdb=" O   TRP A 672 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 677 through 700
      removed outlier: 4.024A  pdb=" N   SER A 681 " --> pdb=" O   GLY A 677 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 720 through 723
    Processing helix  chain 'A' and resid 724 through 729
    Processing helix  chain 'A' and resid 733 through 749
    Processing helix  chain 'A' and resid 758 through 781
    Processing helix  chain 'A' and resid 787 through 805
      removed outlier: 3.549A  pdb=" N   LEU A 800 " --> pdb=" O   THR A 796 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   ILE A 803 " --> pdb=" O   ASN A 799 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 808 through 818
      removed outlier: 3.548A  pdb=" N   ILE A 815 " --> pdb=" O   LYS A 811 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 823 through 833
      removed outlier: 3.898A  pdb=" N   GLN A 832 " --> pdb=" O   ASN A 828 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   GLY A 833 " --> pdb=" O   SER A 829 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 28
    Processing helix  chain 'B' and resid 66 through 86
      removed outlier: 4.036A  pdb=" N   LEU B  70 " --> pdb=" O   SER B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 117
      removed outlier: 4.166A  pdb=" N   LYS B 111 " --> pdb=" O   VAL B 107 " (cutoff:3.500A)
      Proline residue:  B 112  - end of helix
      removed outlier: 3.767A  pdb=" N   LEU B 117 " --> pdb=" O   SER B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 160
      removed outlier: 3.531A  pdb=" N   VAL B 152 " --> pdb=" O   GLU B 148 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   LYS B 155 " --> pdb=" O   MET B 151 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   PHE B 156 " --> pdb=" O   VAL B 152 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   PHE B 159 " --> pdb=" O   LYS B 155 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   PHE B 160 " --> pdb=" O   PHE B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 176
      removed outlier: 3.895A  pdb=" N   ALA B 176 " --> pdb=" O   LEU B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 205
      removed outlier: 4.577A  pdb=" N   GLN B 193 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LEU B 194 " --> pdb=" O   ASP B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 232
      removed outlier: 3.869A  pdb=" N   ALA B 228 " --> pdb=" O   SER B 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 265
      removed outlier: 3.751A  pdb=" N   ASP B 258 " --> pdb=" O   GLY B 254 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 290
    Processing helix  chain 'B' and resid 306 through 311
    Processing helix  chain 'B' and resid 314 through 318
    Processing helix  chain 'B' and resid 333 through 347
    Processing helix  chain 'B' and resid 347 through 356
      removed outlier: 3.585A  pdb=" N   CYS B 351 " --> pdb=" O   ASP B 347 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   GLU B 356 " --> pdb=" O   SER B 352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 377 through 382
      removed outlier: 3.727A  pdb=" N   VAL B 381 " --> pdb=" O   THR B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 385
      No H-bonds generated for 'chain 'B' and resid 383 through 385'
    Processing helix  chain 'B' and resid 389 through 409
    Processing helix  chain 'B' and resid 422 through 425
    Processing helix  chain 'B' and resid 426 through 431
      removed outlier: 4.137A  pdb=" N   TYR B 431 " --> pdb=" O   LEU B 427 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 566 through 591
      removed outlier: 3.539A  pdb=" N   VAL B 591 " --> pdb=" O   LEU B 587 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 596 through 603
      removed outlier: 3.515A  pdb=" N   SER B 602 " --> pdb=" O   LEU B 598 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 604 through 620
      removed outlier: 3.516A  pdb=" N   GLY B 615 " --> pdb=" O   LEU B 611 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 629 through 635
    Processing helix  chain 'B' and resid 637 through 664
      removed outlier: 3.819A  pdb=" N   LEU B 642 " --> pdb=" O   PRO B 638 " (cutoff:3.500A)
      Proline residue:  B 643  - end of helix
      removed outlier: 3.647A  pdb=" N   SER B 649 " --> pdb=" O   THR B 645 " (cutoff:3.500A)
      removed outlier: 4.698A  pdb=" N   THR B 650 " --> pdb=" O   GLY B 646 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLN B 654 " --> pdb=" O   THR B 650 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   GLU B 661 " --> pdb=" O   GLU B 657 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 665 through 677
      removed outlier: 3.554A  pdb=" N   ARG B 671 " --> pdb=" O   SER B 667 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ARG B 677 " --> pdb=" O   SER B 673 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 679 through 703
    Processing helix  chain 'B' and resid 727 through 734
    Processing helix  chain 'B' and resid 734 through 747
      removed outlier: 3.879A  pdb=" N   GLY B 747 " --> pdb=" O   LEU B 743 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 761 through 783
      removed outlier: 3.512A  pdb=" N   ALA B 770 " --> pdb=" O   PHE B 766 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL B 779 " --> pdb=" O   TRP B 775 " (cutoff:3.500A)
      Proline residue:  B 780  - end of helix
      removed outlier: 3.543A  pdb=" N   ALA B 783 " --> pdb=" O   VAL B 779 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 789 through 807
      removed outlier: 3.737A  pdb=" N   GLN B 794 " --> pdb=" O   ARG B 790 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   MET B 795 " --> pdb=" O   PRO B 791 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   GLY B 796 " --> pdb=" O   ALA B 792 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   LEU B 798 " --> pdb=" O   GLN B 794 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LEU B 799 " --> pdb=" O   MET B 795 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ILE B 805 " --> pdb=" O   CYS B 801 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 810 through 824
      Proline residue:  B 821  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29
      removed outlier: 3.625A  pdb=" N   LEU A  29 " --> pdb=" O   TYR A  96 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   TYR A  96 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   GLY A  37 " --> pdb=" O   VAL A  99 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LEU A  38 " --> pdb=" O   ILE A 139 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   VAL A 138 " --> pdb=" O   ILE A 162 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   GLN A 161 " --> pdb=" O   LEU A 181 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 123
    Processing sheet with id=AA3, first strand: chain 'A' and resid 233 through 239
      removed outlier: 7.922A  pdb=" N   ILE A 206 " --> pdb=" O   ALA A 235 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   GLN A 237 " --> pdb=" O   ILE A 206 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   VAL A 208 " --> pdb=" O   GLN A 237 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   THR A 239 " --> pdb=" O   VAL A 208 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   VAL A 210 " --> pdb=" O   THR A 239 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   VAL A 271 " --> pdb=" O   TRP A 205 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   VAL A 272 " --> pdb=" O   ILE A 299 " (cutoff:3.500A)
      removed outlier: 5.416A  pdb=" N   PHE A 322 " --> pdb=" O   TRP A 453 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   LEU A 448 " --> pdb=" O   SER A 467 " (cutoff:3.500A)
      removed outlier: 5.002A  pdb=" N   SER A 467 " --> pdb=" O   LEU A 448 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   ILE A 450 " --> pdb=" O   VAL A 465 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 429 through 430
      removed outlier: 3.742A  pdb=" N   PHE A 429 " --> pdb=" O   ILE A 436 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 504 through 507
    Processing sheet with id=AA6, first strand: chain 'A' and resid 524 through 525
    Processing sheet with id=AA7, first strand: chain 'A' and resid 555 through 557
      removed outlier: 3.860A  pdb=" N   VAL A 718 " --> pdb=" O   VAL A 557 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 30 through 31
      removed outlier: 3.588A  pdb=" N   TYR B  97 " --> pdb=" O   MET B  31 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   ALA B 140 " --> pdb=" O   VAL B  36 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   VAL B 141 " --> pdb=" O   VAL B 165 " (cutoff:3.500A)
      removed outlier: 6.112A  pdb=" N   GLN B 164 " --> pdb=" O   PHE B 184 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 44 through 45
    Processing sheet with id=AB1, first strand: chain 'B' and resid 236 through 243
      removed outlier: 7.711A  pdb=" N   VAL B 209 " --> pdb=" O   HIS B 239 " (cutoff:3.500A)
      removed outlier: 9.425A  pdb=" N   GLY B 241 " --> pdb=" O   VAL B 209 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   ALA B 211 " --> pdb=" O   GLY B 241 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   VAL B 243 " --> pdb=" O   ALA B 211 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   GLY B 213 " --> pdb=" O   VAL B 243 " (cutoff:3.500A)
      removed outlier: 4.989A  pdb=" N   VAL B 270 " --> pdb=" O   TRP B 208 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   TRP B 297 " --> pdb=" O   LEU B 322 " (cutoff:3.500A)
      removed outlier: 8.728A  pdb=" N   PHE B 324 " --> pdb=" O   TRP B 297 " (cutoff:3.500A)
      removed outlier: 5.219A  pdb=" N   VAL B 321 " --> pdb=" O   TRP B 459 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   TYR B 454 " --> pdb=" O   ARG B 473 " (cutoff:3.500A)
      removed outlier: 5.051A  pdb=" N   ARG B 473 " --> pdb=" O   TYR B 454 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   LEU B 456 " --> pdb=" O   VAL B 471 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   GLN B 462 " --> pdb=" O   VAL B 465 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   VAL B 465 " --> pdb=" O   GLN B 462 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 434 through 437
      removed outlier: 3.653A  pdb=" N   VAL B 437 " --> pdb=" O   LEU B 440 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 508 through 512
    Processing sheet with id=AB4, first strand: chain 'B' and resid 559 through 560
      removed outlier: 3.827A  pdb=" N   GLU B 706 " --> pdb=" O   ARG B 723 " (cutoff:3.500A)

