Starting phenix.real_space_refine
on Tue Nov 19 00:48:58 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rm1_19348/11_2024/8rm1_19348.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rm1_19348/11_2024/8rm1_19348.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rm1_19348/11_2024/8rm1_19348.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rm1_19348/11_2024/8rm1_19348.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rm1_19348/11_2024/8rm1_19348.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rm1_19348/11_2024/8rm1_19348.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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     108      5.16       5
     C   11421      2.51       5
     N    3015      2.21       5
     O    3369      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 17913
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5890
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 728, 5890
          Classifications: {'peptide': 728}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 686}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 34
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 29
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 29
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Restraints were copied for chains:
    C, B, F, H, G, I
  Time building chain proxies: 14.08, per 1000 atoms: 0.79
  Number of scatterers: 17913
  At special positions: 0
  Unit cell: (131.58, 138.46, 174.58, 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     108     16.00
     O    3369      8.00
     N    3015      7.00
     C   11421      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 228 " - pdb=" SG  CYS A 503 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 235 " - pdb=" SG  CYS A 318 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 256 " - pdb=" SG  CYS A 380 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 403 " - pdb=" SG  CYS A 483 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 417 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 446 " - pdb=" SG  CYS A 454 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 762 " - pdb=" SG  CYS A 770 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 779 " - pdb=" SG  CYS A 788 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 819 " - pdb=" SG  CYS A 837 " distance=2.03

  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
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
      " NAG G   2 " - " BMA G   3 "
      " NAG H   1 " - " NAG H   2 "
      " NAG I   1 " - " NAG I   2 "
      " NAG I   2 " - " BMA I   3 "
    NAG-ASN
      " NAG A1001 " - " ASN A 141 "
      " NAG B1001 " - " ASN B 141 "
      " NAG C1001 " - " ASN C 141 "
      " NAG D   1 " - " ASN A 183 "
      " NAG E   1 " - " ASN A 807 "
      " NAG F   1 " - " ASN B 183 "
      " NAG G   1 " - " ASN B 807 "
      " NAG H   1 " - " ASN C 183 "
      " NAG I   1 " - " ASN C 807 "
  Time building additional restraints: 4.95
  Conformation dependent library (CDL) restraints added in 2.1 seconds
  

