Starting phenix.real_space_refine
on Wed Sep 17 23:26:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vv2_43547/09_2025/8vv2_43547.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vv2_43547/09_2025/8vv2_43547.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vv2_43547/09_2025/8vv2_43547.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vv2_43547/09_2025/8vv2_43547.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vv2_43547/09_2025/8vv2_43547.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vv2_43547/09_2025/8vv2_43547.map"
  }
  resolution = 2.6
  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=   0.002 sd=   0.021
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 6094 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     P      23      5.49       5
     S      35      5.16       5
     C    4365      2.51       5
     N    1212      2.21       5
     O    1389      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7024
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6519
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 852, 6509
          Classifications: {'peptide': 852}
          Incomplete info: {'truncation_to_alanine': 81}
          Link IDs: {'PTRANS': 34, 'TRANS': 817}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 350
          Unresolved non-hydrogen angles: 424
          Unresolved non-hydrogen dihedrals: 292
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ARG:plan': 10, 'GLU:plan': 22, 'TRP:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 9, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 245
      Conformer: "B"
        Number of residues, atoms: 852, 6509
          Classifications: {'peptide': 852}
          Incomplete info: {'truncation_to_alanine': 81}
          Link IDs: {'PTRANS': 34, 'TRANS': 817}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 350
          Unresolved non-hydrogen angles: 424
          Unresolved non-hydrogen dihedrals: 292
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ARG:plan': 10, 'GLU:plan': 22, 'TRP:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 9, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 245
          bond proxies already assigned to first conformer: 6619
    Chain: "C"
      Number of atoms: 475
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 475
          Classifications: {'RNA': 23}
          Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 2, 'rna3p_pur': 6, 'rna3p_pyr': 7}
          Link IDs: {'rna2p': 9, 'rna3p': 13}
          Unresolved chain links: 1
          Chain breaks: 2
          Unresolved chain link angles: 4
          Unresolved chain link dihedrals: 4
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 26
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'  U:plan': 1, '  U%rna3p_pyr:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 28
          Classifications: {'water': 28}
          Link IDs: {None: 27}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AHIS A 578 " occ=0.63
      ... (18 atoms not shown)
      pdb=" NE2BHIS A 578 " occ=0.37
  Time building chain proxies: 2.71, per 1000 atoms: 0.39
  Number of scatterers: 7024
  At special positions: 0
  Unit cell: (74.7, 106.24, 108.73, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      35     16.00
     P      23     15.00
     O    1389      8.00
     N    1212      7.00
     C    4365      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.71
  Conformation dependent library (CDL) restraints added in 396.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1624

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 4 sheets defined
      55.2% alpha, 12.9% beta
      3 base pairs and 7 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 62 through 84
      removed outlier: 3.877A  pdb=" N   TYR A  69 " --> pdb=" O   ILE A  65 " (cutoff:3.500A)
      removed outlier: 4.774A  pdb=" N   LYS A  72 " --> pdb=" O   TRP A  68 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LYS A  76 " --> pdb=" O   LYS A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 107
      removed outlier: 3.569A  pdb=" N   THR A 107 " --> pdb=" O   HIS A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 194
