Starting phenix.real_space_refine
on Wed Mar  4 05:42:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6n52_0346/03_2026/6n52_0346.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6n52_0346/03_2026/6n52_0346.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6n52_0346/03_2026/6n52_0346.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6n52_0346/03_2026/6n52_0346.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6n52_0346/03_2026/6n52_0346.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6n52_0346/03_2026/6n52_0346.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S     108      5.16       5
     C    7096      2.51       5
     N    1878      2.21       5
     O    2026      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11108
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5526
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 774, 5526
          Classifications: {'peptide': 774}
          Incomplete info: {'truncation_to_alanine': 163}
          Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 740}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 598
          Unresolved non-hydrogen angles: 743
          Unresolved non-hydrogen dihedrals: 494
          Unresolved non-hydrogen chiralities: 46
          Planarities with less than four sites: {'HIS:plan': 2, 'ASP:plan': 14, 'GLU:plan': 20, 'ARG:plan': 10, 'ASN:plan1': 8, 'PHE:plan': 6, 'GLN:plan1': 8, 'TYR:plan': 6, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 325
    Chain: "B"
      Number of atoms: 5526
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 774, 5526
          Classifications: {'peptide': 774}
          Incomplete info: {'truncation_to_alanine': 163}
          Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 740}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 598
          Unresolved non-hydrogen angles: 743
          Unresolved non-hydrogen dihedrals: 494
          Unresolved non-hydrogen chiralities: 46
          Planarities with less than four sites: {'HIS:plan': 2, 'ASP:plan': 14, 'GLU:plan': 20, 'ARG:plan': 10, 'ASN:plan1': 8, 'PHE:plan': 6, 'GLN:plan1': 8, 'TYR:plan': 6, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 325
    Chain: "A"
      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: "B"
      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
  Time building chain proxies: 2.98, per 1000 atoms: 0.27
  Number of scatterers: 11108
  At special positions: 0
  Unit cell: (117.66, 79.5, 183.38, 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    2026      8.00
     N    1878      7.00
     C    7096      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=20, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  57 " - pdb=" SG  CYS A  99 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 241 " - pdb=" SG  CYS A 530 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 276 " - pdb=" SG  CYS A 278 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 365 " - pdb=" SG  CYS A 381 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 419 " - pdb=" SG  CYS A 426 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 511 " - pdb=" SG  CYS A 531 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 515 " - pdb=" SG  CYS A 534 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 537 " - pdb=" SG  CYS A 549 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 552 " - pdb=" SG  CYS A 565 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 644 " - pdb=" SG  CYS A 733 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  57 " - pdb=" SG  CYS B  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 241 " - pdb=" SG  CYS B 530 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 276 " - pdb=" SG  CYS B 278 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 365 " - pdb=" SG  CYS B 381 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 419 " - pdb=" SG  CYS B 426 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 511 " - pdb=" SG  CYS B 531 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 515 " - pdb=" SG  CYS B 534 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 537 " - pdb=" SG  CYS B 549 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 552 " - pdb=" SG  CYS B 565 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 644 " - pdb=" SG  CYS B 733 " 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
    NAG-ASN
      " NAG A 901 " - " ASN A 210 "
      " NAG A 902 " - " ASN A 445 "
      " NAG B 901 " - " ASN B 210 "
      " NAG B 902 " - " ASN B 445 "
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 701.6 milliseconds
  