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4188

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 30 sheets defined
      32.8% alpha, 17.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 175 through 182
    Processing helix  chain 'A' and resid 188 through 205
      removed outlier: 3.847A  pdb=" N   MET A 195 " --> pdb=" O   LEU A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 233
    Processing helix  chain 'A' and resid 271 through 276
      removed outlier: 3.986A  pdb=" N   ASP A 274 " --> pdb=" O   ALA A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 308
      removed outlier: 3.733A  pdb=" N   LEU A 307 " --> pdb=" O   PRO A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 347
    Processing helix  chain 'A' and resid 355 through 358
    Processing helix  chain 'A' and resid 376 through 381
    Processing helix  chain 'A' and resid 382 through 390
      removed outlier: 3.636A  pdb=" N   VAL A 386 " --> pdb=" O   ARG A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 405
      removed outlier: 4.092A  pdb=" N   ASN A 404 " --> pdb=" O   GLY A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 410
      removed outlier: 3.929A  pdb=" N   VAL A 410 " --> pdb=" O   ARG A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 474
    Processing helix  chain 'A' and resid 499 through 507
    Processing helix  chain 'A' and resid 511 through 524
    Processing helix  chain 'A' and resid 576 through 651
      removed outlier: 3.892A  pdb=" N   MET A 582 " --> pdb=" O   LYS A 578 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   THR A 587 " --> pdb=" O   GLY A 583 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   GLY A 588 " --> pdb=" O   TYR A 584 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   ALA A 589 " --> pdb=" O   ALA A 585 " (cutoff:3.500A)
      removed outlier: 5.009A  pdb=" N   VAL A 590 " --> pdb=" O   LEU A 586 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ALA A 621 " --> pdb=" O   THR A 617 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   THR A 622 " --> pdb=" O   LEU A 618 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LEU A 623 " --> pdb=" O   MET A 619 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLY A 631 " --> pdb=" O   SER A 627 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   PHE A 633 " --> pdb=" O   MET A 629 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   ALA A 634 " --> pdb=" O   GLU A 630 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   VAL A 635 " --> pdb=" O   GLY A 631 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   HIS A 641 " --> pdb=" O   HIS A 637 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 663 through 668
    Processing helix  chain 'A' and resid 671 through 681
      removed outlier: 3.573A  pdb=" N   LYS A 676 " --> pdb=" O   ASP A 672 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   VAL A 677 " --> pdb=" O   ASP A 673 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ILE A 678 " --> pdb=" O   GLU A 674 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 868 through 877
      removed outlier: 3.834A  pdb=" N   ILE A 872 " --> pdb=" O   LEU A 868 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 889 through 899
    Processing helix  chain 'B' and resid 175 through 182
    Processing helix  chain 'B' and resid 188 through 205
      removed outlier: 3.847A  pdb=" N   MET B 195 " --> pdb=" O   LEU B 191 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 220 through 233
    Processing helix  chain 'B' and resid 271 through 276
      removed outlier: 3.986A  pdb=" N   ASP B 274 " --> pdb=" O   ALA B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 308
      removed outlier: 3.734A  pdb=" N   LEU B 307 " --> pdb=" O   PRO B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 347
    Processing helix  chain 'B' and resid 355 through 358
    Processing helix  chain 'B' and resid 376 through 381
    Processing helix  chain 'B' and resid 382 through 390
      removed outlier: 3.636A  pdb=" N   VAL B 386 " --> pdb=" O   ARG B 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 401 through 405
      removed outlier: 4.092A  pdb=" N   ASN B 404 " --> pdb=" O   GLY B 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 410
      removed outlier: 3.929A  pdb=" N   VAL B 410 " --> pdb=" O   ARG B 407 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 469 through 474
    Processing helix  chain 'B' and resid 499 through 507
    Processing helix  chain 'B' and resid 511 through 524
    Processing helix  chain 'B' and resid 576 through 651
      removed outlier: 3.893A  pdb=" N   MET B 582 " --> pdb=" O   LYS B 578 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   THR B 587 " --> pdb=" O   GLY B 583 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   GLY B 588 " --> pdb=" O   TYR B 584 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   ALA B 589 " --> pdb=" O   ALA B 585 " (cutoff:3.500A)
      removed outlier: 5.009A  pdb=" N   VAL B 590 " --> pdb=" O   LEU B 586 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   ALA B 621 " --> pdb=" O   THR B 617 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   THR B 622 " --> pdb=" O   LEU B 618 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LEU B 623 " --> pdb=" O   MET B 619 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   GLY B 631 " --> pdb=" O   SER B 627 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   PHE B 633 " --> pdb=" O   MET B 629 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   ALA B 634 " --> pdb=" O   GLU B 630 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   VAL B 635 " --> pdb=" O   GLY B 631 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   HIS B 641 " --> pdb=" O   HIS B 637 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 663 through 668
    Processing helix  chain 'B' and resid 671 through 681
      removed outlier: 3.574A  pdb=" N   LYS B 676 " --> pdb=" O   ASP B 672 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   VAL B 677 " --> pdb=" O   ASP B 673 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ILE B 678 " --> pdb=" O   GLU B 674 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 868 through 877
      removed outlier: 3.834A  pdb=" N   ILE B 872 " --> pdb=" O   LEU B 868 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 889 through 899
    Processing helix  chain 'C' and resid 175 through 182
    Processing helix  chain 'C' and resid 188 through 205
      removed outlier: 3.848A  pdb=" N   MET C 195 " --> pdb=" O   LEU C 191 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 220 through 233
    Processing helix  chain 'C' and resid 271 through 276
      removed outlier: 3.985A  pdb=" N   ASP C 274 " --> pdb=" O   ALA C 271 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 304 through 308
      removed outlier: 3.734A  pdb=" N   LEU C 307 " --> pdb=" O   PRO C 304 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 332 through 347
    Processing helix  chain 'C' and resid 355 through 358
    Processing helix  chain 'C' and resid 376 through 381
    Processing helix  chain 'C' and resid 382 through 390
      removed outlier: 3.636A  pdb=" N   VAL C 386 " --> pdb=" O   ARG C 382 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 401 through 405
      removed outlier: 4.091A  pdb=" N   ASN C 404 " --> pdb=" O   GLY C 401 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 406 through 410
      removed outlier: 3.929A  pdb=" N   VAL C 410 " --> pdb=" O   ARG C 407 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 469 through 474
    Processing helix  chain 'C' and resid 499 through 507
    Processing helix  chain 'C' and resid 511 through 524
    Processing helix  chain 'C' and resid 576 through 651
      removed outlier: 3.894A  pdb=" N   MET C 582 " --> pdb=" O   LYS C 578 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   THR C 587 " --> pdb=" O   GLY C 583 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   GLY C 588 " --> pdb=" O   TYR C 584 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   ALA C 589 " --> pdb=" O   ALA C 585 " (cutoff:3.500A)
      removed outlier: 5.009A  pdb=" N   VAL C 590 " --> pdb=" O   LEU C 586 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   ALA C 621 " --> pdb=" O   THR C 617 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   THR C 622 " --> pdb=" O   LEU C 618 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LEU C 623 " --> pdb=" O   MET C 619 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLY C 631 " --> pdb=" O   SER C 627 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   PHE C 633 " --> pdb=" O   MET C 629 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   ALA C 634 " --> pdb=" O   GLU C 630 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   VAL C 635 " --> pdb=" O   GLY C 631 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   HIS C 641 " --> pdb=" O   HIS C 637 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 663 through 668
    Processing helix  chain 'C' and resid 671 through 681
      removed outlier: 3.574A  pdb=" N   LYS C 676 " --> pdb=" O   ASP C 672 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   VAL C 677 " --> pdb=" O   ASP C 673 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ILE C 678 " --> pdb=" O   GLU C 674 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 868 through 877
      removed outlier: 3.834A  pdb=" N   ILE C 872 " --> pdb=" O   LEU C 868 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 889 through 899
    Processing sheet with id=AA1, first strand: chain 'A' and resid 140 through 141
    Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 152
      removed outlier: 6.883A  pdb=" N   LEU A 757 " --> pdb=" O   ILE A 775 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   ILE A 775 " --> pdb=" O   LEU A 757 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   LEU A 759 " --> pdb=" O   VAL A 773 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   VAL A 773 " --> pdb=" O   LEU A 759 " (cutoff:3.500A)
      removed outlier: 8.116A  pdb=" N   GLU A 761 " --> pdb=" O   ASP A 771 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ASP A 771 " --> pdb=" O   GLU A 761 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 161 through 170
      removed outlier: 3.855A  pdb=" N   ARG A 163 " --> pdb=" O   ILE A 711 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 161 through 170
      removed outlier: 3.855A  pdb=" N   ARG A 163 " --> pdb=" O   ILE A 711 " (cutoff:3.500A)
      removed outlier: 7.287A  pdb=" N   ALA A 700 " --> pdb=" O   GLN A 691 " (cutoff:3.500A)
      removed outlier: 4.815A  pdb=" N   GLN A 691 " --> pdb=" O   ALA A 700 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   GLU A 702 " --> pdb=" O   VAL A 689 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   VAL A 689 " --> pdb=" O   GLU A 702 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   GLY A 704 " --> pdb=" O   TYR A 687 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 495 through 498
    Processing sheet with id=AA6, first strand: chain 'A' and resid 250 through 251
    Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349
    Processing sheet with id=AA8, first strand: chain 'A' and resid 395 through 397
    Processing sheet with id=AA9, first strand: chain 'A' and resid 727 through 728
      removed outlier: 3.574A  pdb=" N   TRP A 791 " --> pdb=" O   THR A 739 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 835 through 837
    Processing sheet with id=AB2, first strand: chain 'B' and resid 140 through 141
    Processing sheet with id=AB3, first strand: chain 'B' and resid 149 through 152
      removed outlier: 6.883A  pdb=" N   LEU B 757 " --> pdb=" O   ILE B 775 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   ILE B 775 " --> pdb=" O   LEU B 757 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   LEU B 759 " --> pdb=" O   VAL B 773 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   VAL B 773 " --> pdb=" O   LEU B 759 " (cutoff:3.500A)
      removed outlier: 8.117A  pdb=" N   GLU B 761 " --> pdb=" O   ASP B 771 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ASP B 771 " --> pdb=" O   GLU B 761 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 161 through 170
      removed outlier: 3.856A  pdb=" N   ARG B 163 " --> pdb=" O   ILE B 711 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 161 through 170
      removed outlier: 3.856A  pdb=" N   ARG B 163 " --> pdb=" O   ILE B 711 " (cutoff:3.500A)
      removed outlier: 7.287A  pdb=" N   ALA B 700 " --> pdb=" O   GLN B 691 " (cutoff:3.500A)
      removed outlier: 4.816A  pdb=" N   GLN B 691 " --> pdb=" O   ALA B 700 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   GLU B 702 " --> pdb=" O   VAL B 689 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   VAL B 689 " --> pdb=" O   GLU B 702 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   GLY B 704 " --> pdb=" O   TYR B 687 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 495 through 498
    Processing sheet with id=AB7, first strand: chain 'B' and resid 250 through 251
    Processing sheet with id=AB8, first strand: chain 'B' and resid 348 through 349
    Processing sheet with id=AB9, first strand: chain 'B' and resid 395 through 397
    Processing sheet with id=AC1, first strand: chain 'B' and resid 727 through 728
      removed outlier: 3.575A  pdb=" N   TRP B 791 " --> pdb=" O   THR B 739 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 835 through 837
    Processing sheet with id=AC3, first strand: chain 'C' and resid 140 through 141
    Processing sheet with id=AC4, first strand: chain 'C' and resid 149 through 152
      removed outlier: 6.882A  pdb=" N   LEU C 757 " --> pdb=" O   ILE C 775 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   ILE C 775 " --> pdb=" O   LEU C 757 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   LEU C 759 " --> pdb=" O   VAL C 773 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   VAL C 773 " --> pdb=" O   LEU C 759 " (cutoff:3.500A)
      removed outlier: 8.117A  pdb=" N   GLU C 761 " --> pdb=" O   ASP C 771 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ASP C 771 " --> pdb=" O   GLU C 761 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'C' and resid 161 through 170
      removed outlier: 3.854A  pdb=" N   ARG C 163 " --> pdb=" O   ILE C 711 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'C' and resid 161 through 170
      removed outlier: 3.854A  pdb=" N   ARG C 163 " --> pdb=" O   ILE C 711 " (cutoff:3.500A)
      removed outlier: 7.286A  pdb=" N   ALA C 700 " --> pdb=" O   GLN C 691 " (cutoff:3.500A)
      removed outlier: 4.816A  pdb=" N   GLN C 691 " --> pdb=" O   ALA C 700 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   GLU C 702 " --> pdb=" O   VAL C 689 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   VAL C 689 " --> pdb=" O   GLU C 702 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   GLY C 704 " --> pdb=" O   TYR C 687 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'C' and resid 495 through 498
    Processing sheet with id=AC8, first strand: chain 'C' and resid 250 through 251
    Processing sheet with id=AC9, first strand: chain 'C' and resid 348 through 349
    Processing sheet with id=AD1, first strand: chain 'C' and resid 395 through 397
    Processing sheet with id=AD2, first strand: chain 'C' and resid 727 through 728
      removed outlier: 3.575A  pdb=" N   TRP C 791 " --> pdb=" O   THR C 739 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'C' and resid 835 through 837