      removed outlier: 3.639A  pdb=" N   GLN A 184 " --> pdb=" O   ALA A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 207
    Processing helix  chain 'A' and resid 209 through 214
      removed outlier: 4.242A  pdb=" N   GLY A 213 " --> pdb=" O   LEU A 209 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   MET A 214 " --> pdb=" O   PRO A 210 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 209 through 214'
    Processing helix  chain 'A' and resid 214 through 225
    Processing helix  chain 'A' and resid 237 through 253
      removed outlier: 4.899A  pdb=" N   THR A 243 " --> pdb=" O   THR A 239 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   GLN A 244 " --> pdb=" O   THR A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 258
    Processing helix  chain 'A' and resid 267 through 282
    Processing helix  chain 'A' and resid 314 through 324
      removed outlier: 3.608A  pdb=" N   LEU A 318 " --> pdb=" O   THR A 314 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   GLN A 322 " --> pdb=" O   LEU A 318 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   SER A 323 " --> pdb=" O   GLN A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 356
    Processing helix  chain 'A' and resid 373 through 380
      removed outlier: 3.695A  pdb=" N   SER A 377 " --> pdb=" O   ALA A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 408
    Processing helix  chain 'A' and resid 433 through 456
      removed outlier: 3.574A  pdb=" N   ALA A 439 " --> pdb=" O   GLU A 435 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ILE A 440 " --> pdb=" O   GLU A 436 " (cutoff:3.500A)
      Proline residue:  A 446  - end of helix
      removed outlier: 3.505A  pdb=" N   GLN A 454 " --> pdb=" O   ARG A 450 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ARG A 455 " --> pdb=" O   GLU A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 467
    Processing helix  chain 'A' and resid 473 through 488
    Processing helix  chain 'A' and resid 499 through 512
    Processing helix  chain 'A' and resid 514 through 518
      removed outlier: 3.760A  pdb=" N   SER A 518 " --> pdb=" O   MET A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 554 through 559
      removed outlier: 3.965A  pdb=" N   THR A 558 " --> pdb=" O   ASN A 554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 605
      removed outlier: 3.891A  pdb=" N   ALA A 605 " --> pdb=" O   ARG A 601 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 618 through 624
    Processing helix  chain 'A' and resid 631 through 635
    Processing helix  chain 'A' and resid 638 through 648
    Processing helix  chain 'A' and resid 652 through 659
      removed outlier: 3.649A  pdb=" N   ARG A 659 " --> pdb=" O   HIS A 655 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 679
    Processing helix  chain 'A' and resid 689 through 698
      removed outlier: 3.620A  pdb=" N   HIS A 694 " --> pdb=" O   PRO A 690 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 701 through 714
    Processing helix  chain 'A' and resid 716 through 729
    Processing helix  chain 'A' and resid 740 through 752
    Processing helix  chain 'A' and resid 758 through 775
    Processing helix  chain 'A' and resid 775 through 787
    Processing helix  chain 'A' and resid 789 through 811
    Processing helix  chain 'A' and resid 820 through 824
    Processing helix  chain 'A' and resid 829 through 841
    Processing helix  chain 'A' and resid 908 through 915
    Processing helix  chain 'A' and resid 941 through 965
      removed outlier: 3.690A  pdb=" N   ILE A 957 " --> pdb=" O   LYS A 953 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 976 through 989
    Processing sheet with id=AA1, first strand: chain 'A' and resid 299 through 301
      removed outlier: 6.820A  pdb=" N   GLY A 293 " --> pdb=" O   TYR A 311 " (cutoff:3.500A)
      removed outlier: 8.872A  pdb=" N   THR A 313 " --> pdb=" O   GLY A 293 " (cutoff:3.500A)
      removed outlier: 7.843A  pdb=" N   GLN A 295 " --> pdb=" O   THR A 313 " (cutoff:3.500A)
      removed outlier: 6.105A  pdb=" N   ARG A 260 " --> pdb=" O   HIS A 332 " (cutoff:3.500A)
      removed outlier: 7.594A  pdb=" N   VAL A 334 " --> pdb=" O   ARG A 260 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   VAL A 262 " --> pdb=" O   VAL A 334 " (cutoff:3.500A)