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2892

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 20 sheets defined
      47.8% alpha, 10.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 48 through 52
      removed outlier: 3.945A  pdb=" N   VAL A  52 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 81
    Processing helix  chain 'A' and resid 101 through 122
    Processing helix  chain 'A' and resid 151 through 163
      removed outlier: 4.120A  pdb=" N   GLN A 157 " --> pdb=" O   SER A 153 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   ASN A 160 " --> pdb=" O   ILE A 156 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LEU A 161 " --> pdb=" O   GLN A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 166
      No H-bonds generated for 'chain 'A' and resid 164 through 166'
    Processing helix  chain 'A' and resid 176 through 181
    Processing helix  chain 'A' and resid 195 through 210
      removed outlier: 3.706A  pdb=" N   VAL A 206 " --> pdb=" O   MET A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 236
      removed outlier: 3.645A  pdb=" N   SER A 226 " --> pdb=" O   ASN A 222 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   GLY A 227 " --> pdb=" O   TYR A 223 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ALA A 236 " --> pdb=" O   LYS A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 266
    Processing helix  chain 'A' and resid 279 through 294
    Processing helix  chain 'A' and resid 305 through 308
      removed outlier: 3.609A  pdb=" N   ALA A 308 " --> pdb=" O   ASP A 305 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 305 through 308'
    Processing helix  chain 'A' and resid 334 through 343
      removed outlier: 3.540A  pdb=" N   ASP A 338 " --> pdb=" O   VAL A 334 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   LYS A 343 " --> pdb=" O   ASP A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 363
      removed outlier: 3.729A  pdb=" N   PHE A 363 " --> pdb=" O   TRP A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 419
      removed outlier: 3.708A  pdb=" N   VAL A 400 " --> pdb=" O   LYS A 396 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ILE A 401 " --> pdb=" O   MET A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 430
    Processing helix  chain 'A' and resid 434 through 443
      removed outlier: 3.819A  pdb=" N   LYS A 443 " --> pdb=" O   GLU A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 598
      removed outlier: 3.988A  pdb=" N   ALA A 582 " --> pdb=" O   PRO A 578 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   ALA A 583 " --> pdb=" O   GLU A 579 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LEU A 595 " --> pdb=" O   LEU A 591 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 612
      removed outlier: 3.689A  pdb=" N   SER A 612 " --> pdb=" O   PRO A 608 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 616 through 636
      removed outlier: 4.044A  pdb=" N   THR A 632 " --> pdb=" O   GLY A 628 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   PHE A 633 " --> pdb=" O   TYR A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 642 through 668
      removed outlier: 4.082A  pdb=" N   GLY A 650 " --> pdb=" O   LEU A 646 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   ILE A 651 " --> pdb=" O   GLN A 647 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   GLY A 652 " --> pdb=" O   ARG A 648 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   LEU A 653 " --> pdb=" O   ILE A 649 " (cutoff:3.500A)
      Proline residue:  A 655  - end of helix
      removed outlier: 3.663A  pdb=" N   SER A 658 " --> pdb=" O   SER A 654 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   ALA A 661 " --> pdb=" O   MET A 657 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   LEU A 662 " --> pdb=" O   SER A 658 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ARG A 668 " --> pdb=" O   THR A 664 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 692 through 715
      removed outlier: 4.243A  pdb=" N   ALA A 697 " --> pdb=" O   GLN A 693 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   PHE A 698 " --> pdb=" O   LEU A 694 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   GLN A 704 " --> pdb=" O   LEU A 700 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   MET A 714 " --> pdb=" O   ALA A 710 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 736 through 761
      Proline residue:  A 743  - end of helix
      removed outlier: 3.594A  pdb=" N   TYR A 746 " --> pdb=" O   THR A 742 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   SER A 753 " --> pdb=" O   LEU A 749 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 765 through 794
      removed outlier: 6.264A  pdb=" N   ALA A 771 " --> pdb=" O   ASN A 767 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   LYS A 772 " --> pdb=" O   PHE A 768 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   TYR A 773 " --> pdb=" O   ASN A 769 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   THR A 780 " --> pdb=" O   PHE A 776 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ILE A 783 " --> pdb=" O   TYR A 779 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   LEU A 786 " --> pdb=" O   CYS A 782 " (cutoff:3.500A)
      removed outlier: 4.748A  pdb=" N   VAL A 789 " --> pdb=" O   TRP A 785 " (cutoff:3.500A)
      Proline residue:  A 790  - end of helix
    Processing helix  chain 'A' and resid 799 through 816
      removed outlier: 3.757A  pdb=" N   VAL A 806 " --> pdb=" O   MET A 802 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   SER A 807 " --> pdb=" O   CYS A 803 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 828 through 832
      removed outlier: 3.698A  pdb=" N   ARG A 831 " --> pdb=" O   LYS A 828 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ASN A 832 " --> pdb=" O   PRO A 829 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 828 through 832'
    Processing helix  chain 'B' and resid 48 through 52
      removed outlier: 3.944A  pdb=" N   VAL B  52 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 81
    Processing helix  chain 'B' and resid 101 through 122
    Processing helix  chain 'B' and resid 151 through 163
      removed outlier: 4.119A  pdb=" N   GLN B 157 " --> pdb=" O   SER B 153 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   ASN B 160 " --> pdb=" O   ILE B 156 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   LEU B 161 " --> pdb=" O   GLN B 157 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 166
      No H-bonds generated for 'chain 'B' and resid 164 through 166'
    Processing helix  chain 'B' and resid 176 through 181
    Processing helix  chain 'B' and resid 195 through 210
      removed outlier: 3.707A  pdb=" N   VAL B 206 " --> pdb=" O   MET B 202 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 236
      removed outlier: 3.644A  pdb=" N   SER B 226 " --> pdb=" O   ASN B 222 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   GLY B 227 " --> pdb=" O   TYR B 223 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ALA B 236 " --> pdb=" O   LYS B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 266
    Processing helix  chain 'B' and resid 279 through 294
    Processing helix  chain 'B' and resid 305 through 308
      removed outlier: 3.609A  pdb=" N   ALA B 308 " --> pdb=" O   ASP B 305 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 305 through 308'
    Processing helix  chain 'B' and resid 334 through 343
      removed outlier: 3.541A  pdb=" N   ASP B 338 " --> pdb=" O   VAL B 334 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   LYS B 343 " --> pdb=" O   ASP B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 354 through 363
      removed outlier: 3.729A  pdb=" N   PHE B 363 " --> pdb=" O   TRP B 359 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 419
      removed outlier: 3.707A  pdb=" N   VAL B 400 " --> pdb=" O   LYS B 396 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ILE B 401 " --> pdb=" O   MET B 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 426 through 430
    Processing helix  chain 'B' and resid 434 through 443
      removed outlier: 3.818A  pdb=" N   LYS B 443 " --> pdb=" O   GLU B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 577 through 598
      removed outlier: 3.988A  pdb=" N   ALA B 582 " --> pdb=" O   PRO B 578 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   ALA B 583 " --> pdb=" O   GLU B 579 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   LEU B 595 " --> pdb=" O   LEU B 591 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 607 through 612
      removed outlier: 3.689A  pdb=" N   SER B 612 " --> pdb=" O   PRO B 608 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 616 through 636
      removed outlier: 4.045A  pdb=" N   THR B 632 " --> pdb=" O   GLY B 628 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   PHE B 633 " --> pdb=" O   TYR B 629 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 642 through 668
      removed outlier: 4.082A  pdb=" N   GLY B 650 " --> pdb=" O   LEU B 646 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   ILE B 651 " --> pdb=" O   GLN B 647 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   GLY B 652 " --> pdb=" O   ARG B 648 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   LEU B 653 " --> pdb=" O   ILE B 649 " (cutoff:3.500A)
      Proline residue:  B 655  - end of helix
      removed outlier: 3.664A  pdb=" N   SER B 658 " --> pdb=" O   SER B 654 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   ALA B 661 " --> pdb=" O   MET B 657 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   LEU B 662 " --> pdb=" O   SER B 658 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ARG B 668 " --> pdb=" O   THR B 664 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 692 through 715
      removed outlier: 4.244A  pdb=" N   ALA B 697 " --> pdb=" O   GLN B 693 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   PHE B 698 " --> pdb=" O   LEU B 694 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   GLN B 704 " --> pdb=" O   LEU B 700 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   MET B 714 " --> pdb=" O   ALA B 710 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 736 through 761
      Proline residue:  B 743  - end of helix
      removed outlier: 3.595A  pdb=" N   TYR B 746 " --> pdb=" O   THR B 742 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   SER B 753 " --> pdb=" O   LEU B 749 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 765 through 794
      removed outlier: 6.265A  pdb=" N   ALA B 771 " --> pdb=" O   ASN B 767 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   LYS B 772 " --> pdb=" O   PHE B 768 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   TYR B 773 " --> pdb=" O   ASN B 769 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   THR B 780 " --> pdb=" O   PHE B 776 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ILE B 783 " --> pdb=" O   TYR B 779 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   LEU B 786 " --> pdb=" O   CYS B 782 " (cutoff:3.500A)
      removed outlier: 4.747A  pdb=" N   VAL B 789 " --> pdb=" O   TRP B 785 " (cutoff:3.500A)
      Proline residue:  B 790  - end of helix
    Processing helix  chain 'B' and resid 799 through 816
      removed outlier: 3.758A  pdb=" N   VAL B 806 " --> pdb=" O   MET B 802 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   SER B 807 " --> pdb=" O   CYS B 803 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 828 through 832
      removed outlier: 3.697A  pdb=" N   ARG B 831 " --> pdb=" O   LYS B 828 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ASN B 832 " --> pdb=" O   PRO B 829 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 828 through 832'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31
      removed outlier: 3.801A  pdb=" N   GLU A  94 " --> pdb=" O   ILE A  37 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   PHE A  41 " --> pdb=" O   ARG A  96 " (cutoff:3.500A)
      removed outlier: 7.407A  pdb=" N   ILE A  36 " --> pdb=" O   ILE A 143 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   GLY A 145 " --> pdb=" O   ILE A  36 " (cutoff:3.500A)
      removed outlier: 8.702A  pdb=" N   ILE A 170 " --> pdb=" O   VAL A 144 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   VAL A 146 " --> pdb=" O   ILE A 170 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 241 through 242
      removed outlier: 9.831A  pdb=" N   TYR A 246 " --> pdb=" O   VAL A 214 " (cutoff:3.500A)
      removed outlier: 8.315A  pdb=" N   ALA A 216 " --> pdb=" O   TYR A 246 " (cutoff:3.500A)
      removed outlier: 8.540A  pdb=" N   ILE A 248 " --> pdb=" O   ALA A 216 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   HIS A 218 " --> pdb=" O   ILE A 248 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 241 through 242
      removed outlier: 6.008A  pdb=" N   VAL A 273 " --> pdb=" O   TYR A 213 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   PHE A 277 " --> pdb=" O   VAL A 217 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   THR A 219 " --> pdb=" O   PHE A 277 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 329
      removed outlier: 3.582A  pdb=" N   TRP A 487 " --> pdb=" O   TYR A 466 " (cutoff:3.500A)
      removed outlier: 5.848A  pdb=" N   ASN A 470 " --> pdb=" O   ASN A 483 " (cutoff:3.500A)
      removed outlier: 5.264A  pdb=" N   ASN A 483 " --> pdb=" O   ASN A 470 " (cutoff:3.500A)
      removed outlier: 7.284A  pdb=" N   LYS A 472 " --> pdb=" O   TYR A 481 " (cutoff:3.500A)
      removed outlier: 6.035A  pdb=" N   TYR A 481 " --> pdb=" O   LYS A 472 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 366
    Processing sheet with id=AA6, first strand: chain 'A' and resid 445 through 447
      removed outlier: 3.686A  pdb=" N   PHE A 446 " --> pdb=" O   ILE A 454 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 520 through 521
    Processing sheet with id=AA8, first strand: chain 'A' and resid 541 through 543
    Processing sheet with id=AA9, first strand: chain 'A' and resid 556 through 557
    Processing sheet with id=AB1, first strand: chain 'A' and resid 719 through 720
    Processing sheet with id=AB2, first strand: chain 'B' and resid 29 through 31
      removed outlier: 3.801A  pdb=" N   GLU B  94 " --> pdb=" O   ILE B  37 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   PHE B  41 " --> pdb=" O   ARG B  96 " (cutoff:3.500A)
      removed outlier: 7.408A  pdb=" N   ILE B  36 " --> pdb=" O   ILE B 143 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   GLY B 145 " --> pdb=" O   ILE B  36 " (cutoff:3.500A)
      removed outlier: 8.702A  pdb=" N   ILE B 170 " --> pdb=" O   VAL B 144 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   VAL B 146 " --> pdb=" O   ILE B 170 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 241 through 242
      removed outlier: 9.831A  pdb=" N   TYR B 246 " --> pdb=" O   VAL B 214 " (cutoff:3.500A)
      removed outlier: 8.315A  pdb=" N   ALA B 216 " --> pdb=" O   TYR B 246 " (cutoff:3.500A)
      removed outlier: 8.541A  pdb=" N   ILE B 248 " --> pdb=" O   ALA B 216 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   HIS B 218 " --> pdb=" O   ILE B 248 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 241 through 242
      removed outlier: 6.008A  pdb=" N   VAL B 273 " --> pdb=" O   TYR B 213 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   PHE B 277 " --> pdb=" O   VAL B 217 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   THR B 219 " --> pdb=" O   PHE B 277 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 325 through 329
      removed outlier: 3.582A  pdb=" N   TRP B 487 " --> pdb=" O   TYR B 466 " (cutoff:3.500A)
      removed outlier: 5.847A  pdb=" N   ASN B 470 " --> pdb=" O   ASN B 483 " (cutoff:3.500A)
      removed outlier: 5.264A  pdb=" N   ASN B 483 " --> pdb=" O   ASN B 470 " (cutoff:3.500A)
      removed outlier: 7.285A  pdb=" N   LYS B 472 " --> pdb=" O   TYR B 481 " (cutoff:3.500A)
      removed outlier: 6.034A  pdb=" N   TYR B 481 " --> pdb=" O   LYS B 472 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 365 through 366
    Processing sheet with id=AB7, first strand: chain 'B' and resid 445 through 447
      removed outlier: 3.685A  pdb=" N   PHE B 446 " --> pdb=" O   ILE B 454 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 520 through 521
    Processing sheet with id=AB9, first strand: chain 'B' and resid 541 through 543
    Processing sheet with id=AC1, first strand: chain 'B' and resid 556 through 557
    Processing sheet with id=AC2, first strand: chain 'B' and resid 719 through 720