    654 hydrogen bonds defined for protein.
    1737 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: 5.94

  Time building geometry restraints manager: 5.63 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 5727
        1.34 -     1.46: 4188
        1.46 -     1.58: 8262
        1.58 -     1.70: 0
        1.70 -     1.82: 159
  Bond restraints: 18336
  Sorted by residual:
  bond pdb=" CA  LEU C 586 "
       pdb=" C   LEU C 586 "
    ideal  model  delta    sigma   weight residual
    1.523  1.564 -0.040 1.80e-02 3.09e+03 4.99e+00
  bond pdb=" CA  LEU A 586 "
       pdb=" C   LEU A 586 "
    ideal  model  delta    sigma   weight residual
    1.523  1.563 -0.040 1.80e-02 3.09e+03 4.98e+00
  bond pdb=" CA  LEU B 586 "
       pdb=" C   LEU B 586 "
    ideal  model  delta    sigma   weight residual
    1.523  1.563 -0.040 1.80e-02 3.09e+03 4.94e+00
  bond pdb=" C1  BMA E   3 "
       pdb=" C2  BMA E   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.548 -0.029 2.00e-02 2.50e+03 2.05e+00
  bond pdb=" C1  BMA G   3 "
       pdb=" C2  BMA G   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.547 -0.028 2.00e-02 2.50e+03 2.01e+00
  ... (remaining 18331 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.95: 24347
        1.95 -     3.90: 478
        3.90 -     5.84: 70
        5.84 -     7.79: 8
        7.79 -     9.74: 12
  Bond angle restraints: 24915
  Sorted by residual:
  angle pdb=" N   ILE A 489 "
        pdb=" CA  ILE A 489 "
        pdb=" C   ILE A 489 "
      ideal   model   delta    sigma   weight residual
     111.62  109.39    2.23 7.90e-01 1.60e+00 8.00e+00
  angle pdb=" N   ILE B 489 "
        pdb=" CA  ILE B 489 "
        pdb=" C   ILE B 489 "
      ideal   model   delta    sigma   weight residual
     111.62  109.40    2.22 7.90e-01 1.60e+00 7.91e+00
  angle pdb=" N   ILE C 489 "
        pdb=" CA  ILE C 489 "
        pdb=" C   ILE C 489 "
      ideal   model   delta    sigma   weight residual
     111.62  109.41    2.21 7.90e-01 1.60e+00 7.86e+00
  angle pdb=" CB  MET C 619 "
        pdb=" CG  MET C 619 "
        pdb=" SD  MET C 619 "
      ideal   model   delta    sigma   weight residual
     112.70  121.07   -8.37 3.00e+00 1.11e-01 7.78e+00
  angle pdb=" CB  MET B 619 "
        pdb=" CG  MET B 619 "
        pdb=" SD  MET B 619 "
      ideal   model   delta    sigma   weight residual
     112.70  121.07   -8.37 3.00e+00 1.11e-01 7.78e+00
  ... (remaining 24910 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.88: 10586
       21.88 -    43.75: 602
       43.75 -    65.63: 101
       65.63 -    87.51: 39
       87.51 -   109.38: 12
  Dihedral angle restraints: 11340
    sinusoidal: 4851
      harmonic: 6489
  Sorted by residual:
  dihedral pdb=" CB  CYS A 779 "
           pdb=" SG  CYS A 779 "
           pdb=" SG  CYS A 788 "
           pdb=" CB  CYS A 788 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  178.53  -85.53     1      1.00e+01 1.00e-02 8.85e+01
  dihedral pdb=" CB  CYS A 256 "
           pdb=" SG  CYS A 256 "
           pdb=" SG  CYS A 380 "
           pdb=" CB  CYS A 380 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  177.14  -84.14     1      1.00e+01 1.00e-02 8.62e+01
  dihedral pdb=" CB  CYS A 417 "
           pdb=" SG  CYS A 417 "
           pdb=" SG  CYS A 432 "
           pdb=" CB  CYS A 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  162.09  -69.09     1      1.00e+01 1.00e-02 6.17e+01
  ... (remaining 11337 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 2370
       0.056 -    0.112: 378
       0.112 -    0.169: 66
       0.169 -    0.225: 0
       0.225 -    0.281: 6
  Chirality restraints: 2820
  Sorted by residual:
  chirality pdb=" C5  BMA E   3 "
            pdb=" C4  BMA E   3 "
            pdb=" C6  BMA E   3 "
            pdb=" O5  BMA E   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.56    0.28 2.00e-01 2.50e+01 1.97e+00
  chirality pdb=" C5  BMA I   3 "
            pdb=" C4  BMA I   3 "
            pdb=" C6  BMA I   3 "
            pdb=" O5  BMA I   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.28 2.00e-01 2.50e+01 1.89e+00
  chirality pdb=" C5  BMA G   3 "
            pdb=" C4  BMA G   3 "
            pdb=" C6  BMA G   3 "
            pdb=" O5  BMA G   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.27 2.00e-01 2.50e+01 1.88e+00
  ... (remaining 2817 not shown)

