Starting phenix.real_space_refine
on Sat Aug 23 10:25:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9c5z_45238/08_2025/9c5z_45238.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9c5z_45238/08_2025/9c5z_45238.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9c5z_45238/08_2025/9c5z_45238.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9c5z_45238/08_2025/9c5z_45238.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9c5z_45238/08_2025/9c5z_45238.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9c5z_45238/08_2025/9c5z_45238.cif"
  }
  resolution = 3.63
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.027
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      60      5.16       5
     C    7401      2.51       5
     N    1846      2.21       5
     O    2144      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11451
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 354, 2791
          Classifications: {'peptide': 354}
          Link IDs: {'PTRANS': 12, 'TRANS': 341}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2899
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 367, 2899
          Classifications: {'peptide': 367}
          Link IDs: {'PTRANS': 12, 'TRANS': 354}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2857
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 363, 2857
          Classifications: {'peptide': 363}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 12, 'TRANS': 350}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 10
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "D"
      Number of atoms: 2820
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 358, 2820
          Classifications: {'peptide': 358}
          Link IDs: {'PTRANS': 12, 'TRANS': 345}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    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
    Chain: "C"
      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: "D"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.52, per 1000 atoms: 0.22
  Number of scatterers: 11451
  At special positions: 0
  Unit cell: (120.84, 131.44, 121.9, 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      60     16.00
     O    2144      8.00
     N    1846      7.00
     C    7401      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS D 750 " - pdb=" SG  CYS D 804 " 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 A1001 " - " ASN A 546 "
      " NAG B1001 " - " ASN B 546 "
      " NAG B1002 " - " ASN B 751 "
      " NAG C1001 " - " ASN C 751 "
      " NAG C1002 " - " ASN C 546 "
      " NAG D1001 " - " ASN D 546 "
  Time building additional restraints: 0.87
  Conformation dependent library (CDL) restraints added in 400.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2648

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 16 sheets defined
      51.0% alpha, 6.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 461 through 475
    Processing helix  chain 'A' and resid 520 through 525
    Processing helix  chain 'A' and resid 560 through 582
    Processing helix  chain 'A' and resid 632 through 665
      removed outlier: 3.904A  pdb=" N   GLU A 665 " --> pdb=" O   VAL A 661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 677
      removed outlier: 3.546A  pdb=" N   LYS A 676 " --> pdb=" O   ASP A 672 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 690 through 696
      removed outlier: 3.752A  pdb=" N   LYS A 696 " --> pdb=" O   THR A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 699 through 712
    Processing helix  chain 'A' and resid 723 through 730
      removed outlier: 3.756A  pdb=" N   THR A 730 " --> pdb=" O   GLN A 726 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 739 through 749
    Processing helix  chain 'A' and resid 774 through 789
      removed outlier: 3.573A  pdb=" N   ILE A 778 " --> pdb=" O   TYR A 774 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 789 through 801
      removed outlier: 3.578A  pdb=" N   MET A 793 " --> pdb=" O   GLY A 789 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 802 through 804
      No H-bonds generated for 'chain 'A' and resid 802 through 804'
    Processing helix  chain 'A' and resid 821 through 834
      removed outlier: 3.585A  pdb=" N   SER A 834 " --> pdb=" O   GLY A 830 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 457
      No H-bonds generated for 'chain 'B' and resid 455 through 457'
    Processing helix  chain 'B' and resid 461 through 474
    Processing helix  chain 'B' and resid 502 through 507
    Processing helix  chain 'B' and resid 520 through 525
    Processing helix  chain 'B' and resid 550 through 557
      removed outlier: 4.169A  pdb=" N   PHE B 555 " --> pdb=" O   GLY B 551 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 560 through 584
    Processing helix  chain 'B' and resid 634 through 662
    Processing helix  chain 'B' and resid 670 through 677
      removed outlier: 3.537A  pdb=" N   GLN B 677 " --> pdb=" O   ASP B 673 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 688 through 695
    Processing helix  chain 'B' and resid 702 through 712
      removed outlier: 3.742A  pdb=" N   ARG B 712 " --> pdb=" O   PHE B 708 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 721 through 731
    Processing helix  chain 'B' and resid 739 through 749
    Processing helix  chain 'B' and resid 774 through 789
      removed outlier: 4.056A  pdb=" N   ILE B 780 " --> pdb=" O   ASP B 776 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 789 through 798
      removed outlier: 3.722A  pdb=" N   TRP B 798 " --> pdb=" O   MET B 794 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 821 through 842
      removed outlier: 3.916A  pdb=" N   ILE B 825 " --> pdb=" O   GLY B 821 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   PHE B 842 " --> pdb=" O   ALA B 838 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 454 through 457
      removed outlier: 4.038A  pdb=" N   ASP C 457 " --> pdb=" O   TYR C 454 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 454 through 457'
    Processing helix  chain 'C' and resid 461 through 474
    Processing helix  chain 'C' and resid 499 through 507
      removed outlier: 3.819A  pdb=" N   ARG C 503 " --> pdb=" O   ASN C 499 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ASP C 507 " --> pdb=" O   ARG C 503 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 520 through 527
      removed outlier: 3.997A  pdb=" N   VAL C 526 " --> pdb=" O   VAL C 522 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 553 through 557
    Processing helix  chain 'C' and resid 560 through 584
    Processing helix  chain 'C' and resid 631 through 665
      removed outlier: 3.649A  pdb=" N   GLU C 662 " --> pdb=" O   PHE C 658 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ARG C 663 " --> pdb=" O   LEU C 659 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 670 through 677
    Processing helix  chain 'C' and resid 691 through 697
    Processing helix  chain 'C' and resid 699 through 712