    526 hydrogen bonds defined for protein.
    1512 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: 2.05

  Time building geometry restraints manager: 1.30 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: 3598
        1.34 -     1.46: 2698
        1.46 -     1.58: 4910
        1.58 -     1.70: 0
        1.70 -     1.82: 152
  Bond restraints: 11358
  Sorted by residual:
  bond pdb=" C   SER A 654 "
       pdb=" N   PRO A 655 "
    ideal  model  delta    sigma   weight residual
    1.337  1.365 -0.028 1.24e-02 6.50e+03 4.94e+00
  bond pdb=" C1  NAG B 901 "
       pdb=" O5  NAG B 901 "
    ideal  model  delta    sigma   weight residual
    1.406  1.450 -0.044 2.00e-02 2.50e+03 4.84e+00
  bond pdb=" C   SER B 654 "
       pdb=" N   PRO B 655 "
    ideal  model  delta    sigma   weight residual
    1.337  1.364 -0.027 1.24e-02 6.50e+03 4.82e+00
  bond pdb=" C1  NAG A 901 "
       pdb=" O5  NAG A 901 "
    ideal  model  delta    sigma   weight residual
    1.406  1.446 -0.040 2.00e-02 2.50e+03 4.02e+00
  bond pdb=" C1  NAG A 902 "
       pdb=" O5  NAG A 902 "
    ideal  model  delta    sigma   weight residual
    1.406  1.441 -0.035 2.00e-02 2.50e+03 3.01e+00
  ... (remaining 11353 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 15063
        1.75 -     3.50: 397
        3.50 -     5.26: 36
        5.26 -     7.01: 16
        7.01 -     8.76: 10
  Bond angle restraints: 15522
  Sorted by residual:
  angle pdb=" C   VAL A 499 "
        pdb=" N   TRP A 500 "
        pdb=" CA  TRP A 500 "
      ideal   model   delta    sigma   weight residual
     121.54  130.30   -8.76 1.91e+00 2.74e-01 2.10e+01
  angle pdb=" C   VAL B 499 "
        pdb=" N   TRP B 500 "
        pdb=" CA  TRP B 500 "
      ideal   model   delta    sigma   weight residual
     121.54  130.25   -8.71 1.91e+00 2.74e-01 2.08e+01
  angle pdb=" N   VAL B 191 "
        pdb=" CA  VAL B 191 "
        pdb=" C   VAL B 191 "
      ideal   model   delta    sigma   weight residual
     112.29  108.05    4.24 9.40e-01 1.13e+00 2.04e+01
  angle pdb=" N   VAL A 191 "
        pdb=" CA  VAL A 191 "
        pdb=" C   VAL A 191 "
      ideal   model   delta    sigma   weight residual
     112.29  108.10    4.19 9.40e-01 1.13e+00 1.99e+01
  angle pdb=" N   ILE B 824 "
        pdb=" CA  ILE B 824 "
        pdb=" C   ILE B 824 "
      ideal   model   delta    sigma   weight residual
     111.91  109.21    2.70 8.90e-01 1.26e+00 9.17e+00
  ... (remaining 15517 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.26: 6530
       15.26 -    30.53: 172
       30.53 -    45.79: 70
       45.79 -    61.06: 4
       61.06 -    76.32: 4
  Dihedral angle restraints: 6780
    sinusoidal: 2284
      harmonic: 4496
  Sorted by residual:
  dihedral pdb=" CB  CYS A 241 "
           pdb=" SG  CYS A 241 "
           pdb=" SG  CYS A 530 "
           pdb=" CB  CYS A 530 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -150.69   64.69     1      1.00e+01 1.00e-02 5.50e+01
  dihedral pdb=" CB  CYS B 241 "
           pdb=" SG  CYS B 241 "
           pdb=" SG  CYS B 530 "
           pdb=" CB  CYS B 530 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -150.69   64.69     1      1.00e+01 1.00e-02 5.50e+01
  dihedral pdb=" CA  PHE A 804 "
           pdb=" C   PHE A 804 "
           pdb=" N   SER A 805 "
           pdb=" CA  SER A 805 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.19  -22.81     0      5.00e+00 4.00e-02 2.08e+01
  ... (remaining 6777 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1078
       0.035 -    0.070: 494
       0.070 -    0.105: 184
       0.105 -    0.140: 55
       0.140 -    0.175: 9
  Chirality restraints: 1820
  Sorted by residual:
  chirality pdb=" CB  VAL A 610 "
            pdb=" CA  VAL A 610 "
            pdb=" CG1 VAL A 610 "
            pdb=" CG2 VAL A 610 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.17 2.00e-01 2.50e+01 7.62e-01
  chirality pdb=" CB  VAL B 610 "
            pdb=" CA  VAL B 610 "
            pdb=" CG1 VAL B 610 "
            pdb=" CG2 VAL B 610 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.17 2.00e-01 2.50e+01 7.59e-01
  chirality pdb=" CA  SER B 654 "
            pdb=" N   SER B 654 "
            pdb=" C   SER B 654 "
            pdb=" CB  SER B 654 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.28e-01
  ... (remaining 1817 not shown)