      removed outlier: 7.394A  pdb=" N   ASP A 336 " --> pdb=" O   VAL A 262 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   THR A 264 " --> pdb=" O   ASP A 336 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 395 through 398
      removed outlier: 6.102A  pdb=" N   VAL A 396 " --> pdb=" O   CYS A 613 " (cutoff:3.500A)
      removed outlier: 7.287A  pdb=" N   HIS A 615 " --> pdb=" O   VAL A 396 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   TYR A 398 " --> pdb=" O   HIS A 615 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   ALA A 492 " --> pdb=" O   TYR A 567 " (cutoff:3.500A)
      removed outlier: 7.734A  pdb=" N   ILE A 569 " --> pdb=" O   ALA A 492 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   LEU A 494 " --> pdb=" O   ILE A 569 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   ILE A 493 " --> pdb=" O   VAL A 550 " (cutoff:3.500A)
      removed outlier: 7.414A  pdb=" N   ALA A 552 " --> pdb=" O   ILE A 493 " (cutoff:3.500A)
      removed outlier: 5.813A  pdb=" N   VAL A 495 " --> pdb=" O   ALA A 552 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 573 through 580
      removed outlier: 4.057A  pdb=" N   SER A 586 " --> pdb=" O   LYS A 893 " (cutoff:3.500A)
      removed outlier: 5.313A  pdb=" N   ILE A 899 " --> pdb=" O   VAL A 868 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   VAL A 861 " --> pdb=" O   VAL A 869 " (cutoff:3.500A)
      removed outlier: 7.459A  pdb=" N   ILE A 871 " --> pdb=" O   VAL A 859 " (cutoff:3.500A)
      removed outlier: 10.627A  pdb=" N   VAL A 859 " --> pdb=" O   ILE A 871 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   MET A 858 " --> pdb=" O   ASN A 851 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   ASN A 851 " --> pdb=" O   MET A 858 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   TRP A 887 " --> pdb=" O   VAL A 907 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 919 through 924

    366 hydrogen bonds defined for protein.
    1068 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      6 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      3 basepair parallelities
      7 stacking parallelities
  Total time for adding SS restraints: 1.22

  Time building geometry restraints manager: 0.92 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1192
        1.32 -     1.44: 1850
        1.44 -     1.57: 4031
        1.57 -     1.69: 42
        1.69 -     1.81: 55
  Bond restraints: 7170
  Sorted by residual:
  bond pdb=" N   TRP A 445 "
       pdb=" CA  TRP A 445 "
    ideal  model  delta    sigma   weight residual
    1.462  1.486 -0.024 7.70e-03 1.69e+04 9.75e+00
  bond pdb=" C   PRO A 446 "
       pdb=" O   PRO A 446 "
    ideal  model  delta    sigma   weight residual
    1.237  1.198  0.039 1.29e-02 6.01e+03 9.05e+00
  bond pdb=" CA  ALA A 439 "
       pdb=" CB  ALA A 439 "
    ideal  model  delta    sigma   weight residual
    1.530  1.487  0.043 1.56e-02 4.11e+03 7.56e+00
  bond pdb=" N   LYS A 854 "
       pdb=" CA  LYS A 854 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.034 1.33e-02 5.65e+03 6.57e+00
  bond pdb=" O5'   U C  19 "
       pdb=" C5'   U C  19 "
    ideal  model  delta    sigma   weight residual
    1.424  1.458 -0.034 1.50e-02 4.44e+03 5.03e+00
  ... (remaining 7165 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.85: 9691
        2.85 -     5.70: 126
        5.70 -     8.55: 14
        8.55 -    11.40: 4
       11.40 -    14.25: 5
  Bond angle restraints: 9840
  Sorted by residual:
  angle pdb=" C3'   G C  17 "
        pdb=" O3'   G C  17 "
        pdb=" P     U C  18 "
      ideal   model   delta    sigma   weight residual
     120.20  134.45  -14.25 1.50e+00 4.44e-01 9.03e+01
  angle pdb=" C3'   U C  19 "
        pdb=" O3'   U C  19 "
        pdb=" P     G C  20 "
      ideal   model   delta    sigma   weight residual
     120.20  106.26   13.94 1.50e+00 4.44e-01 8.64e+01
  angle pdb=" C3'   U C  21 "
        pdb=" O3'   U C  21 "
        pdb=" P     U C  22 "
      ideal   model   delta    sigma   weight residual
     120.20  107.07   13.13 1.50e+00 4.44e-01 7.66e+01
  angle pdb=" C3'   U C  23 "