    556 hydrogen bonds defined for protein.
    1605 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: 2.17

  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:
        1.22 -     1.34: 3900
        1.34 -     1.47: 3086
        1.47 -     1.59: 5411
        1.59 -     1.71: 0
        1.71 -     1.84: 134
  Bond restraints: 12531
  Sorted by residual:
  bond pdb=" N   ARG A 554 "
       pdb=" CA  ARG A 554 "
    ideal  model  delta    sigma   weight residual
    1.455  1.496 -0.041 1.09e-02 8.42e+03 1.39e+01
  bond pdb=" N   ARG B 556 "
       pdb=" CA  ARG B 556 "
    ideal  model  delta    sigma   weight residual
    1.453  1.504 -0.051 1.41e-02 5.03e+03 1.33e+01
  bond pdb=" N   LYS A 553 "
       pdb=" CA  LYS A 553 "
    ideal  model  delta    sigma   weight residual
    1.457  1.504 -0.047 1.29e-02 6.01e+03 1.31e+01
  bond pdb=" N   ARG B 557 "
       pdb=" CA  ARG B 557 "
    ideal  model  delta    sigma   weight residual
    1.457  1.503 -0.045 1.29e-02 6.01e+03 1.24e+01
  bond pdb=" CA  LYS A 553 "
       pdb=" C   LYS A 553 "
    ideal  model  delta    sigma   weight residual
    1.523  1.550 -0.027 1.34e-02 5.57e+03 4.13e+00
  ... (remaining 12526 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.45: 16901
        2.45 -     4.91: 162
        4.91 -     7.36: 9
        7.36 -     9.82: 1
        9.82 -    12.27: 1
  Bond angle restraints: 17074
  Sorted by residual:
  angle pdb=" O   PHE B 555 "
        pdb=" C   PHE B 555 "
        pdb=" N   ARG B 556 "
      ideal   model   delta    sigma   weight residual
     123.03  118.33    4.70 1.13e+00 7.83e-01 1.73e+01
  angle pdb=" CB  PRO B 638 "
        pdb=" CG  PRO B 638 "
        pdb=" CD  PRO B 638 "
      ideal   model   delta    sigma   weight residual
     106.10   93.83   12.27 3.20e+00 9.77e-02 1.47e+01
  angle pdb=" CA  PRO B 638 "
        pdb=" N   PRO B 638 "
        pdb=" CD  PRO B 638 "
      ideal   model   delta    sigma   weight residual
     112.00  106.69    5.31 1.40e+00 5.10e-01 1.44e+01
  angle pdb=" N   PRO B 638 "
        pdb=" CD  PRO B 638 "
        pdb=" CG  PRO B 638 "
      ideal   model   delta    sigma   weight residual
     103.20   97.77    5.43 1.50e+00 4.44e-01 1.31e+01
  angle pdb=" CA  PRO B 638 "
        pdb=" CB  PRO B 638 "
        pdb=" CG  PRO B 638 "
      ideal   model   delta    sigma   weight residual
     104.50   98.02    6.48 1.90e+00 2.77e-01 1.16e+01
  ... (remaining 17069 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 6455
       17.91 -    35.82: 721
       35.82 -    53.73: 210
       53.73 -    71.64: 54
       71.64 -    89.55: 13
  Dihedral angle restraints: 7453
    sinusoidal: 2924
      harmonic: 4529
  Sorted by residual:
  dihedral pdb=" CB  CYS B 370 "
           pdb=" SG  CYS B 370 "
           pdb=" SG  CYS B 373 "
           pdb=" CB  CYS B 373 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -173.25   87.25     1      1.00e+01 1.00e-02 9.14e+01
  dihedral pdb=" CB  CYS A 538 "
           pdb=" SG  CYS A 538 "
           pdb=" SG  CYS A 551 "
           pdb=" CB  CYS A 551 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  160.73  -67.73     1      1.00e+01 1.00e-02 5.96e+01
  dihedral pdb=" CB  CYS A 233 "
           pdb=" SG  CYS A 233 "
           pdb=" SG  CYS A 513 "
           pdb=" CB  CYS A 513 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -148.43   62.43     1      1.00e+01 1.00e-02 5.16e+01
  ... (remaining 7450 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 1166
       0.026 -    0.051: 482
       0.051 -    0.077: 167
       0.077 -    0.103: 84
       0.103 -    0.128: 45
  Chirality restraints: 1944
  Sorted by residual:
  chirality pdb=" CA  VAL A 271 "
            pdb=" N   VAL A 271 "
            pdb=" C   VAL A 271 "
            pdb=" CB  VAL A 271 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.12e-01
  chirality pdb=" CA  ILE B 235 "
            pdb=" N   ILE B 235 "
            pdb=" C   ILE B 235 "
            pdb=" CB  ILE B 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.00e-01
  chirality pdb=" CA  ILE A 332 "
            pdb=" N   ILE A 332 "
            pdb=" C   ILE A 332 "
            pdb=" CB  ILE A 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.82e-01
  ... (remaining 1941 not shown)