  Planarity restraints: 1996
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 577 "    0.034 5.00e-02 4.00e+02   5.14e-02 4.22e+00
        pdb=" N   PRO B 578 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO B 578 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B 578 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 577 "   -0.034 5.00e-02 4.00e+02   5.14e-02 4.22e+00
        pdb=" N   PRO A 578 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO A 578 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 578 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 779 "   -0.009 2.00e-02 2.50e+03   1.32e-02 3.48e+00
        pdb=" CG  TYR B 779 "    0.032 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 779 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 779 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 779 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 779 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 779 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B 779 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1993 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.84: 3682
        2.84 -     3.36: 10215
        3.36 -     3.87: 18278
        3.87 -     4.39: 19558
        4.39 -     4.90: 33371
  Nonbonded interactions: 85104
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 223 "
            pdb=" OD1 ASP B 305 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" OH  TYR A 223 "
            pdb=" OD1 ASP A 305 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" NE2 GLN A 163 "
            pdb=" O   LEU A 184 "
     model   vdw
     2.334 3.120
  nonbonded pdb=" NE2 GLN B 163 "
            pdb=" O   LEU B 184 "
     model   vdw
     2.335 3.120
  nonbonded pdb=" OG  SER B 176 "
            pdb=" OD1 ASP B 178 "
     model   vdw
     2.340 3.040
  ... (remaining 85099 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.750
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.370
  Find NCS groups from input model:        0.090
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
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      :  0.004   0.048  11382  Z= 0.183
  Angle     :  0.715  10.608  15574  Z= 0.401
  Chirality :  0.046   0.175   1820
  Planarity :  0.006   0.051   1992
  Dihedral  :  8.654  76.320   3828
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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 are not related in a simple way.
  whole: -4.16 (0.16), residues: 1536
  helix: -2.63 (0.14), residues: 688
  sheet: -2.65 (0.36), residues: 162
  loop : -2.82 (0.20), residues: 686

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 291 
 TYR   0.032   0.002   TYR B 779 
 PHE   0.027   0.002   PHE A 165 
 TRP   0.022   0.003   TRP A 307 
 HIS   0.007   0.001   HIS B 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (11358)
  covalent geometry    : angle       0.69852 (15522)
  SS BOND              : bond        0.00252 (   20)
  SS BOND              : angle       0.85633 (   40)
  hydrogen bonds       : bond        0.15758 (  524)
  hydrogen bonds       : angle       6.39049 ( 1512)
  link_NAG-ASN         : bond        0.00361 (    4)
  link_NAG-ASN         : angle       5.49700 (   12)

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

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

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  311 TYR cc_start: 0.8213 (p90) cc_final: 0.7929 (p90)
REVERT: A  778 MET cc_start: 0.8348 (mmm) cc_final: 0.7787 (tpp)
REVERT: A  802 MET cc_start: 0.9143 (ttm) cc_final: 0.8694 (ppp)
REVERT: B  442 MET cc_start: 0.8204 (tpp) cc_final: 0.7985 (tpt)
REVERT: B  778 MET cc_start: 0.8299 (mmm) cc_final: 0.7743 (tpp)
REVERT: B  802 MET cc_start: 0.9159 (ttm) cc_final: 0.8708 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.0851
  time to fit residues: 15.7268
Evaluate side-chains
  69 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:    9.9990
   chunk 130 optimal weight:    0.4980
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    8.9990
   chunk 77 optimal weight:    8.9990
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    0.6980
   chunk 149 optimal weight:   10.0000
   overall best weight:    3.8386

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

Flipped N/Q/H residues before XYZ refinement:
A 101 HIS
** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 218 HIS
A 704 GLN
B 101 HIS
** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 218 HIS
B 704 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.061714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.043148 restraints weight = 77934.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.044153 restraints weight = 43634.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.044859 restraints weight = 29938.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.045018 restraints weight = 23122.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.045547 restraints weight = 20725.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.2236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11382  Z= 0.191
  Angle     :  0.611  11.081  15574  Z= 0.314
  Chirality :  0.042   0.141   1820
  Planarity :  0.005   0.053   1992
  Dihedral  :  4.890  39.175   1734
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  6.05 %
    Favored  : 93.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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 are not related in a simple way.
  whole: -2.23 (0.20), residues: 1536
  helix: -0.73 (0.18), residues: 688
  sheet: -2.19 (0.36), residues: 186
  loop : -1.98 (0.23), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  78 
 TYR   0.014   0.001   TYR B 209 
 PHE   0.019   0.002   PHE B 165 
 TRP   0.011   0.002   TRP A 575 
 HIS   0.004   0.001   HIS A 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 (11358)
  covalent geometry    : angle       0.60274 (15522)
  SS BOND              : bond        0.00190 (   20)
  SS BOND              : angle       1.01003 (   40)
  hydrogen bonds       : bond        0.03065 (  524)
  hydrogen bonds       : angle       4.70865 ( 1512)
  link_NAG-ASN         : bond        0.00128 (    4)
  link_NAG-ASN         : angle       3.26299 (   12)

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

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

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.406 
Fit side-chains
REVERT: A  414 MET cc_start: 0.8867 (ttm) cc_final: 0.8442 (mtt)
REVERT: A  778 MET cc_start: 0.8250 (mmm) cc_final: 0.7506 (tmm)
REVERT: A  802 MET cc_start: 0.9220 (ttm) cc_final: 0.8863 (ppp)
REVERT: B  414 MET cc_start: 0.8915 (ttm) cc_final: 0.8524 (mtt)
REVERT: B  778 MET cc_start: 0.8213 (mmm) cc_final: 0.7730 (tpp)
REVERT: B  802 MET cc_start: 0.9224 (ttm) cc_final: 0.8865 (ppp)
  outliers start: 8
  outliers final: 2
  residues processed: 82
  average time/residue: 0.0799
  time to fit residues: 10.4421
Evaluate side-chains
  64 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 62
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain B residue  286 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 48 optimal weight:   30.0000
   chunk 22 optimal weight:   20.0000
   chunk 25 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0070
   chunk 103 optimal weight:   10.0000
   chunk 53 optimal weight:   30.0000
   chunk 79 optimal weight:    7.9990
   chunk 3 optimal weight:    0.0770
   chunk 29 optimal weight:    9.9990
   chunk 92 optimal weight:    0.8980
   chunk 135 optimal weight:    5.9990
   overall best weight:    1.5158