    Processing helix  chain 'C' and resid 720 through 731
    Processing helix  chain 'C' and resid 739 through 749
    Processing helix  chain 'C' and resid 773 through 789
    Processing helix  chain 'C' and resid 789 through 800
      removed outlier: 3.512A  pdb=" N   MET C 793 " --> pdb=" O   GLY C 789 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 822 through 836
      removed outlier: 3.814A  pdb=" N   VAL C 826 " --> pdb=" O   GLY C 822 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   PHE C 836 " --> pdb=" O   VAL C 832 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 461 through 474
    Processing helix  chain 'D' and resid 520 through 527
    Processing helix  chain 'D' and resid 553 through 557
      removed outlier: 3.710A  pdb=" N   LEU D 556 " --> pdb=" O   PHE D 553 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 560 through 580
    Processing helix  chain 'D' and resid 634 through 665
      removed outlier: 3.653A  pdb=" N   GLU D 665 " --> pdb=" O   VAL D 661 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 688 through 696
    Processing helix  chain 'D' and resid 701 through 712
    Processing helix  chain 'D' and resid 712 through 717
    Processing helix  chain 'D' and resid 720 through 731
    Processing helix  chain 'D' and resid 739 through 749
    Processing helix  chain 'D' and resid 773 through 787
      removed outlier: 3.860A  pdb=" N   LYS D 777 " --> pdb=" O   PRO D 773 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 790 through 800
      removed outlier: 3.635A  pdb=" N   MET D 794 " --> pdb=" O   LYS D 790 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 816 through 841
      removed outlier: 5.964A  pdb=" N   GLY D 822 " --> pdb=" O   GLN D 818 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   ILE D 823 " --> pdb=" O   ASN D 819 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   PHE D 824 " --> pdb=" O   ILE D 820 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   GLU D 841 " --> pdb=" O   VAL D 837 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 436
      removed outlier: 6.801A  pdb=" N   VAL A 435 " --> pdb=" O   ARG A 481 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 535 through 536
    Processing sheet with id=AA3, first strand: chain 'A' and resid 681 through 683
      removed outlier: 8.916A  pdb=" N   TYR A 733 " --> pdb=" O   ARG A 543 " (cutoff:3.500A)
      removed outlier: 4.906A  pdb=" N   ARG A 543 " --> pdb=" O   TYR A 733 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   PHE A 735 " --> pdb=" O   LEU A 541 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 433 through 437
    Processing sheet with id=AA5, first strand: chain 'B' and resid 445 through 446
    Processing sheet with id=AA6, first strand: chain 'B' and resid 527 through 529
    Processing sheet with id=AA7, first strand: chain 'B' and resid 734 through 738
    Processing sheet with id=AA8, first strand: chain 'B' and resid 684 through 685
      removed outlier: 6.107A  pdb=" N   ALA B 684 " --> pdb=" O   VAL B 718 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'C' and resid 433 through 435
    Processing sheet with id=AB1, first strand: chain 'C' and resid 445 through 446
    Processing sheet with id=AB2, first strand: chain 'C' and resid 514 through 515
      removed outlier: 4.187A  pdb=" N   ALA C 515 " --> pdb=" O   GLY C 765 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   GLY C 765 " --> pdb=" O   ALA C 515 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 735 through 738
    Processing sheet with id=AB4, first strand: chain 'D' and resid 479 through 482
      removed outlier: 6.325A  pdb=" N   ILE D 434 " --> pdb=" O   LEU D 512 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 445 through 446
    Processing sheet with id=AB6, first strand: chain 'D' and resid 534 through 536
    Processing sheet with id=AB7, first strand: chain 'D' and resid 681 through 684
      removed outlier: 6.813A  pdb=" N   GLU D 681 " --> pdb=" O   ALA D 734 " (cutoff:3.500A)
      removed outlier: 8.404A  pdb=" N   LEU D 736 " --> pdb=" O   GLU D 681 " (cutoff:3.500A)
      removed outlier: 7.229A  pdb=" N   GLY D 683 " --> pdb=" O   LEU D 736 " (cutoff:3.500A)
      removed outlier: 9.418A  pdb=" N   GLU D 738 " --> pdb=" O   GLY D 683 " (cutoff:3.500A)
      removed outlier: 8.007A  pdb=" N   TYR D 733 " --> pdb=" O   ARG D 543 " (cutoff:3.500A)
      removed outlier: 4.738A  pdb=" N   ARG D 543 " --> pdb=" O   TYR D 733 " (cutoff:3.500A)

    541 hydrogen bonds defined for protein.
    1590 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: 1.73

  Time building geometry restraints manager: 1.21 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: 3595
        1.34 -     1.46: 2800
        1.46 -     1.58: 5189
        1.58 -     1.70: 0
        1.70 -     1.82: 104
  Bond restraints: 11688
  Sorted by residual:
  bond pdb=" C1  NAG B1002 "
       pdb=" O5  NAG B1002 "
    ideal  model  delta    sigma   weight residual
    1.406  1.496 -0.090 2.00e-02 2.50e+03 2.01e+01
  bond pdb=" N   MET B 664 "
       pdb=" CA  MET B 664 "
    ideal  model  delta    sigma   weight residual
    1.456  1.484 -0.028 1.22e-02 6.72e+03 5.20e+00
  bond pdb=" N   MET D 664 "
       pdb=" CA  MET D 664 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.19e-02 7.06e+03 5.19e+00
  bond pdb=" C1  NAG C1001 "
       pdb=" O5  NAG C1001 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 2.01e+00
  bond pdb=" C1  NAG B1001 "
       pdb=" O5  NAG B1001 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.92e+00
  ... (remaining 11683 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.70: 15480
        1.70 -     3.40: 276
        3.40 -     5.10: 40
        5.10 -     6.80: 13
        6.80 -     8.50: 8
  Bond angle restraints: 15817
  Sorted by residual:
  angle pdb=" CB  MET B 793 "
        pdb=" CG  MET B 793 "
        pdb=" SD  MET B 793 "
      ideal   model   delta    sigma   weight residual
     112.70  121.20   -8.50 3.00e+00 1.11e-01 8.03e+00
  angle pdb=" C   GLN D 677 "
        pdb=" N   THR D 678 "
        pdb=" CA  THR D 678 "
      ideal   model   delta    sigma   weight residual
     121.54  126.67   -5.13 1.91e+00 2.74e-01 7.20e+00
  angle pdb=" N   MET D 664 "
        pdb=" CA  MET D 664 "
        pdb=" C   MET D 664 "
      ideal   model   delta    sigma   weight residual
     111.07  108.26    2.81 1.07e+00 8.73e-01 6.91e+00
  angle pdb=" CA  MET D 664 "
        pdb=" C   MET D 664 "
        pdb=" O   MET D 664 "
      ideal   model   delta    sigma   weight residual
     120.82  118.19    2.63 1.05e+00 9.07e-01 6.26e+00
  angle pdb=" CA  MET B 664 "
        pdb=" C   MET B 664 "
        pdb=" O   MET B 664 "
      ideal   model   delta    sigma   weight residual
     121.16  118.45    2.71 1.12e+00 7.97e-01 5.84e+00
  ... (remaining 15812 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.41: 6483
       23.41 -    46.82: 438
       46.82 -    70.22: 50
       70.22 -    93.63: 16
       93.63 -   117.04: 23
  Dihedral angle restraints: 7010
    sinusoidal: 2869