  Planarity restraints: 3162
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 533 "    0.056 5.00e-02 4.00e+02   8.54e-02 1.17e+01
        pdb=" N   PRO A 534 "   -0.148 5.00e-02 4.00e+02
        pdb=" CA  PRO A 534 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO A 534 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET C 533 "    0.056 5.00e-02 4.00e+02   8.53e-02 1.16e+01
        pdb=" N   PRO C 534 "   -0.148 5.00e-02 4.00e+02
        pdb=" CA  PRO C 534 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO C 534 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 533 "   -0.056 5.00e-02 4.00e+02   8.53e-02 1.16e+01
        pdb=" N   PRO B 534 "    0.148 5.00e-02 4.00e+02
        pdb=" CA  PRO B 534 "   -0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO B 534 "   -0.046 5.00e-02 4.00e+02
  ... (remaining 3159 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 129
        2.60 -     3.18: 14567
        3.18 -     3.75: 25274
        3.75 -     4.33: 34822
        4.33 -     4.90: 58650
  Nonbonded interactions: 133442
  Sorted by model distance:
  nonbonded pdb=" SG  CYS C 779 "
            pdb=" SG  CYS C 788 "
     model   vdw
     2.028 3.760
  nonbonded pdb=" SG  CYS B 779 "
            pdb=" SG  CYS B 788 "
     model   vdw
     2.029 3.760
  nonbonded pdb=" SG  CYS B 446 "
            pdb=" SG  CYS B 454 "
     model   vdw
     2.030 3.760
  nonbonded pdb=" SG  CYS C 446 "
            pdb=" SG  CYS C 454 "
     model   vdw
     2.030 3.760
  nonbonded pdb=" SG  CYS B 235 "
            pdb=" SG  CYS B 318 "
     model   vdw
     2.031 3.760
  ... (remaining 133437 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'F'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'G'
  selection = chain 'I'
}

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:             2.400
  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:          0.730
  Check model and map are aligned:         0.110
  Set scattering table:                    0.160
  Process input model:                     43.800
  Find NCS groups from input model:        0.650
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   50.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
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   0.040  18336  Z= 0.202
  Angle     :  0.659   9.740  24915  Z= 0.336
  Chirality :  0.044   0.281   2820
  Planarity :  0.005   0.085   3153
  Dihedral  : 14.776 109.384   7125
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  0.61 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.18), residues: 2148
  helix:  1.35 (0.21), residues: 648
  sheet:  0.12 (0.26), residues: 423
  loop : -1.66 (0.17), residues: 1077

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 720 
 HIS   0.003   0.001   HIS B 624 
 PHE   0.008   0.001   PHE C 838 
 TYR   0.011   0.001   TYR C 688 
 ARG   0.003   0.000   ARG A 652 

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

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

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 213
  time to evaluate  : 1.990 
Fit side-chains
REVERT: A  198 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7648 (pt0)
REVERT: A  248 ASN cc_start: 0.6424 (t0) cc_final: 0.5975 (t0)
REVERT: A  521 ASN cc_start: 0.7770 (t0) cc_final: 0.7548 (t0)
REVERT: B  198 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7701 (pt0)
REVERT: B  248 ASN cc_start: 0.6276 (t0) cc_final: 0.5776 (t0)
REVERT: C  198 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7689 (pt0)
REVERT: C  248 ASN cc_start: 0.6397 (t0) cc_final: 0.5970 (t0)
REVERT: C  899 GLU cc_start: 0.7702 (tp30) cc_final: 0.7250 (tp30)
  outliers start: 9
  outliers final: 0
  residues processed: 218
  average time/residue: 0.2897
  time to fit residues: 98.2206
Evaluate side-chains
  172 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 169
  time to evaluate  : 2.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 GLU
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain C residue  198 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 182 optimal weight:    9.9990
   chunk 163 optimal weight:    8.9990
   chunk 90 optimal weight:    7.9990
   chunk 55 optimal weight:    3.9990
   chunk 110 optimal weight:    2.9990
   chunk 87 optimal weight:    8.9990
   chunk 169 optimal weight:    0.7980
   chunk 65 optimal weight:    5.9990
   chunk 102 optimal weight:   20.0000
   chunk 126 optimal weight:    3.9990
   chunk 196 optimal weight:    0.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 335 GLN
A 591 GLN
A 595 GLN
B 230 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.1386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  18336  Z= 0.338
  Angle     :  0.690  12.112  24915  Z= 0.346
  Chirality :  0.049   0.263   2820
  Planarity :  0.005   0.069   3153
  Dihedral  :  8.088  61.829   2784
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  5.00 %
    Favored  : 93.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.18), residues: 2148
  helix:  1.38 (0.21), residues: 648
  sheet: -0.16 (0.26), residues: 411
  loop : -1.86 (0.16), residues: 1089

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 720 
 HIS   0.005   0.001   HIS C 624 
 PHE   0.020   0.002   PHE C 517 
 TYR   0.022   0.002   TYR B 707 
 ARG   0.002   0.000   ARG C 763 