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

Flipped N/Q/H residues before XYZ refinement:
** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.062435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.043870 restraints weight = 77498.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.044870 restraints weight = 45345.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.045626 restraints weight = 29928.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.046056 restraints weight = 22560.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.046387 restraints weight = 19269.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.2546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  11382  Z= 0.104
  Angle     :  0.528   7.975  15574  Z= 0.266
  Chirality :  0.041   0.192   1820
  Planarity :  0.004   0.047   1992
  Dihedral  :  4.377  35.854   1734
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  6.05 %
    Favored  : 93.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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 are not related in a simple way.
  whole: -1.47 (0.21), residues: 1536
  helix:  0.16 (0.19), residues: 692
  sheet: -2.21 (0.34), residues: 208
  loop : -1.74 (0.25), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  78 
 TYR   0.008   0.001   TYR A 340 
 PHE   0.013   0.001   PHE A 165 
 TRP   0.009   0.001   TRP B 557 
 HIS   0.002   0.001   HIS B  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 (11358)
  covalent geometry    : angle       0.52113 (15522)
  SS BOND              : bond        0.00117 (   20)
  SS BOND              : angle       0.78900 (   40)
  hydrogen bonds       : bond        0.02733 (  524)
  hydrogen bonds       : angle       4.33704 ( 1512)
  link_NAG-ASN         : bond        0.00193 (    4)
  link_NAG-ASN         : angle       2.82557 (   12)

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

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

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.410 
Fit side-chains
REVERT: A  189 MET cc_start: 0.8398 (mmt) cc_final: 0.8081 (mmm)
REVERT: A  778 MET cc_start: 0.8292 (mmm) cc_final: 0.7538 (tmm)
REVERT: A  802 MET cc_start: 0.9265 (ttm) cc_final: 0.8889 (ppp)
REVERT: B   72 MET cc_start: 0.9350 (ttp) cc_final: 0.8818 (ppp)
REVERT: B  778 MET cc_start: 0.8279 (mmm) cc_final: 0.7472 (tmm)
REVERT: B  802 MET cc_start: 0.9254 (ttm) cc_final: 0.8895 (ppp)
  outliers start: 7
  outliers final: 2
  residues processed: 73
  average time/residue: 0.0768
  time to fit residues: 9.1566
Evaluate side-chains
  62 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 60
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain B residue  286 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 138 optimal weight:    5.9990
   chunk 1 optimal weight:   10.0000
   chunk 89 optimal weight:    3.9990
   chunk 5 optimal weight:    0.1980
   chunk 24 optimal weight:    5.9990
   chunk 153 optimal weight:   40.0000
   chunk 115 optimal weight:    9.9990
   chunk 39 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 44 optimal weight:    9.9990
   overall best weight:    2.8388

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

Flipped N/Q/H residues before XYZ refinement:
B 163 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.061547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.042841 restraints weight = 76992.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.043819 restraints weight = 45944.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.044548 restraints weight = 30753.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.044763 restraints weight = 23790.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.045290 restraints weight = 20745.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.2976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11382  Z= 0.140
  Angle     :  0.540   6.920  15574  Z= 0.274
  Chirality :  0.042   0.258   1820
  Planarity :  0.004   0.046   1992
  Dihedral  :  4.473  38.629   1734
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  6.35 %
    Favored  : 92.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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 are not related in a simple way.
  whole: -0.95 (0.22), residues: 1536
  helix:  0.59 (0.19), residues: 694
  sheet: -1.94 (0.36), residues: 188
  loop : -1.51 (0.25), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 310 
 TYR   0.007   0.001   TYR B 209 
 PHE   0.017   0.001   PHE B 165 
 TRP   0.008   0.001   TRP B 557 
 HIS   0.003   0.001   HIS A  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (11358)
  covalent geometry    : angle       0.53437 (15522)
  SS BOND              : bond        0.00112 (   20)
  SS BOND              : angle       0.65101 (   40)
  hydrogen bonds       : bond        0.02649 (  524)
  hydrogen bonds       : angle       4.42900 ( 1512)
  link_NAG-ASN         : bond        0.00173 (    4)
  link_NAG-ASN         : angle       2.86350 (   12)

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

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

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
REVERT: A  202 MET cc_start: 0.9144 (mmt) cc_final: 0.8861 (mmt)
REVERT: A  234 MET cc_start: 0.8805 (mtp) cc_final: 0.8562 (mtp)
REVERT: A  778 MET cc_start: 0.8258 (mmm) cc_final: 0.7547 (tmm)
REVERT: A  802 MET cc_start: 0.9269 (ttm) cc_final: 0.8920 (ppp)
REVERT: B   72 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.8896 (ppp)
REVERT: B  202 MET cc_start: 0.9130 (mmt) cc_final: 0.8846 (mmt)
REVERT: B  234 MET cc_start: 0.8808 (mtp) cc_final: 0.8591 (mtp)
REVERT: B  778 MET cc_start: 0.8200 (mmm) cc_final: 0.7532 (tmm)
REVERT: B  802 MET cc_start: 0.9272 (ttm) cc_final: 0.8926 (ppp)
  outliers start: 9
  outliers final: 2
  residues processed: 69
  average time/residue: 0.0882
  time to fit residues: 9.5090
Evaluate side-chains
  66 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 63
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain B residue   72 MET
Chi-restraints excluded: chain B residue  286 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 130 optimal weight:   40.0000
   chunk 87 optimal weight:    0.9980
   chunk 59 optimal weight:   20.0000
   chunk 105 optimal weight:   10.0000
   chunk 72 optimal weight:   20.0000
   chunk 0 optimal weight:   10.0000
   chunk 2 optimal weight:   10.0000
   chunk 35 optimal weight:    9.9990
   chunk 92 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 122 optimal weight:   10.0000
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.059516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.041088 restraints weight = 75424.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.042110 restraints weight = 42653.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.042786 restraints weight = 28748.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.042964 restraints weight = 22147.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.043365 restraints weight = 19645.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.3774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  11382  Z= 0.227
  Angle     :  0.632   8.131  15574  Z= 0.322
  Chirality :  0.043   0.134   1820
  Planarity :  0.004   0.047   1992
  Dihedral  :  5.012  43.710   1734
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  7.42 %
    Favored  : 91.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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 are not related in a simple way.
  whole: -0.88 (0.22), residues: 1536
  helix:  0.55 (0.19), residues: 698
  sheet: -1.99 (0.36), residues: 188
  loop : -1.34 (0.26), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 465 
 TYR   0.010   0.001   TYR A 340 
 PHE   0.017   0.002   PHE A 165 
 TRP   0.012   0.002   TRP B 354 
 HIS   0.005   0.001   HIS A  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00474 (11358)
  covalent geometry    : angle       0.62596 (15522)
  SS BOND              : bond        0.00199 (   20)
  SS BOND              : angle       0.64756 (   40)
  hydrogen bonds       : bond        0.03030 (  524)
  hydrogen bonds       : angle       4.74852 ( 1512)
  link_NAG-ASN         : bond        0.00191 (    4)
  link_NAG-ASN         : angle       3.27559 (   12)