      harmonic: 4141
  Sorted by residual:
  dihedral pdb=" CB  CYS D 750 "
           pdb=" SG  CYS D 750 "
           pdb=" SG  CYS D 804 "
           pdb=" CB  CYS D 804 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -172.49   86.49     1      1.00e+01 1.00e-02 9.01e+01
  dihedral pdb=" CA  MET A 737 "
           pdb=" C   MET A 737 "
           pdb=" N   GLU A 738 "
           pdb=" CA  GLU A 738 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.45  -22.55     0      5.00e+00 4.00e-02 2.03e+01
  dihedral pdb=" C2  NAG B1002 "
           pdb=" C1  NAG B1002 "
           pdb=" O5  NAG B1002 "
           pdb=" C5  NAG B1002 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -62.96   54.08 -117.04     1      3.00e+01 1.11e-03 1.55e+01
  ... (remaining 7007 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 1652
       0.076 -    0.152: 151
       0.152 -    0.228: 5
       0.228 -    0.305: 1
       0.305 -    0.381: 1
  Chirality restraints: 1810
  Sorted by residual:
  chirality pdb=" C1  NAG B1002 "
            pdb=" ND2 ASN B 751 "
            pdb=" C2  NAG B1002 "
            pdb=" O5  NAG B1002 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.02   -0.38 2.00e-01 2.50e+01 3.63e+00
  chirality pdb=" C1  NAG C1002 "
            pdb=" ND2 ASN C 546 "
            pdb=" C2  NAG C1002 "
            pdb=" O5  NAG C1002 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.10   -0.30 2.00e-01 2.50e+01 2.29e+00
  chirality pdb=" CB  ILE B 820 "
            pdb=" CA  ILE B 820 "
            pdb=" CG1 ILE B 820 "
            pdb=" CG2 ILE B 820 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.97e-01
  ... (remaining 1807 not shown)

  Planarity restraints: 1979
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 642 "   -0.013 2.00e-02 2.50e+03   1.22e-02 2.62e+00
        pdb=" CG  PHE A 642 "    0.028 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 642 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 642 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 642 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 642 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 642 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 735 "   -0.011 2.00e-02 2.50e+03   1.16e-02 2.34e+00
        pdb=" CG  PHE A 735 "    0.027 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 735 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 735 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 735 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 735 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 735 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR C 779 "   -0.007 2.00e-02 2.50e+03   1.48e-02 2.20e+00
        pdb=" C   THR C 779 "    0.026 2.00e-02 2.50e+03
        pdb=" O   THR C 779 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ILE C 780 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1976 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1384
        2.75 -     3.29: 12125
        3.29 -     3.83: 19335
        3.83 -     4.36: 21429
        4.36 -     4.90: 36390
  Nonbonded interactions: 90663
  Sorted by model distance:
  nonbonded pdb=" O   VAL B 716 "
            pdb=" OH  TYR B 733 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" OG1 THR C 520 "
            pdb=" NH1 ARG C 523 "
     model   vdw
     2.264 3.120
  nonbonded pdb=" O   GLU D 469 "
            pdb=" OG1 THR D 472 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" OG  SER D 670 "
            pdb=" O   ASP D 673 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" O   GLU D 738 "
            pdb=" OG1 THR D 741 "
     model   vdw
     2.293 3.040
  ... (remaining 90658 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 433 through 580 or resid 633 through 681 or (resid 682 and \ 
 (name N or name CA or name C or name O or name CB )) or resid 683 through 814 o \ 
r (resid 815 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 
16 through 1001))
  selection = (chain 'B' and (resid 433 through 580 or resid 633 through 681 or (resid 682 and \ 
 (name N or name CA or name C or name O or name CB )) or resid 683 through 814 o \ 
r (resid 815 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 
16 through 834 or resid 1002))
  selection = (chain 'C' and (resid 433 through 580 or resid 633 through 834 or resid 1002))
  selection = (chain 'D' and (resid 433 through 681 or (resid 682 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 683 through 814 or (resid 815 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 816 through 834 or resid 1 \ 
001))
}

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:             1.470
  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:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.310
  Find NCS groups from input model:        0.270
  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:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7337
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.090  11695  Z= 0.132
  Angle     :  0.605   8.669  15837  Z= 0.297
  Chirality :  0.043   0.381   1810
  Planarity :  0.003   0.031   1973
  Dihedral  : 16.882 117.041   4359
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 12.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.24 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.39 (0.23), residues: 1426
  helix:  1.39 (0.21), residues: 680
  sheet: -1.81 (0.44), residues: 137
  loop : -1.85 (0.25), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 800 
 TYR   0.023   0.001   TYR C 521 
 PHE   0.028   0.001   PHE A 642 
 TRP   0.014   0.001   TRP B 798 
 HIS   0.002   0.001   HIS C 792 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (11688)
  covalent geometry    : angle       0.59393 (15817)
  SS BOND              : bond        0.00004 (    1)
  SS BOND              : angle       0.34914 (    2)
  hydrogen bonds       : bond        0.11539 (  541)
  hydrogen bonds       : angle       5.17741 ( 1590)
  link_NAG-ASN         : bond        0.00877 (    6)
  link_NAG-ASN         : angle       3.46419 (   18)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 232
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  676 LYS cc_start: 0.8952 (ptmt) cc_final: 0.8732 (ptmm)
REVERT: A  677 GLN cc_start: 0.7700 (pp30) cc_final: 0.7295 (pp30)
REVERT: B  793 MET cc_start: 0.7698 (mmm) cc_final: 0.7489 (mmt)
REVERT: C  737 MET cc_start: 0.6903 (ptt) cc_final: 0.6565 (ptt)
REVERT: D  793 MET cc_start: 0.7924 (ttt) cc_final: 0.6886 (mpp)
  outliers start: 2
  outliers final: 0
  residues processed: 232
  average time/residue: 0.0769
  time to fit residues: 27.5323
Evaluate side-chains
  188 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    7.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    0.5980
   chunk 55 optimal weight:    1.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 714 GLN
A 819 ASN
B 497 GLN