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

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

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 183
  time to evaluate  : 2.004 
Fit side-chains
REVERT: A  198 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7703 (pt0)
REVERT: A  248 ASN cc_start: 0.6193 (t0) cc_final: 0.5832 (t0)
REVERT: A  384 GLU cc_start: 0.7749 (mp0) cc_final: 0.7544 (mp0)
REVERT: A  651 GLU cc_start: 0.7328 (tp30) cc_final: 0.7049 (tp30)
REVERT: A  899 GLU cc_start: 0.7844 (tp30) cc_final: 0.7447 (tp30)
REVERT: B  198 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7897 (pt0)
REVERT: B  248 ASN cc_start: 0.6128 (t0) cc_final: 0.5512 (t0)
REVERT: B  298 MET cc_start: 0.6305 (tpt) cc_final: 0.6038 (tpt)
REVERT: B  384 GLU cc_start: 0.7727 (mp0) cc_final: 0.7518 (mp0)
REVERT: C  198 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7798 (pt0)
REVERT: C  248 ASN cc_start: 0.6274 (t0) cc_final: 0.5752 (t0)
REVERT: C  315 ILE cc_start: 0.6929 (mm) cc_final: 0.6652 (mt)
  outliers start: 27
  outliers final: 17
  residues processed: 198
  average time/residue: 0.3083
  time to fit residues: 92.9073
Evaluate side-chains
  190 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 170
  time to evaluate  : 1.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  198 GLU
Chi-restraints excluded: chain A residue  232 PHE
Chi-restraints excluded: chain A residue  584 TYR
Chi-restraints excluded: chain A residue  740 LEU
Chi-restraints excluded: chain B residue  147 GLN
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  214 LEU
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  584 TYR
Chi-restraints excluded: chain B residue  619 MET
Chi-restraints excluded: chain B residue  740 LEU
Chi-restraints excluded: chain C residue  147 GLN
Chi-restraints excluded: chain C residue  161 THR
Chi-restraints excluded: chain C residue  198 GLU
Chi-restraints excluded: chain C residue  214 LEU
Chi-restraints excluded: chain C residue  584 TYR
Chi-restraints excluded: chain C residue  740 LEU
Chi-restraints excluded: chain C residue  883 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 109 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 163 optimal weight:    6.9990
   chunk 133 optimal weight:   10.0000
   chunk 54 optimal weight:    1.9990
   chunk 196 optimal weight:    0.6980
   chunk 212 optimal weight:    1.9990
   chunk 175 optimal weight:    5.9990
   chunk 194 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 157 optimal weight:    7.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 748 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.1491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  18336  Z= 0.201
  Angle     :  0.587  11.691  24915  Z= 0.291
  Chirality :  0.045   0.246   2820
  Planarity :  0.004   0.056   3153
  Dihedral  :  6.564  58.604   2784
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  :  7.07 %
    Favored  : 91.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.18), residues: 2148
  helix:  1.38 (0.21), residues: 669
  sheet: -0.06 (0.26), residues: 405
  loop : -1.90 (0.17), residues: 1074

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 701 
 HIS   0.003   0.001   HIS C 624 
 PHE   0.019   0.001   PHE C 517 
 TYR   0.014   0.001   TYR B 707 
 ARG   0.003   0.000   ARG A 226 

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

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

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 173
  time to evaluate  : 1.949 
Fit side-chains
REVERT: A  198 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7636 (pt0)
REVERT: A  248 ASN cc_start: 0.5995 (t0) cc_final: 0.5581 (t0)
REVERT: A  384 GLU cc_start: 0.7766 (mp0) cc_final: 0.7420 (mp0)
REVERT: A  899 GLU cc_start: 0.7868 (tp30) cc_final: 0.7433 (tp30)
REVERT: B  248 ASN cc_start: 0.6052 (t0) cc_final: 0.5598 (t0)
REVERT: B  315 ILE cc_start: 0.6961 (mm) cc_final: 0.6707 (mt)
REVERT: B  384 GLU cc_start: 0.7771 (mp0) cc_final: 0.7454 (mp0)
REVERT: C  198 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7798 (pt0)
REVERT: C  248 ASN cc_start: 0.6211 (t0) cc_final: 0.5669 (t0)
REVERT: C  315 ILE cc_start: 0.7010 (mm) cc_final: 0.6721 (mt)
  outliers start: 31
  outliers final: 13
  residues processed: 195
  average time/residue: 0.2930
  time to fit residues: 89.7136
Evaluate side-chains
  179 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 164
  time to evaluate  : 2.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  198 GLU
Chi-restraints excluded: chain A residue  584 TYR
Chi-restraints excluded: chain A residue  740 LEU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  214 LEU
Chi-restraints excluded: chain B residue  584 TYR
Chi-restraints excluded: chain B residue  668 LEU
Chi-restraints excluded: chain B residue  740 LEU
Chi-restraints excluded: chain C residue  147 GLN
Chi-restraints excluded: chain C residue  161 THR
Chi-restraints excluded: chain C residue  198 GLU
Chi-restraints excluded: chain C residue  668 LEU
Chi-restraints excluded: chain C residue  740 LEU
Chi-restraints excluded: chain C residue  883 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 194 optimal weight:    0.8980
   chunk 147 optimal weight:    0.5980
   chunk 101 optimal weight:    7.9990
   chunk 21 optimal weight:    6.9990
   chunk 93 optimal weight:    0.7980
   chunk 131 optimal weight:    0.8980
   chunk 197 optimal weight:    1.9990
   chunk 208 optimal weight:    0.0070
   chunk 103 optimal weight:    6.9990
   chunk 186 optimal weight:    1.9990
   chunk 56 optimal weight:    0.3980
   overall best weight:    0.5398

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

Flipped N/Q/H residues before XYZ refinement:
B 230 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.1580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  18336  Z= 0.136
  Angle     :  0.560  12.611  24915  Z= 0.270
  Chirality :  0.043   0.239   2820
  Planarity :  0.004   0.045   3153
  Dihedral  :  5.619  57.658   2781
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  9.44 %
    Favored  : 89.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.18), residues: 2148
  helix:  1.77 (0.22), residues: 645
  sheet: -0.15 (0.25), residues: 429
  loop : -1.77 (0.17), residues: 1074

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 720 
 HIS   0.002   0.001   HIS A 867 
 PHE   0.020   0.001   PHE C 517 
 TYR   0.013   0.001   TYR C 688 
 ARG   0.002   0.000   ARG A 226 