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

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

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.369 
Fit side-chains
REVERT: A  202 MET cc_start: 0.9159 (mmt) cc_final: 0.8868 (mmt)
REVERT: A  469 MET cc_start: 0.8788 (mmm) cc_final: 0.8558 (tpp)
REVERT: A  778 MET cc_start: 0.8184 (mmm) cc_final: 0.7521 (tmm)
REVERT: A  802 MET cc_start: 0.9309 (ttm) cc_final: 0.8944 (tmm)
REVERT: B   72 MET cc_start: 0.9386 (ttp) cc_final: 0.8912 (ppp)
REVERT: B  202 MET cc_start: 0.9133 (mmt) cc_final: 0.8838 (mmt)
REVERT: B  469 MET cc_start: 0.8783 (mmm) cc_final: 0.8531 (tpp)
REVERT: B  778 MET cc_start: 0.8152 (mmm) cc_final: 0.7510 (tmm)
REVERT: B  802 MET cc_start: 0.9305 (ttm) cc_final: 0.8937 (tmm)
  outliers start: 6
  outliers final: 4
  residues processed: 68
  average time/residue: 0.0717
  time to fit residues: 8.1083
Evaluate side-chains
  63 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 59
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  744 LEU
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  744 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 78 optimal weight:   10.0000
   chunk 106 optimal weight:    5.9990
   chunk 100 optimal weight:    0.9980
   chunk 72 optimal weight:    7.9990
   chunk 131 optimal weight:    5.9990
   chunk 99 optimal weight:   10.0000
   chunk 26 optimal weight:    9.9990
   chunk 123 optimal weight:   10.0000
   chunk 49 optimal weight:    8.9990
   chunk 109 optimal weight:    0.5980
   chunk 145 optimal weight:    8.9990
   overall best weight:    4.3186

-------------------------------------------------------------------------------
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 = 0.3543 r_free = 0.3543 target = 0.059651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.041096 restraints weight = 75250.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.042130 restraints weight = 42622.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.042770 restraints weight = 28928.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.043248 restraints weight = 22408.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.043361 restraints weight = 18881.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.4051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11382  Z= 0.193
  Angle     :  0.609  12.432  15574  Z= 0.304
  Chirality :  0.042   0.134   1820
  Planarity :  0.004   0.046   1992
  Dihedral  :  4.809  40.235   1734
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  7.42 %
    Favored  : 91.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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 are not related in a simple way.
  whole: -0.85 (0.22), residues: 1536
  helix:  0.59 (0.19), residues: 710
  sheet: -2.15 (0.35), residues: 192
  loop : -1.30 (0.26), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 465 
 TYR   0.011   0.001   TYR A 340 
 PHE   0.015   0.002   PHE B 165 
 TRP   0.018   0.002   TRP A 500 
 HIS   0.004   0.001   HIS A  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (11358)
  covalent geometry    : angle       0.60282 (15522)
  SS BOND              : bond        0.00173 (   20)
  SS BOND              : angle       0.53813 (   40)
  hydrogen bonds       : bond        0.02885 (  524)
  hydrogen bonds       : angle       4.66944 ( 1512)
  link_NAG-ASN         : bond        0.00181 (    4)
  link_NAG-ASN         : angle       3.17310 (   12)

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

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

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.433 
Fit side-chains
REVERT: A  202 MET cc_start: 0.9223 (mmt) cc_final: 0.8937 (mmt)
REVERT: A  249 TYR cc_start: 0.8103 (t80) cc_final: 0.7703 (t80)
REVERT: A  469 MET cc_start: 0.8738 (mmm) cc_final: 0.8415 (mmm)
REVERT: A  778 MET cc_start: 0.8177 (mmm) cc_final: 0.7524 (tmm)
REVERT: A  802 MET cc_start: 0.9295 (ttm) cc_final: 0.8919 (tmm)
REVERT: A  818 PHE cc_start: 0.9268 (OUTLIER) cc_final: 0.8915 (m-80)
REVERT: B   72 MET cc_start: 0.9385 (OUTLIER) cc_final: 0.8918 (ppp)
REVERT: B  202 MET cc_start: 0.9212 (mmt) cc_final: 0.8922 (mmt)
REVERT: B  249 TYR cc_start: 0.8126 (t80) cc_final: 0.7741 (t80)
REVERT: B  469 MET cc_start: 0.8747 (mmm) cc_final: 0.8474 (mmm)
REVERT: B  778 MET cc_start: 0.8133 (mmm) cc_final: 0.7523 (tmm)
REVERT: B  802 MET cc_start: 0.9298 (ttm) cc_final: 0.8928 (tmm)
REVERT: B  818 PHE cc_start: 0.9240 (OUTLIER) cc_final: 0.8951 (m-80)
  outliers start: 10
  outliers final: 4
  residues processed: 68
  average time/residue: 0.0915
  time to fit residues: 9.9194
Evaluate side-chains
  63 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  744 LEU
Chi-restraints excluded: chain A residue  818 PHE
Chi-restraints excluded: chain B residue   72 MET
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  744 LEU
Chi-restraints excluded: chain B residue  818 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 153 optimal weight:   30.0000
   chunk 37 optimal weight:   20.0000
   chunk 143 optimal weight:    6.9990
   chunk 46 optimal weight:    8.9990
   chunk 44 optimal weight:    9.9990
   chunk 27 optimal weight:   20.0000
   chunk 17 optimal weight:    0.7980
   chunk 2 optimal weight:   10.0000
   chunk 56 optimal weight:   30.0000
   chunk 141 optimal weight:   30.0000
   chunk 74 optimal weight:   10.0000
   overall best weight:    7.3590

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

Flipped N/Q/H residues before XYZ refinement:
A 390 HIS
** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 390 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.057696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.039148 restraints weight = 76315.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.040058 restraints weight = 45342.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.040728 restraints weight = 30471.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.041043 restraints weight = 23530.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.041410 restraints weight = 20426.013|
|-----------------------------------------------------------------------------|
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.4802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.053  11382  Z= 0.320
  Angle     :  0.740  10.871  15574  Z= 0.376
  Chirality :  0.045   0.161   1820
  Planarity :  0.005   0.045   1992
  Dihedral  :  5.533  45.958   1734
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.16 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  8.40 %
    Favored  : 90.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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 are not related in a simple way.
  whole: -1.22 (0.22), residues: 1536
  helix:  0.27 (0.19), residues: 708
  sheet: -2.51 (0.35), residues: 174
  loop : -1.46 (0.26), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 465 
 TYR   0.010   0.002   TYR A 730 
 PHE   0.022   0.002   PHE A 363 
 TRP   0.015   0.002   TRP B 359 
 HIS   0.007   0.002   HIS A  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00665 (11358)
  covalent geometry    : angle       0.73321 (15522)
  SS BOND              : bond        0.00285 (   20)
  SS BOND              : angle       0.75143 (   40)
  hydrogen bonds       : bond        0.03333 (  524)
  hydrogen bonds       : angle       5.17490 ( 1512)
  link_NAG-ASN         : bond        0.00179 (    4)
  link_NAG-ASN         : angle       3.68491 (   12)