** B 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 802 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.155984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.117449 restraints weight = 22498.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.115432 restraints weight = 15773.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.116030 restraints weight = 14886.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.116809 restraints weight = 12782.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.116921 restraints weight = 11881.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.1279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11695  Z= 0.149
  Angle     :  0.627  10.553  15837  Z= 0.305
  Chirality :  0.044   0.327   1810
  Planarity :  0.003   0.032   1973
  Dihedral  :  8.737  73.658   1679
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 12.14 %
    Favored  : 86.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.41 (0.23), residues: 1426
  helix:  1.32 (0.20), residues: 692
  sheet: -1.97 (0.42), residues: 149
  loop : -1.79 (0.25), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 800 
 TYR   0.011   0.001   TYR B 443 
 PHE   0.017   0.001   PHE C 533 
 TRP   0.015   0.001   TRP A 641 
 HIS   0.002   0.001   HIS B 508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (11688)
  covalent geometry    : angle       0.61840 (15817)
  SS BOND              : bond        0.00000 (    1)
  SS BOND              : angle       0.02177 (    2)
  hydrogen bonds       : bond        0.03233 (  541)
  hydrogen bonds       : angle       4.39316 ( 1590)
  link_NAG-ASN         : bond        0.00679 (    6)
  link_NAG-ASN         : angle       3.22301 (   18)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 205
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  564 TRP cc_start: 0.4641 (t60) cc_final: 0.4397 (t60)
REVERT: A  770 MET cc_start: 0.4850 (mmt) cc_final: 0.4633 (mmt)
REVERT: B  542 TYR cc_start: 0.7776 (t80) cc_final: 0.7316 (t80)
REVERT: D  793 MET cc_start: 0.8047 (ttt) cc_final: 0.6783 (mpp)
  outliers start: 11
  outliers final: 9
  residues processed: 209
  average time/residue: 0.0908
  time to fit residues: 29.1760
Evaluate side-chains
  189 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 180
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  645 LEU
Chi-restraints excluded: chain B residue  647 ILE
Chi-restraints excluded: chain B residue  729 LEU
Chi-restraints excluded: chain C residue  445 LEU
Chi-restraints excluded: chain D residue  568 LEU
Chi-restraints excluded: chain D residue  737 MET
Chi-restraints excluded: chain D residue  794 MET
Chi-restraints excluded: chain D residue  802 ASN
Chi-restraints excluded: chain D residue  826 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 106 optimal weight:    7.9990
   chunk 21 optimal weight:    6.9990
   chunk 135 optimal weight:   10.0000
   chunk 57 optimal weight:    5.9990
   chunk 67 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 97 optimal weight:    0.6980
   chunk 96 optimal weight:    0.2980
   chunk 31 optimal weight:    0.9990
   chunk 114 optimal weight:    6.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
A 714 GLN
** B 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 792 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.155527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.117079 restraints weight = 22636.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.115922 restraints weight = 14641.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.115875 restraints weight = 13745.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.116673 restraints weight = 12267.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.116793 restraints weight = 11176.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.1616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  11695  Z= 0.168
  Angle     :  0.627   9.916  15837  Z= 0.305
  Chirality :  0.044   0.339   1810
  Planarity :  0.003   0.029   1973
  Dihedral  :  5.975  55.876   1679
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 15.70 %
    Favored  : 82.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.53 (0.23), residues: 1426
  helix:  1.26 (0.20), residues: 691
  sheet: -2.15 (0.44), residues: 139
  loop : -1.87 (0.25), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 800 
 TYR   0.014   0.001   TYR B 443 
 PHE   0.022   0.001   PHE C 658 
 TRP   0.015   0.001   TRP A 641 
 HIS   0.002   0.001   HIS C 508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 (11688)
  covalent geometry    : angle       0.61797 (15817)
  SS BOND              : bond        0.00249 (    1)
  SS BOND              : angle       0.24596 (    2)
  hydrogen bonds       : bond        0.03156 (  541)
  hydrogen bonds       : angle       4.37992 ( 1590)
  link_NAG-ASN         : bond        0.00656 (    6)
  link_NAG-ASN         : angle       3.16404 (   18)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 199
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  542 TYR cc_start: 0.7843 (t80) cc_final: 0.7294 (t80)
REVERT: B  669 ASP cc_start: 0.8092 (t0) cc_final: 0.7791 (t0)
REVERT: B  787 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7510 (mt-10)
REVERT: D  793 MET cc_start: 0.8173 (ttt) cc_final: 0.6972 (mpp)
  outliers start: 21
  outliers final: 12
  residues processed: 210
  average time/residue: 0.0712
  time to fit residues: 23.3673
Evaluate side-chains
  195 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 183
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain B residue  576 CYS
Chi-restraints excluded: chain B residue  645 LEU
Chi-restraints excluded: chain B residue  647 ILE
Chi-restraints excluded: chain B residue  729 LEU
Chi-restraints excluded: chain C residue  445 LEU
Chi-restraints excluded: chain C residue  522 VAL
Chi-restraints excluded: chain D residue  568 LEU
Chi-restraints excluded: chain D residue  737 MET
Chi-restraints excluded: chain D residue  794 MET
Chi-restraints excluded: chain D residue  826 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 59 optimal weight:    6.9990
   chunk 102 optimal weight:    2.9990
   chunk 23 optimal weight:   20.0000
   chunk 87 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 104 optimal weight:    6.9990
   chunk 120 optimal weight:    0.8980
   chunk 134 optimal weight:    0.8980
   chunk 7 optimal weight:    3.9990
   chunk 129 optimal weight:    4.9990
   chunk 83 optimal weight:    0.0570
   overall best weight:    1.7702

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

Flipped N/Q/H residues before XYZ refinement:
A 491 GLN
A 714 GLN
A 819 ASN
** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.153611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.113122 restraints weight = 22666.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.112185 restraints weight = 15067.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.112979 restraints weight = 14745.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.113398 restraints weight = 12735.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.113688 restraints weight = 11507.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.1976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  11695  Z= 0.197
  Angle     :  0.639   9.130  15837  Z= 0.316