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

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

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 171
  time to evaluate  : 1.885 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  198 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7679 (pt0)
REVERT: A  248 ASN cc_start: 0.5999 (t0) cc_final: 0.5603 (t0)
REVERT: A  651 GLU cc_start: 0.6925 (tp30) cc_final: 0.6687 (tp30)
REVERT: B  248 ASN cc_start: 0.6119 (t0) cc_final: 0.5641 (t0)
REVERT: C  248 ASN cc_start: 0.6133 (t0) cc_final: 0.5578 (t0)
REVERT: C  315 ILE cc_start: 0.7041 (mm) cc_final: 0.6714 (mt)
  outliers start: 21
  outliers final: 11
  residues processed: 183
  average time/residue: 0.2941
  time to fit residues: 83.9092
Evaluate side-chains
  177 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 165
  time to evaluate  : 1.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 GLU
Chi-restraints excluded: chain A residue  232 PHE
Chi-restraints excluded: chain A residue  584 TYR
Chi-restraints excluded: chain A residue  740 LEU
Chi-restraints excluded: chain B residue  214 LEU
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  740 LEU
Chi-restraints excluded: chain C residue  198 GLU
Chi-restraints excluded: chain C residue  353 LEU
Chi-restraints excluded: chain C residue  668 LEU
Chi-restraints excluded: chain C residue  740 LEU
Chi-restraints excluded: chain C residue  883 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 173 optimal weight:    0.9980
   chunk 118 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   chunk 155 optimal weight:    8.9990
   chunk 86 optimal weight:    0.9990
   chunk 178 optimal weight:    5.9990
   chunk 144 optimal weight:    0.4980
   chunk 0 optimal weight:    6.9990
   chunk 106 optimal weight:   10.0000
   chunk 187 optimal weight:    6.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    1.4986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  18336  Z= 0.219
  Angle     :  0.588  10.519  24915  Z= 0.291
  Chirality :  0.045   0.236   2820
  Planarity :  0.004   0.054   3153
  Dihedral  :  5.739  59.150   2781
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 10.45 %
    Favored  : 88.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.18), residues: 2148
  helix:  1.70 (0.21), residues: 648
  sheet: -0.21 (0.25), residues: 429
  loop : -1.82 (0.17), residues: 1071

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 701 
 HIS   0.004   0.001   HIS C 624 
 PHE   0.018   0.002   PHE B 317 
 TYR   0.017   0.001   TYR C 707 
 ARG   0.002   0.000   ARG B 283 

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

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

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 166
  time to evaluate  : 2.226 
Fit side-chains
REVERT: A  230 GLN cc_start: 0.7176 (mt0) cc_final: 0.6945 (mt0)
REVERT: A  248 ASN cc_start: 0.6035 (t0) cc_final: 0.5656 (t0)
REVERT: A  298 MET cc_start: 0.5921 (tpt) cc_final: 0.5716 (tpt)
REVERT: A  579 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8275 (tt)
REVERT: B  248 ASN cc_start: 0.6075 (t0) cc_final: 0.5633 (t0)
REVERT: C  248 ASN cc_start: 0.6172 (t0) cc_final: 0.5620 (t0)
REVERT: C  315 ILE cc_start: 0.7057 (mm) cc_final: 0.6682 (mt)
REVERT: C  578 LYS cc_start: 0.6645 (ptpp) cc_final: 0.5566 (pttt)
  outliers start: 27
  outliers final: 17
  residues processed: 184
  average time/residue: 0.3028
  time to fit residues: 86.7479
Evaluate side-chains
  177 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 159
  time to evaluate  : 1.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  232 PHE
Chi-restraints excluded: chain A residue  579 LEU
Chi-restraints excluded: chain A residue  584 TYR
Chi-restraints excluded: chain A residue  740 LEU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  214 LEU
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  740 LEU
Chi-restraints excluded: chain B residue  771 ASP
Chi-restraints excluded: chain C residue  161 THR
Chi-restraints excluded: chain C residue  198 GLU
Chi-restraints excluded: chain C residue  353 LEU
Chi-restraints excluded: chain C residue  619 MET
Chi-restraints excluded: chain C residue  668 LEU
Chi-restraints excluded: chain C residue  740 LEU
Chi-restraints excluded: chain C residue  771 ASP
Chi-restraints excluded: chain C residue  883 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 188 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 122 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 208 optimal weight:    1.9990
   chunk 173 optimal weight:    5.9990
   chunk 96 optimal weight:    2.9990
   chunk 17 optimal weight:    9.9990
   chunk 69 optimal weight:    1.9990
   chunk 109 optimal weight:   10.0000
   overall best weight:    2.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.2149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  18336  Z= 0.314
  Angle     :  0.654   9.891  24915  Z= 0.326
  Chirality :  0.047   0.247   2820
  Planarity :  0.005   0.066   3153
  Dihedral  :  5.945  59.959   2778
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 10.45 %
    Favored  : 87.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (0.18), residues: 2148
  helix:  1.37 (0.21), residues: 669
  sheet: -0.37 (0.25), residues: 429
  loop : -2.00 (0.17), residues: 1050

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 701 
 HIS   0.005   0.001   HIS B 624 
 PHE   0.015   0.002   PHE C 517 
 TYR   0.019   0.002   TYR B 707 
 ARG   0.003   0.000   ARG A 652 

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

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

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 159
  time to evaluate  : 2.110 
Fit side-chains
REVERT: A  248 ASN cc_start: 0.6032 (t0) cc_final: 0.5753 (t0)
REVERT: B  230 GLN cc_start: 0.7223 (mt0) cc_final: 0.6936 (mt0)
REVERT: B  248 ASN cc_start: 0.6123 (t0) cc_final: 0.5735 (t0)
REVERT: B  309 ASN cc_start: 0.7266 (m110) cc_final: 0.6988 (m-40)
REVERT: B  315 ILE cc_start: 0.7093 (mm) cc_final: 0.6842 (mt)
REVERT: B  579 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8150 (tt)
REVERT: C  248 ASN cc_start: 0.6152 (t0) cc_final: 0.5614 (t0)
REVERT: C  315 ILE cc_start: 0.7072 (mm) cc_final: 0.6773 (mt)
REVERT: C  578 LYS cc_start: 0.6749 (ptpp) cc_final: 0.5748 (pttt)
REVERT: C  579 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8049 (tt)
  outliers start: 38
  outliers final: 23
  residues processed: 184
  average time/residue: 0.2957
  time to fit residues: 84.6249
Evaluate side-chains
  180 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 155
  time to evaluate  : 1.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  232 PHE
Chi-restraints excluded: chain A residue  584 TYR
Chi-restraints excluded: chain A residue  740 LEU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  214 LEU
Chi-restraints excluded: chain B residue  241 LYS
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  579 LEU
Chi-restraints excluded: chain B residue  622 THR
Chi-restraints excluded: chain B residue  668 LEU
Chi-restraints excluded: chain B residue  740 LEU
Chi-restraints excluded: chain B residue  765 LEU
Chi-restraints excluded: chain B residue  773 VAL
Chi-restraints excluded: chain C residue  161 THR
Chi-restraints excluded: chain C residue  198 GLU
Chi-restraints excluded: chain C residue  353 LEU
Chi-restraints excluded: chain C residue  579 LEU
Chi-restraints excluded: chain C residue  668 LEU
Chi-restraints excluded: chain C residue  740 LEU
Chi-restraints excluded: chain C residue  765 LEU
Chi-restraints excluded: chain C residue  771 ASP
Chi-restraints excluded: chain C residue  773 VAL
Chi-restraints excluded: chain C residue  840 VAL
Chi-restraints excluded: chain C residue  883 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 201 optimal weight:    0.9980
   chunk 23 optimal weight:    8.9990
   chunk 119 optimal weight:    3.9990
   chunk 152 optimal weight:    3.9990
   chunk 118 optimal weight:    0.7980
   chunk 175 optimal weight:    3.9990
   chunk 116 optimal weight:    0.7980
   chunk 208 optimal weight:    4.9990
   chunk 130 optimal weight:    0.7980
   chunk 126 optimal weight:    0.9990
   chunk 96 optimal weight:    3.9990
   overall best weight:    0.8782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
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      :  0.002   0.024  18336  Z= 0.156
  Angle     :  0.560  10.176  24915  Z= 0.274
  Chirality :  0.043   0.239   2820
  Planarity :  0.004   0.051   3153
  Dihedral  :  5.331  57.196   2778
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 11.82 %
    Favored  : 87.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.18), residues: 2148
  helix:  1.62 (0.21), residues: 666
  sheet: -0.27 (0.26), residues: 429
  loop : -1.89 (0.18), residues: 1053