  Planarity restraints: 2164
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 556 "    0.592 9.50e-02 1.11e+02   2.65e-01 4.30e+01
        pdb=" NE  ARG B 556 "   -0.034 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 556 "   -0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 556 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 556 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 555 "    0.020 2.00e-02 2.50e+03   3.87e-02 1.50e+01
        pdb=" C   PHE B 555 "   -0.067 2.00e-02 2.50e+03
        pdb=" O   PHE B 555 "    0.025 2.00e-02 2.50e+03
        pdb=" N   ARG B 556 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 557 "   -0.345 9.50e-02 1.11e+02   1.55e-01 1.47e+01
        pdb=" NE  ARG B 557 "    0.021 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 557 "    0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 557 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 557 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 2161 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 115
        2.60 -     3.18: 10704
        3.18 -     3.75: 17548
        3.75 -     4.33: 23619
        4.33 -     4.90: 39776
  Nonbonded interactions: 91762
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 227 "
            pdb=" OE2 GLU B 240 "
     model   vdw
     2.029 3.040
  nonbonded pdb=" OG1 THR B 645 "
            pdb=" OG1 THR B 736 "
     model   vdw
     2.093 3.040
  nonbonded pdb=" OE1 GLU A  81 "
            pdb=" OH  TYR A 389 "
     model   vdw
     2.108 3.040
  nonbonded pdb=" NH2 ARG B  54 "
            pdb=" O   SER B  58 "
     model   vdw
     2.169 3.120
  nonbonded pdb=" O   ALA A 683 "
            pdb=" OG1 THR A 686 "
     model   vdw
     2.221 3.040
  ... (remaining 91757 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.260
  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:             0.020
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     13.480
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  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:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6935
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      :  0.003   0.249  12549  Z= 0.177
  Angle     :  0.612  23.570  17110  Z= 0.319
  Chirality :  0.038   0.128   1944
  Planarity :  0.008   0.265   2164
  Dihedral  : 16.771  89.552   4469
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.07 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  : 21.23 %
    Favored  : 78.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.85 (0.22), residues: 1538
  helix:  0.55 (0.20), residues: 722
  sheet: -1.15 (0.36), residues: 212
  loop : -1.68 (0.24), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG B  30 
 TYR   0.018   0.001   TYR B 529 
 PHE   0.010   0.001   PHE A 558 
 TRP   0.015   0.001   TRP B 698 
 HIS   0.003   0.001   HIS A 397 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (12531)
  covalent geometry    : angle       0.56104 (17074)
  SS BOND              : bond        0.05872 (   18)
  SS BOND              : angle       5.37353 (   36)
  hydrogen bonds       : bond        0.22584 (  556)
  hydrogen bonds       : angle       7.22724 ( 1605)

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

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

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 245
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 LEU cc_start: 0.8457 (tp) cc_final: 0.8219 (tt)
REVERT: A  238 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7743 (tp30)
REVERT: A  315 GLU cc_start: 0.8053 (tp30) cc_final: 0.7467 (tp30)
REVERT: A  473 ARG cc_start: 0.8401 (mtp85) cc_final: 0.8157 (mmm-85)
REVERT: A  479 GLN cc_start: 0.7511 (mm-40) cc_final: 0.7273 (mm-40)
REVERT: A  644 CYS cc_start: 0.6771 (t) cc_final: 0.6327 (p)
REVERT: A  788 VAL cc_start: 0.6314 (t) cc_final: 0.6025 (m)
REVERT: A  792 ASP cc_start: 0.6724 (m-30) cc_final: 0.6236 (m-30)
REVERT: B  193 GLN cc_start: 0.7826 (tt0) cc_final: 0.7596 (tt0)
REVERT: B  443 ARG cc_start: 0.7812 (ttp80) cc_final: 0.7520 (ptm-80)
REVERT: B  699 TYR cc_start: 0.6387 (OUTLIER) cc_final: 0.5894 (p90)
REVERT: B  744 CYS cc_start: 0.7865 (m) cc_final: 0.7642 (t)
  outliers start: 2
  outliers final: 1
  residues processed: 246
  average time/residue: 0.1271
  time to fit residues: 42.7957
Evaluate side-chains
  232 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 230
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  529 TYR
Chi-restraints excluded: chain B residue  699 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 66 optimal weight:    0.0060
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    0.2980
   chunk 103 optimal weight:    0.6980
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9980
   chunk 149 optimal weight:    1.9990
   overall best weight:    0.4796

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

Flipped N/Q/H residues before XYZ refinement:
A 117 HIS
A 283 HIS
A 434 HIS
A 755 ASN
B 207 ASN
B 543 GLN
B 627 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.175542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.133261 restraints weight = 17875.059|
|-----------------------------------------------------------------------------|
r_work (start): 0.3591 rms_B_bonded: 2.56
r_work: 0.3441 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7030
moved from start:          0.1396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  12549  Z= 0.162
  Angle     :  0.643  12.841  17110  Z= 0.328
  Chirality :  0.043   0.140   1944
  Planarity :  0.005   0.057   2164
  Dihedral  :  4.682  55.777   1681
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 19.38 %
    Favored  : 77.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.56 (0.22), residues: 1538
  helix:  0.80 (0.20), residues: 729
  sheet: -0.90 (0.35), residues: 216
  loop : -1.62 (0.24), residues: 593

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  30 
 TYR   0.030   0.002   TYR B 529 
 PHE   0.017   0.001   PHE B 435 
 TRP   0.022   0.001   TRP B 775 
 HIS   0.017   0.001   HIS B 734 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (12531)
  covalent geometry    : angle       0.63990 (17074)
  SS BOND              : bond        0.00391 (   18)
  SS BOND              : angle       1.50895 (   36)
  hydrogen bonds       : bond        0.05752 (  556)
  hydrogen bonds       : angle       4.72252 ( 1605)

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

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

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 226
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 VAL cc_start: 0.8629 (t) cc_final: 0.8301 (p)
REVERT: A  226 ARG cc_start: 0.8318 (tpp80) cc_final: 0.7810 (tpp-160)
REVERT: A  315 GLU cc_start: 0.8106 (tp30) cc_final: 0.7579 (tp30)
REVERT: A  319 LEU cc_start: 0.8568 (mp) cc_final: 0.8244 (mp)
REVERT: A  510 ILE cc_start: 0.8456 (tp) cc_final: 0.8252 (mt)
REVERT: A  644 CYS cc_start: 0.6886 (t) cc_final: 0.6293 (p)
REVERT: A  780 MET cc_start: 0.7500 (tpp) cc_final: 0.7242 (tpp)
REVERT: B  148 GLU cc_start: 0.7427 (mp0) cc_final: 0.6831 (mp0)
REVERT: B  257 GLN cc_start: 0.7692 (mt0) cc_final: 0.7466 (mt0)
REVERT: B  518 CYS cc_start: 0.6537 (m) cc_final: 0.6219 (m)
REVERT: B  647 CYS cc_start: 0.4632 (OUTLIER) cc_final: 0.1921 (p)
REVERT: B  699 TYR cc_start: 0.6740 (OUTLIER) cc_final: 0.6100 (p90)
REVERT: B  732 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6939 (tm)
REVERT: B  768 MET cc_start: 0.7976 (mmt) cc_final: 0.6998 (mmt)
  outliers start: 41
  outliers final: 19
  residues processed: 251
  average time/residue: 0.1282
  time to fit residues: 44.3921
Evaluate side-chains
  236 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 214
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  117 HIS
Chi-restraints excluded: chain A residue  130 ASN
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  397 HIS
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  485 THR
Chi-restraints excluded: chain A residue  497 LYS
Chi-restraints excluded: chain B residue  171 MET
Chi-restraints excluded: chain B residue  178 GLU
Chi-restraints excluded: chain B residue  203 GLU
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  376 ILE
Chi-restraints excluded: chain B residue  529 TYR
Chi-restraints excluded: chain B residue  555 PHE
Chi-restraints excluded: chain B residue  647 CYS
Chi-restraints excluded: chain B residue  699 TYR
Chi-restraints excluded: chain B residue  732 LEU
Chi-restraints excluded: chain B residue  746 LEU
Chi-restraints excluded: chain B residue  776 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 95 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   chunk 106 optimal weight:    0.5980
   chunk 127 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 49 optimal weight:    4.9990
   chunk 45 optimal weight:    0.2980
   chunk 117 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 441 GLN
B 207 ASN
B 265 GLN
** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 627 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.174611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.133105 restraints weight = 18124.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 2.53
r_work: 0.3433 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7062
moved from start:          0.1747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12549  Z= 0.178
  Angle     :  0.617   9.903  17110  Z= 0.316
  Chirality :  0.042   0.158   1944
  Planarity :  0.005   0.061   2164
  Dihedral  :  4.772  55.148   1681
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 20.12 %
    Favored  : 75.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.55 (0.21), residues: 1538
  helix:  0.82 (0.20), residues: 720
  sheet: -0.82 (0.35), residues: 216
  loop : -1.63 (0.24), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 134 
 TYR   0.029   0.002   TYR B 529 
 PHE   0.020   0.002   PHE B 435 
 TRP   0.015   0.001   TRP B 424 
 HIS   0.014   0.001   HIS B 734 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 (12531)
  covalent geometry    : angle       0.61324 (17074)
  SS BOND              : bond        0.00389 (   18)
  SS BOND              : angle       1.68713 (   36)
  hydrogen bonds       : bond        0.05582 (  556)
  hydrogen bonds       : angle       4.55614 ( 1605)