  Chirality :  0.044   0.319   1810
  Planarity :  0.003   0.030   1973
  Dihedral  :  5.527  55.567   1679
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 13.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 18.20 %
    Favored  : 79.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.65 (0.23), residues: 1426
  helix:  1.14 (0.20), residues: 690
  sheet: -2.18 (0.41), residues: 150
  loop : -1.88 (0.25), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 800 
 TYR   0.019   0.001   TYR B 443 
 PHE   0.022   0.001   PHE C 533 
 TRP   0.012   0.001   TRP B 798 
 HIS   0.002   0.001   HIS C 508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 (11688)
  covalent geometry    : angle       0.63100 (15817)
  SS BOND              : bond        0.00020 (    1)
  SS BOND              : angle       0.14132 (    2)
  hydrogen bonds       : bond        0.03237 (  541)
  hydrogen bonds       : angle       4.46019 ( 1590)
  link_NAG-ASN         : bond        0.00640 (    6)
  link_NAG-ASN         : angle       3.03396 (   18)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 193
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
REVERT: A  533 PHE cc_start: 0.7282 (t80) cc_final: 0.6967 (t80)
REVERT: A  737 MET cc_start: 0.7198 (ppp) cc_final: 0.6997 (ppp)
REVERT: B  542 TYR cc_start: 0.7867 (t80) cc_final: 0.7446 (t80)
REVERT: B  669 ASP cc_start: 0.8192 (t0) cc_final: 0.7913 (t0)
REVERT: D  579 PHE cc_start: 0.8579 (t80) cc_final: 0.8378 (t80)
REVERT: D  786 GLN cc_start: 0.7860 (tp40) cc_final: 0.7480 (mp10)
  outliers start: 30
  outliers final: 19
  residues processed: 212
  average time/residue: 0.0747
  time to fit residues: 24.8069
Evaluate side-chains
  198 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 179
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  635 ILE
Chi-restraints excluded: chain B residue  566 TYR
Chi-restraints excluded: chain B residue  576 CYS
Chi-restraints excluded: chain B residue  645 LEU
Chi-restraints excluded: chain B residue  647 ILE
Chi-restraints excluded: chain B residue  729 LEU
Chi-restraints excluded: chain B residue  766 VAL
Chi-restraints excluded: chain C residue  437 THR
Chi-restraints excluded: chain C residue  445 LEU
Chi-restraints excluded: chain C residue  522 VAL
Chi-restraints excluded: chain C residue  718 VAL
Chi-restraints excluded: chain C residue  779 THR
Chi-restraints excluded: chain D residue  559 LEU
Chi-restraints excluded: chain D residue  568 LEU
Chi-restraints excluded: chain D residue  737 MET
Chi-restraints excluded: chain D residue  746 THR
Chi-restraints excluded: chain D residue  826 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 1 optimal weight:    8.9990
   chunk 27 optimal weight:   10.0000
   chunk 127 optimal weight:    0.7980
   chunk 125 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   chunk 35 optimal weight:    0.8980
   chunk 132 optimal weight:    1.9990
   chunk 124 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 714 GLN
** B 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.155662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.123104 restraints weight = 22626.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.124856 restraints weight = 21478.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.125483 restraints weight = 17322.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.126691 restraints weight = 11107.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.127512 restraints weight = 9642.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7355
moved from start:          0.1994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11695  Z= 0.128
  Angle     :  0.606   9.218  15837  Z= 0.295
  Chirality :  0.043   0.298   1810
  Planarity :  0.003   0.030   1973
  Dihedral  :  5.210  56.556   1679
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 20.55 %
    Favored  : 77.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.63 (0.23), residues: 1426
  helix:  1.19 (0.20), residues: 692
  sheet: -2.10 (0.40), residues: 157
  loop : -1.94 (0.26), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 503 
 TYR   0.019   0.001   TYR B 443 
 PHE   0.026   0.001   PHE C 658 
 TRP   0.011   0.001   TRP B 798 
 HIS   0.002   0.000   HIS C 792 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (11688)
  covalent geometry    : angle       0.59864 (15817)
  SS BOND              : bond        0.00009 (    1)
  SS BOND              : angle       0.11070 (    2)
  hydrogen bonds       : bond        0.02965 (  541)
  hydrogen bonds       : angle       4.28289 ( 1590)
  link_NAG-ASN         : bond        0.00701 (    6)
  link_NAG-ASN         : angle       2.77340 (   18)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 201
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  737 MET cc_start: 0.7450 (ppp) cc_final: 0.6830 (ppp)
REVERT: B  542 TYR cc_start: 0.7747 (t80) cc_final: 0.7432 (t80)
REVERT: B  669 ASP cc_start: 0.8060 (t0) cc_final: 0.7833 (t0)
REVERT: B  799 TRP cc_start: 0.8482 (OUTLIER) cc_final: 0.6920 (m-90)
REVERT: C  523 ARG cc_start: 0.8645 (mtt90) cc_final: 0.8245 (mtt90)
REVERT: C  737 MET cc_start: 0.7462 (ptt) cc_final: 0.7115 (ptt)
REVERT: C  800 ARG cc_start: 0.7549 (tmm160) cc_final: 0.7332 (ttp80)
REVERT: D  464 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8160 (pt)
  outliers start: 23
  outliers final: 13
  residues processed: 212
  average time/residue: 0.0816
  time to fit residues: 26.9684
Evaluate side-chains
  201 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 186
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain B residue  576 CYS
Chi-restraints excluded: chain B residue  645 LEU
Chi-restraints excluded: chain B residue  647 ILE
Chi-restraints excluded: chain B residue  717 LEU
Chi-restraints excluded: chain B residue  729 LEU
Chi-restraints excluded: chain B residue  799 TRP
Chi-restraints excluded: chain C residue  437 THR
Chi-restraints excluded: chain C residue  445 LEU
Chi-restraints excluded: chain C residue  718 VAL
Chi-restraints excluded: chain D residue  464 ILE
Chi-restraints excluded: chain D residue  568 LEU
Chi-restraints excluded: chain D residue  746 THR
Chi-restraints excluded: chain D residue  826 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 1 optimal weight:   10.0000
   chunk 45 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 107 optimal weight:   10.0000
   chunk 15 optimal weight:    5.9990
   chunk 32 optimal weight:    7.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 491 GLN
A 714 GLN
** B 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.154027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.115699 restraints weight = 22072.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.114975 restraints weight = 14468.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.115513 restraints weight = 15153.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.116258 restraints weight = 12480.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.116190 restraints weight = 11071.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.2182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  11695  Z= 0.165
  Angle     :  0.624   9.267  15837  Z= 0.309