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 701 
 HIS   0.003   0.001   HIS C 867 
 PHE   0.022   0.001   PHE C 517 
 TYR   0.014   0.001   TYR C 688 
 ARG   0.002   0.000   ARG A 226 

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

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

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 162
  time to evaluate  : 2.025 
Fit side-chains
REVERT: A  248 ASN cc_start: 0.6028 (t0) cc_final: 0.5680 (t0)
REVERT: B  248 ASN cc_start: 0.6131 (t0) cc_final: 0.5708 (t0)
REVERT: B  315 ILE cc_start: 0.7044 (mm) cc_final: 0.6815 (mt)
REVERT: C  248 ASN cc_start: 0.6186 (t0) cc_final: 0.5605 (t0)
REVERT: C  315 ILE cc_start: 0.7031 (mm) cc_final: 0.6691 (mt)
REVERT: C  578 LYS cc_start: 0.6688 (ptpp) cc_final: 0.5752 (pttt)
REVERT: C  579 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8148 (tt)
  outliers start: 17
  outliers final: 11
  residues processed: 175
  average time/residue: 0.2949
  time to fit residues: 80.6110
Evaluate side-chains
  168 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 156
  time to evaluate  : 2.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  232 PHE
Chi-restraints excluded: chain A residue  584 TYR
Chi-restraints excluded: chain A residue  740 LEU
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  668 LEU
Chi-restraints excluded: chain B residue  740 LEU
Chi-restraints excluded: chain B residue  771 ASP
Chi-restraints excluded: chain C residue  579 LEU
Chi-restraints excluded: chain C residue  668 LEU
Chi-restraints excluded: chain C residue  740 LEU
Chi-restraints excluded: chain C residue  883 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 128 optimal weight:    3.9990
   chunk 83 optimal weight:   20.0000
   chunk 124 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   chunk 40 optimal weight:    9.9990
   chunk 132 optimal weight:    0.9980
   chunk 141 optimal weight:    0.6980
   chunk 102 optimal weight:    0.1980
   chunk 19 optimal weight:    0.9980
   chunk 163 optimal weight:    0.7980
   chunk 189 optimal weight:    0.9990
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.2104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  18336  Z= 0.145
  Angle     :  0.553   9.756  24915  Z= 0.268
  Chirality :  0.043   0.236   2820
  Planarity :  0.004   0.048   3153
  Dihedral  :  4.958  57.861   2775
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 11.72 %
    Favored  : 87.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.50 (0.18), residues: 2148
  helix:  1.86 (0.22), residues: 648
  sheet: -0.22 (0.26), residues: 429
  loop : -1.86 (0.18), residues: 1071

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 701 
 HIS   0.004   0.001   HIS C 867 
 PHE   0.021   0.001   PHE A 517 
 TYR   0.012   0.001   TYR B 707 
 ARG   0.002   0.000   ARG A 297 

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

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

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 163
  time to evaluate  : 2.001 
Fit side-chains
   revert: symmetry clash
REVERT: A  142 MET cc_start: 0.7968 (mtt) cc_final: 0.7739 (mtt)
REVERT: A  248 ASN cc_start: 0.6093 (t0) cc_final: 0.5742 (t0)
REVERT: A  292 LEU cc_start: 0.1779 (OUTLIER) cc_final: 0.1421 (mm)
REVERT: A  899 GLU cc_start: 0.7599 (tp30) cc_final: 0.7394 (tp30)
REVERT: B  230 GLN cc_start: 0.7109 (mt0) cc_final: 0.6834 (mt0)
REVERT: B  248 ASN cc_start: 0.6185 (t0) cc_final: 0.5788 (t0)
REVERT: B  292 LEU cc_start: 0.1877 (OUTLIER) cc_final: 0.1659 (mm)
REVERT: C  248 ASN cc_start: 0.6187 (t0) cc_final: 0.5590 (t0)
REVERT: C  292 LEU cc_start: 0.1868 (OUTLIER) cc_final: 0.1556 (mm)
REVERT: C  579 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8170 (tt)
  outliers start: 23
  outliers final: 15
  residues processed: 180
  average time/residue: 0.2837
  time to fit residues: 80.9799
Evaluate side-chains
  178 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 159
  time to evaluate  : 2.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  584 TYR
Chi-restraints excluded: chain A residue  740 LEU
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  622 THR
Chi-restraints excluded: chain B residue  668 LEU
Chi-restraints excluded: chain B residue  740 LEU
Chi-restraints excluded: chain B residue  765 LEU
Chi-restraints excluded: chain C residue  292 LEU
Chi-restraints excluded: chain C residue  353 LEU
Chi-restraints excluded: chain C residue  579 LEU
Chi-restraints excluded: chain C residue  668 LEU
Chi-restraints excluded: chain C residue  740 LEU
Chi-restraints excluded: chain C residue  765 LEU
Chi-restraints excluded: chain C residue  771 ASP
Chi-restraints excluded: chain C residue  883 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 199 optimal weight:    0.7980
   chunk 181 optimal weight:    8.9990
   chunk 194 optimal weight:    0.2980
   chunk 116 optimal weight:    4.9990
   chunk 84 optimal weight:    0.9990
   chunk 152 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 175 optimal weight:    5.9990
   chunk 183 optimal weight:   10.0000
   chunk 193 optimal weight:    0.7980
   chunk 127 optimal weight:    3.9990
   overall best weight:    0.7582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021  18336  Z= 0.144
  Angle     :  0.544   9.681  24915  Z= 0.264
  Chirality :  0.043   0.236   2820
  Planarity :  0.004   0.048   3153
  Dihedral  :  4.784  57.569   2775
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 11.67 %
    Favored  : 87.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.18), residues: 2148
  helix:  1.90 (0.22), residues: 648
  sheet: -0.21 (0.26), residues: 429
  loop : -1.80 (0.18), residues: 1071