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

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

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 211
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7242 (mm-30)
REVERT: A  100 ASP cc_start: 0.7545 (t0) cc_final: 0.7295 (t0)
REVERT: A  136 VAL cc_start: 0.8676 (t) cc_final: 0.8339 (p)
REVERT: A  226 ARG cc_start: 0.8347 (tpp80) cc_final: 0.7830 (tpp-160)
REVERT: A  287 GLU cc_start: 0.7861 (tp30) cc_final: 0.7472 (tp30)
REVERT: A  290 ARG cc_start: 0.7394 (ttm110) cc_final: 0.6986 (ttm110)
REVERT: A  315 GLU cc_start: 0.8112 (tp30) cc_final: 0.7624 (tp30)
REVERT: A  319 LEU cc_start: 0.8560 (mp) cc_final: 0.8215 (mp)
REVERT: A  644 CYS cc_start: 0.6979 (t) cc_final: 0.6346 (p)
REVERT: B  148 GLU cc_start: 0.7408 (mp0) cc_final: 0.6849 (mp0)
REVERT: B  256 VAL cc_start: 0.6742 (m) cc_final: 0.6410 (t)
REVERT: B  558 ARG cc_start: 0.5118 (OUTLIER) cc_final: 0.4704 (mtm110)
REVERT: B  616 LEU cc_start: 0.6624 (OUTLIER) cc_final: 0.6367 (mt)
REVERT: B  661 GLU cc_start: 0.7370 (mp0) cc_final: 0.6935 (mp0)
REVERT: B  699 TYR cc_start: 0.6654 (OUTLIER) cc_final: 0.6080 (p90)
REVERT: B  732 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6977 (tm)
  outliers start: 53
  outliers final: 37
  residues processed: 243
  average time/residue: 0.1122
  time to fit residues: 38.0127
Evaluate side-chains
  250 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 208
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  117 HIS
Chi-restraints excluded: chain A residue  130 ASN
Chi-restraints excluded: chain A residue  173 ASP
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  393 TYR
Chi-restraints excluded: chain A residue  397 HIS
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  485 THR
Chi-restraints excluded: chain A residue  497 LYS
Chi-restraints excluded: chain A residue  518 ILE
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  616 MET
Chi-restraints excluded: chain A residue  756 TYR
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  796 THR
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  178 GLU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  190 ASP
Chi-restraints excluded: chain B residue  203 GLU
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  277 VAL
Chi-restraints excluded: chain B residue  376 ILE
Chi-restraints excluded: chain B residue  524 CYS
Chi-restraints excluded: chain B residue  529 TYR
Chi-restraints excluded: chain B residue  555 PHE
Chi-restraints excluded: chain B residue  558 ARG
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain B residue  616 LEU
Chi-restraints excluded: chain B residue  618 CYS
Chi-restraints excluded: chain B residue  699 TYR
Chi-restraints excluded: chain B residue  712 HIS
Chi-restraints excluded: chain B residue  732 LEU
Chi-restraints excluded: chain B residue  746 LEU
Chi-restraints excluded: chain B residue  776 VAL
Chi-restraints excluded: chain B residue  778 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 148 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9980
   chunk 106 optimal weight:    0.9990
   chunk 102 optimal weight:    0.8980
   chunk 90 optimal weight:    0.9980
   chunk 146 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 136 optimal weight:    1.9990
   chunk 154 optimal weight:    0.3980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 441 GLN
B 193 GLN
B 207 ASN
** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 462 GLN
B 627 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.173128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.131055 restraints weight = 18078.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 2.56
r_work: 0.3383 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7088
moved from start:          0.2088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  12549  Z= 0.224
  Angle     :  0.644   9.762  17110  Z= 0.333
  Chirality :  0.044   0.165   1944
  Planarity :  0.006   0.070   2164
  Dihedral  :  5.048  55.519   1681
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 21.68 %
    Favored  : 73.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.71 (0.21), residues: 1538
  helix:  0.64 (0.20), residues: 724
  sheet: -0.83 (0.35), residues: 218
  loop : -1.69 (0.24), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 134 
 TYR   0.028   0.002   TYR B 529 
 PHE   0.027   0.002   PHE B 435 
 TRP   0.017   0.002   TRP B 208 
 HIS   0.008   0.002   HIS B 734 

Details of bonding type rmsd
  covalent geometry    : bond        0.00538 (12531)
  covalent geometry    : angle       0.64058 (17074)
  SS BOND              : bond        0.00357 (   18)
  SS BOND              : angle       1.50265 (   36)
  hydrogen bonds       : bond        0.05955 (  556)
  hydrogen bonds       : angle       4.53751 ( 1605)

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

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

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 222
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7248 (mm-30)
REVERT: A  100 ASP cc_start: 0.7531 (t0) cc_final: 0.7253 (t0)
REVERT: A  214 THR cc_start: 0.7855 (p) cc_final: 0.7577 (m)
REVERT: A  226 ARG cc_start: 0.8369 (tpp80) cc_final: 0.7838 (tpp-160)
REVERT: A  287 GLU cc_start: 0.7878 (tp30) cc_final: 0.7597 (tp30)
REVERT: A  290 ARG cc_start: 0.7398 (ttm110) cc_final: 0.7052 (ttm110)
REVERT: A  315 GLU cc_start: 0.8085 (tp30) cc_final: 0.7367 (tp30)
REVERT: A  644 CYS cc_start: 0.7017 (t) cc_final: 0.6385 (p)
REVERT: A  690 MET cc_start: 0.4211 (mpt) cc_final: 0.3988 (mpt)
REVERT: B  148 GLU cc_start: 0.7437 (mp0) cc_final: 0.6882 (mp0)
REVERT: B  256 VAL cc_start: 0.6691 (m) cc_final: 0.6073 (t)
REVERT: B  260 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8287 (mm)
REVERT: B  499 CYS cc_start: 0.6212 (OUTLIER) cc_final: 0.5957 (p)
REVERT: B  501 ARG cc_start: 0.6634 (mtp85) cc_final: 0.6426 (mtt-85)
REVERT: B  699 TYR cc_start: 0.6865 (OUTLIER) cc_final: 0.6132 (p90)
REVERT: B  732 LEU cc_start: 0.7145 (OUTLIER) cc_final: 0.6920 (tm)
REVERT: B  782 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8156 (tp)
  outliers start: 63
  outliers final: 38
  residues processed: 259
  average time/residue: 0.1029
  time to fit residues: 37.5180
Evaluate side-chains
  265 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 221
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  130 ASN
Chi-restraints excluded: chain A residue  173 ASP
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  397 HIS
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  485 THR
Chi-restraints excluded: chain A residue  497 LYS
Chi-restraints excluded: chain A residue  505 LYS
Chi-restraints excluded: chain A residue  518 ILE
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  617 VAL
Chi-restraints excluded: chain A residue  621 TYR
Chi-restraints excluded: chain A residue  756 TYR
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  796 THR
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  178 GLU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  216 ASP
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  277 VAL
Chi-restraints excluded: chain B residue  462 GLN
Chi-restraints excluded: chain B residue  499 CYS
Chi-restraints excluded: chain B residue  524 CYS
Chi-restraints excluded: chain B residue  529 TYR
Chi-restraints excluded: chain B residue  555 PHE
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain B residue  618 CYS
Chi-restraints excluded: chain B residue  699 TYR
Chi-restraints excluded: chain B residue  700 LEU
Chi-restraints excluded: chain B residue  712 HIS
Chi-restraints excluded: chain B residue  732 LEU
Chi-restraints excluded: chain B residue  776 VAL
Chi-restraints excluded: chain B residue  782 LEU
Chi-restraints excluded: chain B residue  793 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 144 optimal weight:    3.9990
   chunk 53 optimal weight:    0.7980
   chunk 69 optimal weight:    0.6980
   chunk 92 optimal weight:    0.9980
   chunk 63 optimal weight:   30.0000
   chunk 15 optimal weight:    0.2980
   chunk 5 optimal weight:    2.9990
   chunk 135 optimal weight:    0.0470
   chunk 127 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9980
   chunk 82 optimal weight:    0.2980
   overall best weight:    0.4278