  Chirality :  0.044   0.296   1810
  Planarity :  0.003   0.030   1973
  Dihedral  :  5.113  56.019   1679
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 21.28 %
    Favored  : 76.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.65 (0.23), residues: 1426
  helix:  1.16 (0.20), residues: 692
  sheet: -2.09 (0.40), residues: 162
  loop : -1.94 (0.26), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 503 
 TYR   0.015   0.001   TYR B 443 
 PHE   0.018   0.001   PHE C 533 
 TRP   0.017   0.001   TRP C 798 
 HIS   0.001   0.000   HIS C 792 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 (11688)
  covalent geometry    : angle       0.61715 (15817)
  SS BOND              : bond        0.00029 (    1)
  SS BOND              : angle       0.11457 (    2)
  hydrogen bonds       : bond        0.03117 (  541)
  hydrogen bonds       : angle       4.34997 ( 1590)
  link_NAG-ASN         : bond        0.00658 (    6)
  link_NAG-ASN         : angle       2.78584 (   18)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 199
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  542 TYR cc_start: 0.7723 (t80) cc_final: 0.7467 (t80)
REVERT: B  669 ASP cc_start: 0.8102 (t0) cc_final: 0.7881 (t0)
REVERT: B  793 MET cc_start: 0.8068 (tpp) cc_final: 0.7867 (tpp)
REVERT: B  799 TRP cc_start: 0.8629 (OUTLIER) cc_final: 0.7111 (m-90)
REVERT: D  464 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8312 (pt)
REVERT: D  741 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8470 (m)
  outliers start: 27
  outliers final: 19
  residues processed: 216
  average time/residue: 0.0682
  time to fit residues: 23.1392
Evaluate side-chains
  207 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 185
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  635 ILE
Chi-restraints excluded: chain B residue  435 VAL
Chi-restraints excluded: chain B residue  566 TYR
Chi-restraints excluded: chain B residue  576 CYS
Chi-restraints excluded: chain B residue  645 LEU
Chi-restraints excluded: chain B residue  647 ILE
Chi-restraints excluded: chain B residue  717 LEU
Chi-restraints excluded: chain B residue  729 LEU
Chi-restraints excluded: chain B residue  766 VAL
Chi-restraints excluded: chain B residue  799 TRP
Chi-restraints excluded: chain C residue  437 THR
Chi-restraints excluded: chain C residue  445 LEU
Chi-restraints excluded: chain C residue  718 VAL
Chi-restraints excluded: chain C residue  779 THR
Chi-restraints excluded: chain D residue  464 ILE
Chi-restraints excluded: chain D residue  568 LEU
Chi-restraints excluded: chain D residue  741 THR
Chi-restraints excluded: chain D residue  746 THR
Chi-restraints excluded: chain D residue  826 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 106 optimal weight:    1.9990
   chunk 112 optimal weight:   10.0000
   chunk 116 optimal weight:    2.9990
   chunk 98 optimal weight:    3.9990
   chunk 138 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 45 optimal weight:    0.5980
   chunk 104 optimal weight:    9.9990
   chunk 6 optimal weight:    6.9990
   chunk 102 optimal weight:    2.9990
   chunk 139 optimal weight:    0.8980
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
A 654 ASN
A 714 GLN
** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.152094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.111246 restraints weight = 22610.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.109851 restraints weight = 16352.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.111299 restraints weight = 14463.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.111252 restraints weight = 12812.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.111443 restraints weight = 11458.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.2341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  11695  Z= 0.194
  Angle     :  0.654  10.138  15837  Z= 0.324
  Chirality :  0.045   0.297   1810
  Planarity :  0.003   0.031   1973
  Dihedral  :  5.174  55.714   1679
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 13.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 21.76 %
    Favored  : 75.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.76 (0.22), residues: 1426
  helix:  1.07 (0.20), residues: 691
  sheet: -2.17 (0.39), residues: 162
  loop : -1.97 (0.26), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 503 
 TYR   0.015   0.001   TYR B 443 
 PHE   0.030   0.002   PHE C 658 
 TRP   0.018   0.001   TRP B 798 
 HIS   0.002   0.000   HIS C 508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 (11688)
  covalent geometry    : angle       0.64752 (15817)
  SS BOND              : bond        0.00041 (    1)
  SS BOND              : angle       0.12340 (    2)
  hydrogen bonds       : bond        0.03295 (  541)
  hydrogen bonds       : angle       4.45075 ( 1590)
  link_NAG-ASN         : bond        0.00644 (    6)
  link_NAG-ASN         : angle       2.80070 (   18)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 191
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  766 VAL cc_start: 0.7236 (m) cc_final: 0.6991 (t)
REVERT: B  542 TYR cc_start: 0.7720 (t80) cc_final: 0.7445 (t80)
REVERT: B  669 ASP cc_start: 0.8067 (t0) cc_final: 0.7814 (t0)
REVERT: B  799 TRP cc_start: 0.8661 (OUTLIER) cc_final: 0.7288 (m-90)
REVERT: D  579 PHE cc_start: 0.8407 (t80) cc_final: 0.8204 (t80)
REVERT: D  741 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.8498 (m)
REVERT: D  786 GLN cc_start: 0.7710 (tp40) cc_final: 0.7222 (mp10)
  outliers start: 32
  outliers final: 21
  residues processed: 210
  average time/residue: 0.0641
  time to fit residues: 21.6795
Evaluate side-chains
  202 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 179
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  635 ILE
Chi-restraints excluded: chain B residue  435 VAL
Chi-restraints excluded: chain B residue  566 TYR
Chi-restraints excluded: chain B residue  576 CYS
Chi-restraints excluded: chain B residue  645 LEU
Chi-restraints excluded: chain B residue  647 ILE
Chi-restraints excluded: chain B residue  717 LEU
Chi-restraints excluded: chain B residue  729 LEU
Chi-restraints excluded: chain B residue  750 CYS
Chi-restraints excluded: chain B residue  766 VAL
Chi-restraints excluded: chain B residue  799 TRP
Chi-restraints excluded: chain C residue  437 THR
Chi-restraints excluded: chain C residue  460 GLU
Chi-restraints excluded: chain C residue  718 VAL
Chi-restraints excluded: chain C residue  779 THR
Chi-restraints excluded: chain D residue  559 LEU
Chi-restraints excluded: chain D residue  568 LEU
Chi-restraints excluded: chain D residue  741 THR
Chi-restraints excluded: chain D residue  746 THR
Chi-restraints excluded: chain D residue  826 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 138 optimal weight:    0.8980