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

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

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.425 
Fit side-chains
REVERT: A  469 MET cc_start: 0.8742 (mmm) cc_final: 0.8342 (mmm)
REVERT: A  494 MET cc_start: 0.7662 (mmm) cc_final: 0.7324 (tpt)
REVERT: A  778 MET cc_start: 0.8233 (mmm) cc_final: 0.7403 (tpp)
REVERT: A  802 MET cc_start: 0.9330 (ttm) cc_final: 0.8959 (tmm)
REVERT: B   72 MET cc_start: 0.9321 (OUTLIER) cc_final: 0.9044 (ppp)
REVERT: B  202 MET cc_start: 0.9048 (mmt) cc_final: 0.8821 (mmt)
REVERT: B  469 MET cc_start: 0.8743 (mmm) cc_final: 0.8343 (mmm)
REVERT: B  494 MET cc_start: 0.7660 (mmm) cc_final: 0.7026 (tpp)
REVERT: B  778 MET cc_start: 0.8192 (mmm) cc_final: 0.7410 (tpp)
REVERT: B  802 MET cc_start: 0.9335 (ttm) cc_final: 0.8957 (tmm)
REVERT: B  818 PHE cc_start: 0.9327 (OUTLIER) cc_final: 0.8979 (m-80)
  outliers start: 7
  outliers final: 4
  residues processed: 62
  average time/residue: 0.0779
  time to fit residues: 7.9649
Evaluate side-chains
  60 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  744 LEU
Chi-restraints excluded: chain B residue   72 MET
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  744 LEU
Chi-restraints excluded: chain B residue  818 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 131 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 112 optimal weight:    9.9990
   chunk 149 optimal weight:   20.0000
   chunk 101 optimal weight:    1.9990
   chunk 133 optimal weight:   30.0000
   chunk 22 optimal weight:   10.0000
   chunk 122 optimal weight:    5.9990
   chunk 136 optimal weight:   30.0000
   chunk 140 optimal weight:   20.0000
   chunk 9 optimal weight:    7.9990
   overall best weight:    4.5990

-------------------------------------------------------------------------------
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 = 0.3511 r_free = 0.3511 target = 0.058876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.040234 restraints weight = 74339.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.041203 restraints weight = 43600.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.041946 restraints weight = 29670.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.042403 restraints weight = 22096.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.042608 restraints weight = 18880.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.4817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11382  Z= 0.206
  Angle     :  0.642  13.121  15574  Z= 0.320
  Chirality :  0.043   0.147   1820
  Planarity :  0.004   0.043   1992
  Dihedral  :  5.119  41.968   1734
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  8.50 %
    Favored  : 90.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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 are not related in a simple way.
  whole: -1.02 (0.22), residues: 1536
  helix:  0.49 (0.19), residues: 710
  sheet: -2.52 (0.32), residues: 210
  loop : -1.28 (0.27), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 465 
 TYR   0.012   0.001   TYR A 340 
 PHE   0.016   0.002   PHE B 165 
 TRP   0.013   0.002   TRP A 557 
 HIS   0.005   0.001   HIS A  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 (11358)
  covalent geometry    : angle       0.63529 (15522)
  SS BOND              : bond        0.00199 (   20)
  SS BOND              : angle       0.54302 (   40)
  hydrogen bonds       : bond        0.02948 (  524)
  hydrogen bonds       : angle       4.86581 ( 1512)
  link_NAG-ASN         : bond        0.00195 (    4)
  link_NAG-ASN         : angle       3.42245 (   12)

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

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

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.413 
Fit side-chains
REVERT: A  249 TYR cc_start: 0.8234 (t80) cc_final: 0.7821 (t80)
REVERT: A  494 MET cc_start: 0.7689 (mmm) cc_final: 0.7111 (tpp)
REVERT: A  720 MET cc_start: 0.9174 (ppp) cc_final: 0.8463 (pmm)
REVERT: A  778 MET cc_start: 0.8156 (mmm) cc_final: 0.7564 (tmm)
REVERT: A  802 MET cc_start: 0.9314 (ttm) cc_final: 0.8936 (tmm)
REVERT: B   72 MET cc_start: 0.9390 (OUTLIER) cc_final: 0.8972 (ppp)
REVERT: B  202 MET cc_start: 0.9207 (mmt) cc_final: 0.8962 (mmt)
REVERT: B  249 TYR cc_start: 0.8225 (t80) cc_final: 0.7821 (t80)
REVERT: B  429 MET cc_start: 0.8246 (mmt) cc_final: 0.8034 (mmt)
REVERT: B  494 MET cc_start: 0.7668 (mmm) cc_final: 0.7079 (tpp)
REVERT: B  720 MET cc_start: 0.9157 (ppp) cc_final: 0.8448 (pmm)
REVERT: B  778 MET cc_start: 0.8138 (mmm) cc_final: 0.7334 (tpp)
REVERT: B  802 MET cc_start: 0.9337 (ttm) cc_final: 0.8970 (tmm)
REVERT: B  818 PHE cc_start: 0.9314 (OUTLIER) cc_final: 0.8969 (m-80)
  outliers start: 6
  outliers final: 4
  residues processed: 61
  average time/residue: 0.0812
  time to fit residues: 8.1168
Evaluate side-chains
  62 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  744 LEU
Chi-restraints excluded: chain B residue   72 MET
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  744 LEU
Chi-restraints excluded: chain B residue  818 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 55 optimal weight:    5.9990
   chunk 88 optimal weight:    6.9990
   chunk 123 optimal weight:    5.9990
   chunk 148 optimal weight:   40.0000
   chunk 78 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 124 optimal weight:    7.9990
   chunk 11 optimal weight:    3.9990
   chunk 61 optimal weight:    9.9990
   chunk 141 optimal weight:    6.9990
   chunk 95 optimal weight:   10.0000
   overall best weight:    5.9990

-------------------------------------------------------------------------------
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 = 0.3492 r_free = 0.3492 target = 0.058053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.039542 restraints weight = 73915.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.040507 restraints weight = 43211.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.041204 restraints weight = 29329.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.041621 restraints weight = 22566.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.041732 restraints weight = 19143.542|
|-----------------------------------------------------------------------------|
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.5159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046  11382  Z= 0.265
  Angle     :  0.688   9.110  15574  Z= 0.347
  Chirality :  0.044   0.136   1820
  Planarity :  0.004   0.043   1992
  Dihedral  :  5.308  43.910   1734
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.16 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  8.50 %
    Favored  : 90.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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 are not related in a simple way.
  whole: -1.10 (0.22), residues: 1536
  helix:  0.44 (0.20), residues: 710
  sheet: -2.57 (0.32), residues: 210
  loop : -1.32 (0.27), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 465 
 TYR   0.010   0.001   TYR A 340 
 PHE   0.018   0.002   PHE B 363 
 TRP   0.012   0.002   TRP B 359 
 HIS   0.005   0.001   HIS A  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00556 (11358)
  covalent geometry    : angle       0.68126 (15522)
  SS BOND              : bond        0.00229 (   20)
  SS BOND              : angle       0.58707 (   40)
  hydrogen bonds       : bond        0.03106 (  524)
  hydrogen bonds       : angle       5.02428 ( 1512)
  link_NAG-ASN         : bond        0.00198 (    4)
  link_NAG-ASN         : angle       3.52108 (   12)