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

Flipped N/Q/H residues before XYZ refinement:
A 117 HIS
A 441 GLN
B 207 ASN
** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.173161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.132183 restraints weight = 18020.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.3584 rms_B_bonded: 2.44
r_work: 0.3445 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7040
moved from start:          0.2230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12549  Z= 0.139
  Angle     :  0.589  12.912  17110  Z= 0.298
  Chirality :  0.041   0.143   1944
  Planarity :  0.005   0.074   2164
  Dihedral  :  4.851  57.038   1681
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 22.27 %
    Favored  : 73.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.42 (0.22), residues: 1538
  helix:  0.95 (0.20), residues: 715
  sheet: -0.72 (0.36), residues: 218
  loop : -1.58 (0.24), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 134 
 TYR   0.027   0.002   TYR B 529 
 PHE   0.016   0.001   PHE B 435 
 TRP   0.013   0.001   TRP B 208 
 HIS   0.006   0.001   HIS B 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (12531)
  covalent geometry    : angle       0.58672 (17074)
  SS BOND              : bond        0.00259 (   18)
  SS BOND              : angle       1.35296 (   36)
  hydrogen bonds       : bond        0.04838 (  556)
  hydrogen bonds       : angle       4.29902 ( 1605)

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

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

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 212
  time to evaluate  : 0.575 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7121 (mm-30)
REVERT: A  100 ASP cc_start: 0.7451 (t0) cc_final: 0.7202 (t0)
REVERT: A  126 GLU cc_start: 0.7489 (tp30) cc_final: 0.7086 (tp30)
REVERT: A  136 VAL cc_start: 0.8686 (t) cc_final: 0.8346 (p)
REVERT: A  226 ARG cc_start: 0.8324 (tpp80) cc_final: 0.7803 (tpp-160)
REVERT: A  287 GLU cc_start: 0.7877 (tp30) cc_final: 0.7487 (tp30)
REVERT: A  290 ARG cc_start: 0.7360 (ttm110) cc_final: 0.7010 (ttm110)
REVERT: A  315 GLU cc_start: 0.8084 (tp30) cc_final: 0.7479 (tp30)
REVERT: A  479 GLN cc_start: 0.7524 (mm-40) cc_final: 0.7270 (mm-40)
REVERT: A  644 CYS cc_start: 0.7093 (t) cc_final: 0.6492 (p)
REVERT: B  148 GLU cc_start: 0.7412 (mp0) cc_final: 0.6853 (mp0)
REVERT: B  501 ARG cc_start: 0.6565 (mtp85) cc_final: 0.6346 (mtt-85)
REVERT: B  558 ARG cc_start: 0.5234 (OUTLIER) cc_final: 0.4881 (mtm110)
REVERT: B  699 TYR cc_start: 0.6793 (OUTLIER) cc_final: 0.6070 (p90)
REVERT: B  732 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6831 (tm)
REVERT: B  782 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8177 (tp)
  outliers start: 54
  outliers final: 41
  residues processed: 245
  average time/residue: 0.1324
  time to fit residues: 45.2204
Evaluate side-chains
  257 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 211
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  117 HIS
Chi-restraints excluded: chain A residue  130 ASN
Chi-restraints excluded: chain A residue  173 ASP
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  397 HIS
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  410 CYS
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  454 GLN
Chi-restraints excluded: chain A residue  497 LYS
Chi-restraints excluded: chain A residue  505 LYS
Chi-restraints excluded: chain A residue  518 ILE
Chi-restraints excluded: chain A residue  621 TYR
Chi-restraints excluded: chain A residue  756 TYR
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  796 THR
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  178 GLU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  277 VAL
Chi-restraints excluded: chain B residue  341 HIS
Chi-restraints excluded: chain B residue  524 CYS
Chi-restraints excluded: chain B residue  529 TYR
Chi-restraints excluded: chain B residue  555 PHE
Chi-restraints excluded: chain B residue  558 ARG
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain B residue  618 CYS
Chi-restraints excluded: chain B residue  699 TYR
Chi-restraints excluded: chain B residue  712 HIS
Chi-restraints excluded: chain B residue  713 MET
Chi-restraints excluded: chain B residue  716 THR
Chi-restraints excluded: chain B residue  732 LEU
Chi-restraints excluded: chain B residue  746 LEU
Chi-restraints excluded: chain B residue  769 LEU
Chi-restraints excluded: chain B residue  776 VAL
Chi-restraints excluded: chain B residue  778 PHE
Chi-restraints excluded: chain B residue  782 LEU
Chi-restraints excluded: chain B residue  788 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 92 optimal weight:    0.4980
   chunk 29 optimal weight:    0.6980
   chunk 93 optimal weight:    0.6980
   chunk 64 optimal weight:    0.0370
   chunk 53 optimal weight:    0.2980
   chunk 39 optimal weight:    0.8980
   chunk 139 optimal weight:   10.0000
   chunk 81 optimal weight:    0.8980
   chunk 101 optimal weight:    1.9990
   chunk 123 optimal weight:    0.0370
   chunk 76 optimal weight:    0.0020
   overall best weight:    0.1744

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

Flipped N/Q/H residues before XYZ refinement:
A 441 GLN
B 207 ASN
B 341 HIS
** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 436 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.174968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.133980 restraints weight = 18005.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 2.48
r_work: 0.3472 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7009
moved from start:          0.2428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  12549  Z= 0.110
  Angle     :  0.565  10.925  17110  Z= 0.283
  Chirality :  0.039   0.138   1944
  Planarity :  0.004   0.056   2164
  Dihedral  :  4.662  59.879   1681
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 23.31 %
    Favored  : 73.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.22), residues: 1538
  helix:  1.23 (0.20), residues: 708
  sheet: -0.61 (0.36), residues: 216
  loop : -1.42 (0.24), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 134 
 TYR   0.024   0.001   TYR B 529 
 PHE   0.011   0.001   PHE A 338 
 TRP   0.011   0.001   TRP A 588 
 HIS   0.024   0.001   HIS A 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 (12531)
  covalent geometry    : angle       0.56092 (17074)
  SS BOND              : bond        0.00269 (   18)
  SS BOND              : angle       1.50760 (   36)
  hydrogen bonds       : bond        0.03938 (  556)
  hydrogen bonds       : angle       4.07587 ( 1605)