   chunk 69 optimal weight:    0.8980
   chunk 99 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 67 optimal weight:    0.6980
   chunk 104 optimal weight:    0.9990
   chunk 22 optimal weight:    8.9990
   chunk 96 optimal weight:    0.8980
   chunk 137 optimal weight:    7.9990
   chunk 139 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 714 GLN
** B 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.154681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.115770 restraints weight = 22599.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.114939 restraints weight = 21510.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.115401 restraints weight = 15984.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.116242 restraints weight = 14268.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.116716 restraints weight = 12599.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.2369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11695  Z= 0.134
  Angle     :  0.645  11.305  15837  Z= 0.313
  Chirality :  0.044   0.292   1810
  Planarity :  0.003   0.030   1973
  Dihedral  :  5.006  56.572   1679
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 12.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 22.82 %
    Favored  : 74.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.63 (0.23), residues: 1426
  helix:  1.18 (0.20), residues: 691
  sheet: -2.02 (0.40), residues: 161
  loop : -1.97 (0.26), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 503 
 TYR   0.009   0.001   TYR B 443 
 PHE   0.013   0.001   PHE A 533 
 TRP   0.015   0.001   TRP A 641 
 HIS   0.002   0.001   HIS C 792 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (11688)
  covalent geometry    : angle       0.63868 (15817)
  SS BOND              : bond        0.00017 (    1)
  SS BOND              : angle       0.06137 (    2)
  hydrogen bonds       : bond        0.03110 (  541)
  hydrogen bonds       : angle       4.33388 ( 1590)
  link_NAG-ASN         : bond        0.00677 (    6)
  link_NAG-ASN         : angle       2.77519 (   18)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 200
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  533 PHE cc_start: 0.6980 (t80) cc_final: 0.6493 (t80)
REVERT: B  542 TYR cc_start: 0.7585 (t80) cc_final: 0.7354 (t80)
REVERT: B  799 TRP cc_start: 0.8561 (OUTLIER) cc_final: 0.7347 (m-90)
REVERT: C  523 ARG cc_start: 0.8864 (mtt90) cc_final: 0.8520 (mtt90)
REVERT: D  741 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8317 (m)
  outliers start: 28
  outliers final: 19
  residues processed: 218
  average time/residue: 0.0768
  time to fit residues: 26.4810
Evaluate side-chains
  214 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 193
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  635 ILE
Chi-restraints excluded: chain B residue  435 VAL
Chi-restraints excluded: chain B residue  526 VAL
Chi-restraints excluded: chain B residue  566 TYR
Chi-restraints excluded: chain B residue  576 CYS
Chi-restraints excluded: chain B residue  645 LEU
Chi-restraints excluded: chain B residue  647 ILE
Chi-restraints excluded: chain B residue  729 LEU
Chi-restraints excluded: chain B residue  750 CYS
Chi-restraints excluded: chain B residue  766 VAL
Chi-restraints excluded: chain B residue  799 TRP
Chi-restraints excluded: chain C residue  437 THR
Chi-restraints excluded: chain C residue  445 LEU
Chi-restraints excluded: chain C residue  718 VAL
Chi-restraints excluded: chain C residue  779 THR
Chi-restraints excluded: chain D residue  568 LEU
Chi-restraints excluded: chain D residue  741 THR
Chi-restraints excluded: chain D residue  746 THR
Chi-restraints excluded: chain D residue  826 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9980
   chunk 80 optimal weight:    0.6980
   chunk 89 optimal weight:    0.9980
   chunk 137 optimal weight:    0.4980
   chunk 11 optimal weight:    3.9990
   chunk 67 optimal weight:    0.3980
   chunk 141 optimal weight:    4.9990
   chunk 23 optimal weight:   10.0000
   chunk 29 optimal weight:    6.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 714 GLN
** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.155569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.122896 restraints weight = 22478.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.123607 restraints weight = 22401.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.124204 restraints weight = 20111.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.126854 restraints weight = 13561.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.126994 restraints weight = 9577.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7348
moved from start:          0.2389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  11695  Z= 0.129
  Angle     :  0.636  10.726  15837  Z= 0.311
  Chirality :  0.044   0.304   1810
  Planarity :  0.003   0.030   1973
  Dihedral  :  4.904  56.501   1679
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 12.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 23.46 %
    Favored  : 74.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.60 (0.23), residues: 1426
  helix:  1.23 (0.20), residues: 689
  sheet: -1.90 (0.42), residues: 156
  loop : -2.00 (0.25), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 503 
 TYR   0.008   0.001   TYR B 443 
 PHE   0.029   0.001   PHE C 658 
 TRP   0.020   0.001   TRP A 641 
 HIS   0.002   0.001   HIS C 792 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (11688)
  covalent geometry    : angle       0.63006 (15817)
  SS BOND              : bond        0.00011 (    1)
  SS BOND              : angle       0.05418 (    2)
  hydrogen bonds       : bond        0.03077 (  541)
  hydrogen bonds       : angle       4.30810 ( 1590)
  link_NAG-ASN         : bond        0.00687 (    6)
  link_NAG-ASN         : angle       2.68109 (   18)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 203
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  654 ASN cc_start: 0.8287 (t0) cc_final: 0.7397 (t0)
REVERT: A  737 MET cc_start: 0.7723 (ppp) cc_final: 0.7500 (ppp)
REVERT: A  770 MET cc_start: 0.4953 (mmt) cc_final: 0.4743 (mmt)
REVERT: B  542 TYR cc_start: 0.7704 (t80) cc_final: 0.7502 (t80)
REVERT: B  669 ASP cc_start: 0.8139 (t0) cc_final: 0.7851 (t0)
REVERT: B  787 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7689 (mt-10)
REVERT: B  799 TRP cc_start: 0.8480 (OUTLIER) cc_final: 0.7181 (m-90)
REVERT: D  743 GLU cc_start: 0.8003 (pp20) cc_final: 0.7218 (pp20)
  outliers start: 26
  outliers final: 18
  residues processed: 216
  average time/residue: 0.0745
  time to fit residues: 25.8132
Evaluate side-chains
  212 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 193
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  635 ILE
Chi-restraints excluded: chain B residue  445 LEU
Chi-restraints excluded: chain B residue  566 TYR
Chi-restraints excluded: chain B residue  576 CYS
Chi-restraints excluded: chain B residue  645 LEU
Chi-restraints excluded: chain B residue  647 ILE