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 701 
 HIS   0.004   0.001   HIS C 867 
 PHE   0.020   0.001   PHE B 517 
 TYR   0.013   0.001   TYR A 707 
 ARG   0.001   0.000   ARG B 580 

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

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

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 165
  time to evaluate  : 2.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 ASN cc_start: 0.6099 (t0) cc_final: 0.5713 (t0)
REVERT: A  292 LEU cc_start: 0.1732 (OUTLIER) cc_final: 0.1498 (mm)
REVERT: B  248 ASN cc_start: 0.6304 (t0) cc_final: 0.5876 (t0)
REVERT: B  292 LEU cc_start: 0.1825 (OUTLIER) cc_final: 0.1612 (mm)
REVERT: C  248 ASN cc_start: 0.6169 (t0) cc_final: 0.5585 (t0)
REVERT: C  292 LEU cc_start: 0.1827 (OUTLIER) cc_final: 0.1524 (mm)
REVERT: C  388 LEU cc_start: 0.7014 (mp) cc_final: 0.6257 (tp)
REVERT: C  579 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8119 (tt)
  outliers start: 22
  outliers final: 15
  residues processed: 182
  average time/residue: 0.2846
  time to fit residues: 81.9391
Evaluate side-chains
  183 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 164
  time to evaluate  : 2.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  740 LEU
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  622 THR
Chi-restraints excluded: chain B residue  668 LEU
Chi-restraints excluded: chain B residue  740 LEU
Chi-restraints excluded: chain B residue  765 LEU
Chi-restraints excluded: chain B residue  771 ASP
Chi-restraints excluded: chain C residue  292 LEU
Chi-restraints excluded: chain C residue  353 LEU
Chi-restraints excluded: chain C residue  579 LEU
Chi-restraints excluded: chain C residue  668 LEU
Chi-restraints excluded: chain C residue  740 LEU
Chi-restraints excluded: chain C residue  765 LEU
Chi-restraints excluded: chain C residue  883 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 205 optimal weight:    5.9990
   chunk 125 optimal weight:    3.9990
   chunk 97 optimal weight:    7.9990
   chunk 142 optimal weight:    4.9990
   chunk 215 optimal weight:   10.0000
   chunk 198 optimal weight:    1.9990
   chunk 171 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 132 optimal weight:    1.9990
   chunk 105 optimal weight:    0.5980
   chunk 136 optimal weight:    2.9990
   overall best weight:    2.3188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.2338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  18336  Z= 0.297
  Angle     :  0.629   9.880  24915  Z= 0.313
  Chirality :  0.047   0.246   2820
  Planarity :  0.005   0.058   3153
  Dihedral  :  5.242  59.791   2775
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 11.87 %
    Favored  : 87.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.18), residues: 2148
  helix:  1.65 (0.21), residues: 648
  sheet: -0.39 (0.25), residues: 435
  loop : -1.95 (0.17), residues: 1065

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 701 
 HIS   0.006   0.001   HIS C 624 
 PHE   0.021   0.002   PHE A 517 
 TYR   0.019   0.001   TYR C 707 
 ARG   0.003   0.000   ARG A 283 

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

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

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4296 Ramachandran restraints generated.
    2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 160
  time to evaluate  : 2.049 
Fit side-chains
REVERT: A  248 ASN cc_start: 0.6055 (t0) cc_final: 0.5757 (t0)
REVERT: A  292 LEU cc_start: 0.1703 (OUTLIER) cc_final: 0.1341 (mm)
REVERT: A  309 ASN cc_start: 0.7187 (m110) cc_final: 0.6887 (m-40)
REVERT: B  248 ASN cc_start: 0.6257 (t0) cc_final: 0.5880 (t0)
REVERT: B  292 LEU cc_start: 0.1852 (OUTLIER) cc_final: 0.1615 (mm)
REVERT: B  309 ASN cc_start: 0.7246 (m110) cc_final: 0.6942 (m-40)
REVERT: C  248 ASN cc_start: 0.6240 (t0) cc_final: 0.5663 (t0)
REVERT: C  292 LEU cc_start: 0.1836 (OUTLIER) cc_final: 0.1522 (mm)
REVERT: C  315 ILE cc_start: 0.7084 (mm) cc_final: 0.6674 (mt)
REVERT: C  579 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8146 (tt)
  outliers start: 20
  outliers final: 15
  residues processed: 177
  average time/residue: 0.3014
  time to fit residues: 84.7067
Evaluate side-chains
  178 residues out of total 2004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 159
  time to evaluate  : 2.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  740 LEU
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain B residue  214 LEU
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  622 THR
Chi-restraints excluded: chain B residue  668 LEU
Chi-restraints excluded: chain B residue  740 LEU
Chi-restraints excluded: chain B residue  765 LEU
Chi-restraints excluded: chain C residue  292 LEU
Chi-restraints excluded: chain C residue  353 LEU
Chi-restraints excluded: chain C residue  579 LEU
Chi-restraints excluded: chain C residue  668 LEU
Chi-restraints excluded: chain C residue  740 LEU
Chi-restraints excluded: chain C residue  765 LEU
Chi-restraints excluded: chain C residue  883 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 216
   random chunks:
   chunk 182 optimal weight:    0.2980
   chunk 52 optimal weight:    0.7980
   chunk 158 optimal weight:    7.9990
   chunk 25 optimal weight:    8.9990
   chunk 47 optimal weight:    0.9990
   chunk 171 optimal weight:    6.9990
   chunk 71 optimal weight:    9.9990
   chunk 176 optimal weight:    5.9990
   chunk 21 optimal weight:    8.9990
   chunk 31 optimal weight:    9.9990
   chunk 150 optimal weight:    0.5980
   overall best weight:    1.7384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.191765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.117151 restraints weight = 23371.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 2.71
r_work: 0.3010 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.2364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  18336  Z= 0.236
  Angle     :  0.599   9.855  24915  Z= 0.296
  Chirality :  0.045   0.242   2820
  Planarity :  0.005   0.057   3153
  Dihedral  :  5.191  59.390   2775
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 11.87 %
    Favored  : 87.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.18), residues: 2148
  helix:  1.65 (0.21), residues: 648
  sheet: -0.33 (0.26), residues: 429
  loop : -1.93 (0.17), residues: 1071

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 701 
 HIS   0.004   0.001   HIS C 624 
 PHE   0.021   0.002   PHE A 517 
 TYR   0.016   0.001   TYR C 707 
 ARG   0.003   0.000   ARG B 652 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3541.24 seconds
wall clock time: 66 minutes 13.60 seconds (3973.60 seconds total)