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

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

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 219
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 LEU cc_start: 0.8252 (mt) cc_final: 0.8047 (mm)
REVERT: A   97 GLU cc_start: 0.7333 (tp30) cc_final: 0.7080 (mm-30)
REVERT: A  136 VAL cc_start: 0.8692 (t) cc_final: 0.8373 (p)
REVERT: A  226 ARG cc_start: 0.8281 (tpp80) cc_final: 0.7778 (tpp-160)
REVERT: A  287 GLU cc_start: 0.7857 (tp30) cc_final: 0.7494 (tp30)
REVERT: A  290 ARG cc_start: 0.7291 (ttm110) cc_final: 0.6957 (ttm110)
REVERT: A  315 GLU cc_start: 0.8119 (tp30) cc_final: 0.7607 (tp30)
REVERT: A  644 CYS cc_start: 0.7124 (t) cc_final: 0.6352 (p)
REVERT: A  778 THR cc_start: 0.7464 (m) cc_final: 0.7196 (t)
REVERT: B  148 GLU cc_start: 0.7418 (mp0) cc_final: 0.6883 (mp0)
REVERT: B  260 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8280 (mm)
REVERT: B  520 ASP cc_start: 0.7585 (t0) cc_final: 0.7141 (t0)
REVERT: B  558 ARG cc_start: 0.5178 (OUTLIER) cc_final: 0.4795 (mtm110)
REVERT: B  616 LEU cc_start: 0.6524 (OUTLIER) cc_final: 0.6268 (mt)
REVERT: B  699 TYR cc_start: 0.6801 (OUTLIER) cc_final: 0.6042 (p90)
REVERT: B  775 TRP cc_start: 0.7336 (m100) cc_final: 0.7129 (m100)
REVERT: B  782 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8101 (tp)
  outliers start: 43
  outliers final: 31
  residues processed: 246
  average time/residue: 0.1306
  time to fit residues: 44.7230
Evaluate side-chains
  243 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 207
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  117 HIS
Chi-restraints excluded: chain A residue  130 ASN
Chi-restraints excluded: chain A residue  173 ASP
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  393 TYR
Chi-restraints excluded: chain A residue  397 HIS
Chi-restraints excluded: chain A residue  410 CYS
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  485 THR
Chi-restraints excluded: chain A residue  505 LYS
Chi-restraints excluded: chain A residue  518 ILE
Chi-restraints excluded: chain A residue  591 PHE
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  756 TYR
Chi-restraints excluded: chain A residue  796 THR
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  178 GLU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  341 HIS
Chi-restraints excluded: chain B residue  529 TYR
Chi-restraints excluded: chain B residue  555 PHE
Chi-restraints excluded: chain B residue  558 ARG
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain B residue  616 LEU
Chi-restraints excluded: chain B residue  699 TYR
Chi-restraints excluded: chain B residue  712 HIS
Chi-restraints excluded: chain B residue  713 MET
Chi-restraints excluded: chain B residue  769 LEU
Chi-restraints excluded: chain B residue  776 VAL
Chi-restraints excluded: chain B residue  778 PHE
Chi-restraints excluded: chain B residue  782 LEU
Chi-restraints excluded: chain B residue  788 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 130 optimal weight:    2.9990
   chunk 75 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   chunk 129 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0170
   chunk 69 optimal weight:    0.9990
   chunk 131 optimal weight:    1.9990
   chunk 152 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 111 optimal weight:    1.9990
   chunk 80 optimal weight:    0.7980
   overall best weight:    0.7418

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

Flipped N/Q/H residues before XYZ refinement:
A 117 HIS
A 441 GLN
** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 193 GLN
B 207 ASN
B 341 HIS
** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.172674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.133847 restraints weight = 17969.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.3603 rms_B_bonded: 2.56
r_work: 0.3432 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7067
moved from start:          0.2500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  12549  Z= 0.196
  Angle     :  0.634  14.980  17110  Z= 0.321
  Chirality :  0.043   0.262   1944
  Planarity :  0.005   0.055   2164
  Dihedral  :  4.860  53.706   1681
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 22.12 %
    Favored  : 73.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.40 (0.21), residues: 1538
  helix:  0.90 (0.20), residues: 724
  sheet: -0.64 (0.36), residues: 218
  loop : -1.55 (0.24), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 134 
 TYR   0.024   0.002   TYR B 529 
 PHE   0.023   0.002   PHE B 435 
 TRP   0.015   0.001   TRP B 208 
 HIS   0.033   0.002   HIS B 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 (12531)
  covalent geometry    : angle       0.62930 (17074)
  SS BOND              : bond        0.00264 (   18)
  SS BOND              : angle       1.75778 (   36)
  hydrogen bonds       : bond        0.05190 (  556)
  hydrogen bonds       : angle       4.27152 ( 1605)

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

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

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 219
  time to evaluate  : 0.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7153 (mm-30)
REVERT: A  100 ASP cc_start: 0.7366 (t0) cc_final: 0.7133 (t0)
REVERT: A  226 ARG cc_start: 0.8350 (tpp80) cc_final: 0.7799 (tpp-160)
REVERT: A  315 GLU cc_start: 0.8092 (tp30) cc_final: 0.7615 (tp30)
REVERT: A  644 CYS cc_start: 0.7043 (t) cc_final: 0.6147 (p)
REVERT: B  148 GLU cc_start: 0.7376 (mp0) cc_final: 0.6839 (mp0)
REVERT: B  260 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8322 (mm)
REVERT: B  398 TYR cc_start: 0.8071 (OUTLIER) cc_final: 0.7759 (m-80)
REVERT: B  520 ASP cc_start: 0.7593 (t0) cc_final: 0.7274 (t0)
REVERT: B  558 ARG cc_start: 0.5367 (OUTLIER) cc_final: 0.4948 (mtm110)
REVERT: B  616 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.6284 (mt)
REVERT: B  699 TYR cc_start: 0.6881 (OUTLIER) cc_final: 0.6110 (p90)
REVERT: B  743 LEU cc_start: 0.8246 (mm) cc_final: 0.7989 (mm)
REVERT: B  782 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8162 (tp)
REVERT: B  818 MET cc_start: 0.2998 (mmt) cc_final: 0.2782 (mmt)
  outliers start: 60
  outliers final: 46
  residues processed: 258
  average time/residue: 0.1300
  time to fit residues: 46.3729
Evaluate side-chains
  267 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 214
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  117 HIS
Chi-restraints excluded: chain A residue  130 ASN
Chi-restraints excluded: chain A residue  173 ASP
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  397 HIS
Chi-restraints excluded: chain A residue  410 CYS
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  454 GLN
Chi-restraints excluded: chain A residue  485 THR
Chi-restraints excluded: chain A residue  497 LYS
Chi-restraints excluded: chain A residue  518 ILE
Chi-restraints excluded: chain A residue  591 PHE
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  617 VAL
Chi-restraints excluded: chain A residue  621 TYR
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  756 TYR
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  796 THR
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   63 THR
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  178 GLU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  190 ASP
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain B residue  258 ASP
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  277 VAL
Chi-restraints excluded: chain B residue  398 TYR
Chi-restraints excluded: chain B residue  524 CYS
Chi-restraints excluded: chain B residue  529 TYR
Chi-restraints excluded: chain B residue  555 PHE
Chi-restraints excluded: chain B residue  558 ARG
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain B residue  616 LEU
Chi-restraints excluded: chain B residue  699 TYR
Chi-restraints excluded: chain B residue  707 VAL
Chi-restraints excluded: chain B residue  712 HIS
Chi-restraints excluded: chain B residue  716 THR
Chi-restraints excluded: chain B residue  746 LEU
Chi-restraints excluded: chain B residue  769 LEU
Chi-restraints excluded: chain B residue  776 VAL
Chi-restraints excluded: chain B residue  778 PHE
Chi-restraints excluded: chain B residue  782 LEU
Chi-restraints excluded: chain B residue  788 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 75 optimal weight:    0.4980
   chunk 41 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 101 optimal weight:    0.9980
   chunk 107 optimal weight:    0.1980
   chunk 138 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 122 optimal weight:    0.5980
   chunk 113 optimal weight:    0.5980
   chunk 78 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 117 HIS
A 441 GLN
** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 207 ASN
** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.173272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.134827 restraints weight = 17909.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 2.52
r_work: 0.3446 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7044
moved from start:          0.2602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  12549  Z= 0.150
  Angle     :  0.603  12.398  17110  Z= 0.305
  Chirality :  0.041   0.274   1944
  Planarity :  0.005   0.056   2164
  Dihedral  :  4.786  53.030   1681
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 22.87 %
    Favored  : 73.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.27 (0.21), residues: 1538
  helix:  1.01 (0.20), residues: 718
  sheet: -0.56 (0.36), residues: 216
  loop : -1.46 (0.24), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  30 
 TYR   0.021   0.001   TYR B 529 
 PHE   0.017   0.001   PHE B 435 
 TRP   0.022   0.001   TRP B 424 
 HIS   0.009   0.001   HIS B 734 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (12531)
  covalent geometry    : angle       0.60081 (17074)
  SS BOND              : bond        0.00322 (   18)
  SS BOND              : angle       1.36923 (   36)
  hydrogen bonds       : bond        0.04690 (  556)
  hydrogen bonds       : angle       4.19119 ( 1605)