Chi-restraints excluded: chain B residue  717 LEU
Chi-restraints excluded: chain B residue  729 LEU
Chi-restraints excluded: chain B residue  750 CYS
Chi-restraints excluded: chain B residue  766 VAL
Chi-restraints excluded: chain B residue  799 TRP
Chi-restraints excluded: chain C residue  437 THR
Chi-restraints excluded: chain C residue  718 VAL
Chi-restraints excluded: chain C residue  779 THR
Chi-restraints excluded: chain D residue  568 LEU
Chi-restraints excluded: chain D residue  746 THR
Chi-restraints excluded: chain D residue  826 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 28 optimal weight:    7.9990
   chunk 1 optimal weight:    0.7980
   chunk 20 optimal weight:    9.9990
   chunk 80 optimal weight:    0.8980
   chunk 36 optimal weight:    0.0970
   chunk 60 optimal weight:    0.5980
   chunk 64 optimal weight:    0.8980
   chunk 72 optimal weight:    3.9990
   chunk 112 optimal weight:    9.9990
   chunk 130 optimal weight:    5.9990
   chunk 92 optimal weight:    0.9980
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
A 654 ASN
** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.156408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.116786 restraints weight = 22636.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.115388 restraints weight = 18332.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.116001 restraints weight = 14053.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.116934 restraints weight = 12658.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.117104 restraints weight = 11345.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
moved from start:          0.2509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11695  Z= 0.127
  Angle     :  0.639  10.622  15837  Z= 0.311
  Chirality :  0.044   0.286   1810
  Planarity :  0.003   0.031   1973
  Dihedral  :  4.845  56.533   1679
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 23.79 %
    Favored  : 74.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.62 (0.23), residues: 1426
  helix:  1.21 (0.20), residues: 690
  sheet: -1.91 (0.41), residues: 163
  loop : -2.03 (0.25), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 503 
 TYR   0.007   0.001   TYR D 733 
 PHE   0.017   0.001   PHE D 579 
 TRP   0.042   0.001   TRP D 706 
 HIS   0.002   0.000   HIS C 792 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (11688)
  covalent geometry    : angle       0.63363 (15817)
  SS BOND              : bond        0.00009 (    1)
  SS BOND              : angle       0.02486 (    2)
  hydrogen bonds       : bond        0.03026 (  541)
  hydrogen bonds       : angle       4.28717 ( 1590)
  link_NAG-ASN         : bond        0.00672 (    6)
  link_NAG-ASN         : angle       2.65021 (   18)

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

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

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2852 Ramachandran restraints generated.
    1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 197
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  514 VAL cc_start: 0.7580 (t) cc_final: 0.7283 (p)
REVERT: A  737 MET cc_start: 0.7433 (ppp) cc_final: 0.7101 (ppp)
REVERT: A  770 MET cc_start: 0.4854 (mmt) cc_final: 0.4652 (mmt)
REVERT: B  542 TYR cc_start: 0.7734 (t80) cc_final: 0.7490 (t80)
REVERT: B  669 ASP cc_start: 0.8344 (t0) cc_final: 0.8027 (t0)
REVERT: B  799 TRP cc_start: 0.8470 (OUTLIER) cc_final: 0.7143 (m-90)
REVERT: C  523 ARG cc_start: 0.8865 (mtt90) cc_final: 0.8646 (mtt90)
REVERT: C  737 MET cc_start: 0.7493 (ptt) cc_final: 0.7273 (ptt)
REVERT: D  743 GLU cc_start: 0.7950 (pp20) cc_final: 0.7598 (pp20)
  outliers start: 23
  outliers final: 18
  residues processed: 209
  average time/residue: 0.0802
  time to fit residues: 26.2824
Evaluate side-chains
  208 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 189
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  548 THR
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  635 ILE
Chi-restraints excluded: chain A residue  827 LEU
Chi-restraints excluded: chain B residue  435 VAL
Chi-restraints excluded: chain B residue  445 LEU
Chi-restraints excluded: chain B residue  566 TYR
Chi-restraints excluded: chain B residue  576 CYS
Chi-restraints excluded: chain B residue  645 LEU
Chi-restraints excluded: chain B residue  717 LEU
Chi-restraints excluded: chain B residue  766 VAL
Chi-restraints excluded: chain B residue  799 TRP
Chi-restraints excluded: chain C residue  437 THR
Chi-restraints excluded: chain C residue  718 VAL
Chi-restraints excluded: chain C residue  779 THR
Chi-restraints excluded: chain D residue  568 LEU
Chi-restraints excluded: chain D residue  746 THR
Chi-restraints excluded: chain D residue  826 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 142
   random chunks:
   chunk 94 optimal weight:    3.9990
   chunk 29 optimal weight:    6.9990
   chunk 74 optimal weight:    0.9980
   chunk 84 optimal weight:    0.9980
   chunk 15 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9980
   chunk 126 optimal weight:    0.4980
   chunk 130 optimal weight:    5.9990
   chunk 122 optimal weight:    5.9990
   chunk 95 optimal weight:    3.9990
   chunk 82 optimal weight:    0.6980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 819 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.156092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.116690 restraints weight = 22643.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.115433 restraints weight = 18153.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.115918 restraints weight = 14577.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.116801 restraints weight = 13273.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.116868 restraints weight = 12278.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.2527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11695  Z= 0.136
  Angle     :  0.641  10.295  15837  Z= 0.313
  Chirality :  0.044   0.289   1810
  Planarity :  0.003   0.030   1973
  Dihedral  :  4.826  56.355   1679
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 24.11 %
    Favored  : 74.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.62 (0.23), residues: 1426
  helix:  1.22 (0.20), residues: 690
  sheet: -1.89 (0.41), residues: 163
  loop : -2.04 (0.25), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 503 
 TYR   0.008   0.001   TYR B 443 
 PHE   0.015   0.001   PHE A 533 
 TRP   0.030   0.001   TRP D 706 
 HIS   0.002   0.000   HIS C 792 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (11688)
  covalent geometry    : angle       0.63480 (15817)
  SS BOND              : bond        0.00009 (    1)
  SS BOND              : angle       0.01755 (    2)
  hydrogen bonds       : bond        0.03041 (  541)
  hydrogen bonds       : angle       4.26782 ( 1590)
  link_NAG-ASN         : bond        0.00665 (    6)
  link_NAG-ASN         : angle       2.64179 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1723.10 seconds
wall clock time: 30 minutes 37.38 seconds (1837.38 seconds total)