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

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

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.415 
Fit side-chains
REVERT: A  202 MET cc_start: 0.9011 (mmt) cc_final: 0.8755 (mmt)
REVERT: A  469 MET cc_start: 0.8432 (tpp) cc_final: 0.7760 (tpp)
REVERT: A  494 MET cc_start: 0.7747 (mmm) cc_final: 0.7237 (tpp)
REVERT: A  720 MET cc_start: 0.9056 (ppp) cc_final: 0.8266 (mpp)
REVERT: A  778 MET cc_start: 0.8155 (mmm) cc_final: 0.7316 (tpp)
REVERT: A  802 MET cc_start: 0.9364 (ttm) cc_final: 0.9023 (tmm)
REVERT: A  818 PHE cc_start: 0.9321 (OUTLIER) cc_final: 0.8878 (m-80)
REVERT: B   72 MET cc_start: 0.9311 (OUTLIER) cc_final: 0.8909 (ppp)
REVERT: B  202 MET cc_start: 0.9082 (mmt) cc_final: 0.8853 (mmt)
REVERT: B  494 MET cc_start: 0.7723 (mmm) cc_final: 0.7214 (tpp)
REVERT: B  720 MET cc_start: 0.9008 (ppp) cc_final: 0.8194 (mpp)
REVERT: B  778 MET cc_start: 0.8163 (mmm) cc_final: 0.7331 (tpp)
REVERT: B  802 MET cc_start: 0.9373 (ttm) cc_final: 0.9077 (tmm)
REVERT: B  818 PHE cc_start: 0.9367 (OUTLIER) cc_final: 0.8998 (m-80)
  outliers start: 9
  outliers final: 4
  residues processed: 64
  average time/residue: 0.0783
  time to fit residues: 8.2798
Evaluate side-chains
  62 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  744 LEU
Chi-restraints excluded: chain A residue  818 PHE
Chi-restraints excluded: chain B residue   72 MET
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  744 LEU
Chi-restraints excluded: chain B residue  818 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   chunk 120 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 41 optimal weight:    7.9990
   chunk 86 optimal weight:    9.9990
   chunk 62 optimal weight:    6.9990
   chunk 60 optimal weight:   30.0000
   chunk 135 optimal weight:    7.9990
   chunk 122 optimal weight:    9.9990
   overall best weight:    3.5990

-------------------------------------------------------------------------------
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 = 0.3519 r_free = 0.3519 target = 0.059256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.040707 restraints weight = 75045.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.041715 restraints weight = 43978.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.042282 restraints weight = 29377.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.042801 restraints weight = 23129.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.042969 restraints weight = 19293.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.5133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  11382  Z= 0.167
  Angle     :  0.622  11.408  15574  Z= 0.308
  Chirality :  0.042   0.135   1820
  Planarity :  0.004   0.041   1992
  Dihedral  :  4.922  40.476   1734
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  8.59 %
    Favored  : 90.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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 are not related in a simple way.
  whole: -0.81 (0.22), residues: 1536
  helix:  0.73 (0.20), residues: 706
  sheet: -2.52 (0.32), residues: 210
  loop : -1.19 (0.27), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 465 
 TYR   0.009   0.001   TYR A 340 
 PHE   0.015   0.001   PHE A 165 
 TRP   0.012   0.002   TRP A 557 
 HIS   0.003   0.001   HIS A  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (11358)
  covalent geometry    : angle       0.61615 (15522)
  SS BOND              : bond        0.00158 (   20)
  SS BOND              : angle       0.50982 (   40)
  hydrogen bonds       : bond        0.02827 (  524)
  hydrogen bonds       : angle       4.77507 ( 1512)
  link_NAG-ASN         : bond        0.00214 (    4)
  link_NAG-ASN         : angle       3.27046 (   12)

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

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

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3072 Ramachandran restraints generated.
    1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.459 
Fit side-chains
REVERT: A  202 MET cc_start: 0.9073 (mmt) cc_final: 0.8762 (mmt)
REVERT: A  249 TYR cc_start: 0.8156 (t80) cc_final: 0.7757 (t80)
REVERT: A  469 MET cc_start: 0.8407 (tpp) cc_final: 0.7709 (tpp)
REVERT: A  494 MET cc_start: 0.7786 (mmm) cc_final: 0.7277 (tpp)
REVERT: A  778 MET cc_start: 0.8074 (mmm) cc_final: 0.7251 (tpp)
REVERT: A  802 MET cc_start: 0.9363 (ttm) cc_final: 0.9041 (tmm)
REVERT: A  818 PHE cc_start: 0.9304 (OUTLIER) cc_final: 0.8864 (m-80)
REVERT: B   72 MET cc_start: 0.9397 (OUTLIER) cc_final: 0.8939 (ppp)
REVERT: B  202 MET cc_start: 0.9193 (mmt) cc_final: 0.8936 (mmt)
REVERT: B  249 TYR cc_start: 0.8178 (t80) cc_final: 0.7796 (t80)
REVERT: B  469 MET cc_start: 0.8422 (tpp) cc_final: 0.7726 (tpp)
REVERT: B  494 MET cc_start: 0.7753 (mmm) cc_final: 0.7220 (tpp)
REVERT: B  778 MET cc_start: 0.8062 (mmm) cc_final: 0.7241 (tpp)
REVERT: B  802 MET cc_start: 0.9363 (ttm) cc_final: 0.9052 (tmm)
REVERT: B  818 PHE cc_start: 0.9334 (OUTLIER) cc_final: 0.8967 (m-80)
  outliers start: 9
  outliers final: 4
  residues processed: 64
  average time/residue: 0.0839
  time to fit residues: 8.9322
Evaluate side-chains
  63 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  744 LEU
Chi-restraints excluded: chain A residue  818 PHE
Chi-restraints excluded: chain B residue   72 MET
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  744 LEU
Chi-restraints excluded: chain B residue  818 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 82 optimal weight:    6.9990
   chunk 73 optimal weight:    0.0270
   chunk 99 optimal weight:   20.0000
   chunk 75 optimal weight:   20.0000
   chunk 116 optimal weight:    3.9990
   chunk 78 optimal weight:    9.9990
   chunk 120 optimal weight:    9.9990
   chunk 25 optimal weight:    8.9990
   chunk 92 optimal weight:    0.9990
   chunk 140 optimal weight:    0.0000
   chunk 41 optimal weight:    9.9990
   overall best weight:    2.4048

-------------------------------------------------------------------------------
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 = 0.3536 r_free = 0.3536 target = 0.059983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.041555 restraints weight = 74458.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.042590 restraints weight = 43151.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.043352 restraints weight = 29093.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.043823 restraints weight = 21497.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.043911 restraints weight = 18249.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.5119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11382  Z= 0.124
  Angle     :  0.580  10.433  15574  Z= 0.286
  Chirality :  0.041   0.134   1820
  Planarity :  0.004   0.039   1992
  Dihedral  :  4.569  37.585   1734
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  8.50 %
    Favored  : 90.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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 are not related in a simple way.
  whole: -0.50 (0.23), residues: 1536
  helix:  1.14 (0.20), residues: 694
  sheet: -2.49 (0.32), residues: 210
  loop : -1.16 (0.27), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 465 
 TYR   0.009   0.001   TYR A 340 
 PHE   0.012   0.001   PHE B 601 
 TRP   0.010   0.001   TRP A 557 
 HIS   0.003   0.001   HIS A 391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (11358)
  covalent geometry    : angle       0.57528 (15522)
  SS BOND              : bond        0.00111 (   20)
  SS BOND              : angle       0.47604 (   40)
  hydrogen bonds       : bond        0.02541 (  524)
  hydrogen bonds       : angle       4.56561 ( 1512)
  link_NAG-ASN         : bond        0.00214 (    4)
  link_NAG-ASN         : angle       2.88588 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2000.73 seconds
wall clock time: 35 minutes 8.06 seconds (2108.06 seconds total)