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

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

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 213
  time to evaluate  : 0.478 
Fit side-chains
   revert: symmetry clash
REVERT: A   97 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.7115 (mm-30)
REVERT: A  100 ASP cc_start: 0.7478 (t0) cc_final: 0.7253 (t0)
REVERT: A  226 ARG cc_start: 0.8329 (tpp80) cc_final: 0.7811 (tpp-160)
REVERT: A  315 GLU cc_start: 0.8086 (tp30) cc_final: 0.7613 (tp30)
REVERT: A  644 CYS cc_start: 0.7036 (t) cc_final: 0.6153 (p)
REVERT: B  148 GLU cc_start: 0.7351 (mp0) cc_final: 0.6828 (mp0)
REVERT: B  260 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8358 (mm)
REVERT: B  398 TYR cc_start: 0.8071 (OUTLIER) cc_final: 0.7698 (m-80)
REVERT: B  520 ASP cc_start: 0.7586 (t0) cc_final: 0.7264 (t0)
REVERT: B  558 ARG cc_start: 0.5384 (OUTLIER) cc_final: 0.4985 (mtm110)
REVERT: B  616 LEU cc_start: 0.6589 (OUTLIER) cc_final: 0.6318 (mt)
REVERT: B  618 CYS cc_start: 0.5825 (t) cc_final: 0.5369 (m)
REVERT: B  654 GLN cc_start: 0.5547 (OUTLIER) cc_final: 0.4268 (mt0)
REVERT: B  699 TYR cc_start: 0.6845 (OUTLIER) cc_final: 0.6123 (p90)
REVERT: B  743 LEU cc_start: 0.8242 (mm) cc_final: 0.7964 (mm)
REVERT: B  782 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8140 (tp)
  outliers start: 54
  outliers final: 42
  residues processed: 251
  average time/residue: 0.1317
  time to fit residues: 45.8811
Evaluate side-chains
  263 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 213
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   97 GLU
Chi-restraints excluded: chain A residue  117 HIS
Chi-restraints excluded: chain A residue  130 ASN
Chi-restraints excluded: chain A residue  173 ASP
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  397 HIS
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  485 THR
Chi-restraints excluded: chain A residue  497 LYS
Chi-restraints excluded: chain A residue  518 ILE
Chi-restraints excluded: chain A residue  591 PHE
Chi-restraints excluded: chain A residue  617 VAL
Chi-restraints excluded: chain A residue  621 TYR
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  654 GLN
Chi-restraints excluded: chain A residue  756 TYR
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  796 THR
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  178 GLU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  398 TYR
Chi-restraints excluded: chain B residue  524 CYS
Chi-restraints excluded: chain B residue  529 TYR
Chi-restraints excluded: chain B residue  555 PHE
Chi-restraints excluded: chain B residue  558 ARG
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain B residue  616 LEU
Chi-restraints excluded: chain B residue  654 GLN
Chi-restraints excluded: chain B residue  699 TYR
Chi-restraints excluded: chain B residue  707 VAL
Chi-restraints excluded: chain B residue  712 HIS
Chi-restraints excluded: chain B residue  716 THR
Chi-restraints excluded: chain B residue  769 LEU
Chi-restraints excluded: chain B residue  776 VAL
Chi-restraints excluded: chain B residue  778 PHE
Chi-restraints excluded: chain B residue  782 LEU
Chi-restraints excluded: chain B residue  788 VAL
Chi-restraints excluded: chain B residue  801 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 133 optimal weight:    0.5980
   chunk 56 optimal weight:    0.7980
   chunk 84 optimal weight:    0.6980
   chunk 116 optimal weight:    0.3980
   chunk 126 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 73 optimal weight:    1.9990
   chunk 115 optimal weight:    0.3980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 117 HIS
A 441 GLN
** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 193 GLN
B 207 ASN
** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.172732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.131768 restraints weight = 17825.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3588 rms_B_bonded: 2.47
r_work: 0.3445 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7035
moved from start:          0.2699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12549  Z= 0.159
  Angle     :  0.609  11.910  17110  Z= 0.308
  Chirality :  0.042   0.274   1944
  Planarity :  0.005   0.055   2164
  Dihedral  :  4.788  52.648   1681
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 22.79 %
    Favored  : 72.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.27 (0.21), residues: 1538
  helix:  1.02 (0.20), residues: 718
  sheet: -0.57 (0.36), residues: 216
  loop : -1.49 (0.24), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  30 
 TYR   0.018   0.002   TYR B 529 
 PHE   0.018   0.001   PHE B 435 
 TRP   0.019   0.001   TRP B 424 
 HIS   0.007   0.001   HIS A 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 (12531)
  covalent geometry    : angle       0.60674 (17074)
  SS BOND              : bond        0.00226 (   18)
  SS BOND              : angle       1.39984 (   36)
  hydrogen bonds       : bond        0.04736 (  556)
  hydrogen bonds       : angle       4.18810 ( 1605)

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

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

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 215
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 ASP cc_start: 0.7496 (t0) cc_final: 0.7242 (t0)
REVERT: A  136 VAL cc_start: 0.8677 (t) cc_final: 0.8322 (p)
REVERT: A  226 ARG cc_start: 0.8287 (tpp80) cc_final: 0.7768 (tpp-160)
REVERT: A  315 GLU cc_start: 0.8051 (tp30) cc_final: 0.7544 (tp30)
REVERT: A  479 GLN cc_start: 0.7591 (mm-40) cc_final: 0.7380 (mm-40)
REVERT: A  644 CYS cc_start: 0.7022 (t) cc_final: 0.6187 (p)
REVERT: B  148 GLU cc_start: 0.7392 (mp0) cc_final: 0.6849 (mp0)
REVERT: B  260 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8330 (mm)
REVERT: B  398 TYR cc_start: 0.8079 (OUTLIER) cc_final: 0.7695 (m-80)
REVERT: B  520 ASP cc_start: 0.7573 (t0) cc_final: 0.7263 (t0)
REVERT: B  558 ARG cc_start: 0.5500 (OUTLIER) cc_final: 0.5101 (mtm110)
REVERT: B  616 LEU cc_start: 0.6525 (OUTLIER) cc_final: 0.6252 (mt)
REVERT: B  618 CYS cc_start: 0.5807 (t) cc_final: 0.5375 (m)
REVERT: B  654 GLN cc_start: 0.5525 (OUTLIER) cc_final: 0.4249 (mt0)
REVERT: B  699 TYR cc_start: 0.6885 (OUTLIER) cc_final: 0.6151 (p90)
REVERT: B  743 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7947 (mm)
REVERT: B  768 MET cc_start: 0.7672 (tpp) cc_final: 0.6975 (mmt)
REVERT: B  782 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8108 (tp)
  outliers start: 57
  outliers final: 44
  residues processed: 254
  average time/residue: 0.1239
  time to fit residues: 43.8227
Evaluate side-chains
  261 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 209
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  117 HIS
Chi-restraints excluded: chain A residue  130 ASN
Chi-restraints excluded: chain A residue  173 ASP
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  397 HIS
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  485 THR
Chi-restraints excluded: chain A residue  497 LYS
Chi-restraints excluded: chain A residue  518 ILE
Chi-restraints excluded: chain A residue  591 PHE
Chi-restraints excluded: chain A residue  617 VAL
Chi-restraints excluded: chain A residue  621 TYR
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  654 GLN
Chi-restraints excluded: chain A residue  756 TYR
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  796 THR
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  178 GLU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain B residue  258 ASP
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  277 VAL
Chi-restraints excluded: chain B residue  398 TYR
Chi-restraints excluded: chain B residue  524 CYS
Chi-restraints excluded: chain B residue  529 TYR
Chi-restraints excluded: chain B residue  555 PHE
Chi-restraints excluded: chain B residue  558 ARG
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain B residue  616 LEU
Chi-restraints excluded: chain B residue  654 GLN
Chi-restraints excluded: chain B residue  699 TYR
Chi-restraints excluded: chain B residue  707 VAL
Chi-restraints excluded: chain B residue  712 HIS
Chi-restraints excluded: chain B residue  716 THR
Chi-restraints excluded: chain B residue  743 LEU
Chi-restraints excluded: chain B residue  769 LEU
Chi-restraints excluded: chain B residue  776 VAL
Chi-restraints excluded: chain B residue  778 PHE
Chi-restraints excluded: chain B residue  782 LEU
Chi-restraints excluded: chain B residue  788 VAL
Chi-restraints excluded: chain B residue  801 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 91 optimal weight:    0.4980
   chunk 56 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0570
   chunk 116 optimal weight:    0.0070
   chunk 27 optimal weight:    0.6980
   chunk 70 optimal weight:    0.6980
   chunk 100 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.3916

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

Flipped N/Q/H residues before XYZ refinement:
A 117 HIS
A 441 GLN
** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 207 ASN
** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.173476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.132671 restraints weight = 17923.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 2.48
r_work: 0.3452 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7024
moved from start:          0.2796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12549  Z= 0.134
  Angle     :  0.605  14.606  17110  Z= 0.305
  Chirality :  0.041   0.274   1944
  Planarity :  0.005   0.061   2164
  Dihedral  :  4.680  52.359   1681
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 23.09 %
    Favored  : 73.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.16 (0.22), residues: 1538
  helix:  1.13 (0.20), residues: 712
  sheet: -0.53 (0.36), residues: 216
  loop : -1.41 (0.24), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  30 
 TYR   0.017   0.001   TYR B 394 
 PHE   0.014   0.001   PHE B 435 
 TRP   0.018   0.001   TRP B 424 
 HIS   0.009   0.001   HIS A 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (12531)
  covalent geometry    : angle       0.60100 (17074)
  SS BOND              : bond        0.00292 (   18)
  SS BOND              : angle       1.62150 (   36)
  hydrogen bonds       : bond        0.04358 (  556)
  hydrogen bonds       : angle       4.13260 ( 1605)

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

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

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3076 Ramachandran restraints generated.
    1538 Oldfield, 0 Emsley, 1538 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 207
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 ASP cc_start: 0.7516 (t0) cc_final: 0.7275 (t0)
REVERT: A  226 ARG cc_start: 0.8270 (tpp80) cc_final: 0.7760 (tpp-160)
REVERT: A  479 GLN cc_start: 0.7554 (mm-40) cc_final: 0.7339 (mm-40)
REVERT: A  644 CYS cc_start: 0.6991 (t) cc_final: 0.6159 (p)
REVERT: B  148 GLU cc_start: 0.7394 (mp0) cc_final: 0.6861 (mp0)
REVERT: B  260 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8306 (mm)
REVERT: B  520 ASP cc_start: 0.7532 (t0) cc_final: 0.7202 (t0)
REVERT: B  558 ARG cc_start: 0.5479 (OUTLIER) cc_final: 0.5086 (mtm110)
REVERT: B  616 LEU cc_start: 0.6559 (OUTLIER) cc_final: 0.6245 (mm)
REVERT: B  654 GLN cc_start: 0.5561 (OUTLIER) cc_final: 0.4243 (mt0)
REVERT: B  699 TYR cc_start: 0.6917 (OUTLIER) cc_final: 0.6186 (p90)
REVERT: B  768 MET cc_start: 0.7572 (tpp) cc_final: 0.7026 (mmt)
REVERT: B  782 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8118 (tp)
  outliers start: 50
  outliers final: 38
  residues processed: 243
  average time/residue: 0.1262
  time to fit residues: 42.6432
Evaluate side-chains
  251 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 207
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  130 ASN
Chi-restraints excluded: chain A residue  173 ASP
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  397 HIS
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  485 THR
Chi-restraints excluded: chain A residue  497 LYS
Chi-restraints excluded: chain A residue  518 ILE
Chi-restraints excluded: chain A residue  591 PHE
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  621 TYR
Chi-restraints excluded: chain A residue  654 GLN
Chi-restraints excluded: chain A residue  756 TYR
Chi-restraints excluded: chain A residue  796 THR
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain B residue  178 GLU
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  237 ILE
Chi-restraints excluded: chain B residue  240 GLU
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  277 VAL
Chi-restraints excluded: chain B residue  524 CYS
Chi-restraints excluded: chain B residue  529 TYR
Chi-restraints excluded: chain B residue  555 PHE
Chi-restraints excluded: chain B residue  558 ARG
Chi-restraints excluded: chain B residue  584 LEU
Chi-restraints excluded: chain B residue  616 LEU
Chi-restraints excluded: chain B residue  654 GLN
Chi-restraints excluded: chain B residue  699 TYR
Chi-restraints excluded: chain B residue  707 VAL
Chi-restraints excluded: chain B residue  712 HIS
Chi-restraints excluded: chain B residue  716 THR
Chi-restraints excluded: chain B residue  769 LEU
Chi-restraints excluded: chain B residue  776 VAL
Chi-restraints excluded: chain B residue  778 PHE
Chi-restraints excluded: chain B residue  782 LEU
Chi-restraints excluded: chain B residue  788 VAL
Chi-restraints excluded: chain B residue  801 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 71 optimal weight:    0.8980
   chunk 75 optimal weight:    0.6980
   chunk 39 optimal weight:    0.0050
   chunk 36 optimal weight:    0.0980
   chunk 110 optimal weight:    0.6980
   chunk 130 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 150 optimal weight:    1.9990
   chunk 12 optimal weight:    0.3980
   chunk 111 optimal weight:    1.9990
   overall best weight:    0.3794

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

Flipped N/Q/H residues before XYZ refinement:
A 441 GLN
** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 207 ASN
** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.173829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.132944 restraints weight = 17774.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3598 rms_B_bonded: 2.47
r_work: 0.3459 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7015
moved from start:          0.2907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12549  Z= 0.132
  Angle     :  0.587  10.388  17110  Z= 0.297
  Chirality :  0.041   0.262   1944
  Planarity :  0.005   0.054   2164
  Dihedral  :  4.457  52.025   1681
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 23.53 %
    Favored  : 73.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.09 (0.22), residues: 1538
  helix:  1.20 (0.20), residues: 712
  sheet: -0.49 (0.36), residues: 216
  loop : -1.41 (0.24), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  30 
 TYR   0.020   0.001   TYR B 286 
 PHE   0.014   0.001   PHE B 435 
 TRP   0.017   0.001   TRP B 424 
 HIS   0.006   0.001   HIS B 405 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (12531)
  covalent geometry    : angle       0.58361 (17074)
  SS BOND              : bond        0.00248 (   18)
  SS BOND              : angle       1.53797 (   36)
  hydrogen bonds       : bond        0.04224 (  556)
  hydrogen bonds       : angle       4.05216 ( 1605)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2872.55 seconds
wall clock time: 50 minutes 1.61 seconds (3001.61 seconds total)