        pdb=" O3'   U C  23 "
        pdb=" P     U C  24 "
      ideal   model   delta    sigma   weight residual
     120.20  108.14   12.06 1.50e+00 4.44e-01 6.47e+01
  angle pdb=" C3'   U C  22 "
        pdb=" O3'   U C  22 "
        pdb=" P     U C  23 "
      ideal   model   delta    sigma   weight residual
     120.20  109.32   10.88 1.50e+00 4.44e-01 5.26e+01
  ... (remaining 9835 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.26: 3861
       21.26 -    42.52: 384
       42.52 -    63.78: 131
       63.78 -    85.04: 23
       85.04 -   106.30: 3
  Dihedral angle restraints: 4402
    sinusoidal: 1900
      harmonic: 2502
  Sorted by residual:
  dihedral pdb=" CA  LYS A 972 "
           pdb=" C   LYS A 972 "
           pdb=" N   ASP A 973 "
           pdb=" CA  ASP A 973 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.45   20.55     0      5.00e+00 4.00e-02 1.69e+01
  dihedral pdb=" CA  TYR A 842 "
           pdb=" C   TYR A 842 "
           pdb=" N   PRO A 843 "
           pdb=" CA  PRO A 843 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.49  -18.51     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CG  ARG A 747 "
           pdb=" CD  ARG A 747 "
           pdb=" NE  ARG A 747 "
           pdb=" CZ  ARG A 747 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -39.60  -50.40     2      1.50e+01 4.44e-03 1.27e+01
  ... (remaining 4399 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.106: 1103
       0.106 -    0.213: 60
       0.213 -    0.319: 4
       0.319 -    0.425: 3
       0.425 -    0.532: 2
  Chirality restraints: 1172
  Sorted by residual:
  chirality pdb=" P     U C  18 "
            pdb=" OP1   U C  18 "
            pdb=" OP2   U C  18 "
            pdb=" O5'   U C  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.94   -0.53 2.00e-01 2.50e+01 7.06e+00
  chirality pdb=" P     U C  19 "
            pdb=" OP1   U C  19 "
            pdb=" OP2   U C  19 "
            pdb=" O5'   U C  19 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.87   -0.46 2.00e-01 2.50e+01 5.34e+00
  chirality pdb=" P     U C  27 "
            pdb=" OP1   U C  27 "
            pdb=" OP2   U C  27 "
            pdb=" O5'   U C  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.77   -0.36 2.00e-01 2.50e+01 3.22e+00
  ... (remaining 1169 not shown)

  Planarity restraints: 1171
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 450 "    0.322 9.50e-02 1.11e+02   1.44e-01 1.28e+01
        pdb=" NE  ARG A 450 "   -0.019 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 450 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 450 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 450 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 735 "    0.037 5.00e-02 4.00e+02   5.66e-02 5.13e+00
        pdb=" N   PRO A 736 "   -0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO A 736 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 736 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G C  12 "   -0.028 2.00e-02 2.50e+03   1.17e-02 4.14e+00
        pdb=" N9    G C  12 "    0.026 2.00e-02 2.50e+03
        pdb=" C8    G C  12 "    0.002 2.00e-02 2.50e+03
        pdb=" N7    G C  12 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    G C  12 "    0.006 2.00e-02 2.50e+03
        pdb=" C6    G C  12 "   -0.006 2.00e-02 2.50e+03
        pdb=" O6    G C  12 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1    G C  12 "   -0.006 2.00e-02 2.50e+03
        pdb=" C2    G C  12 "    0.001 2.00e-02 2.50e+03
        pdb=" N2    G C  12 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    G C  12 "    0.005 2.00e-02 2.50e+03
        pdb=" C4    G C  12 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1168 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1274
        2.77 -     3.30: 6604
        3.30 -     3.83: 11976
        3.83 -     4.37: 14186
        4.37 -     4.90: 23879
  Nonbonded interactions: 57919
  Sorted by model distance:
  nonbonded pdb=" N   GLU A 374 "
            pdb=" OE1 GLU A 374 "
     model   vdw
     2.231 3.120
  nonbonded pdb=" OD1 ASP A 402 "
            pdb=" OH  TYR A 456 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OE1 GLU A 576 "
            pdb=" NE2AHIS A 578 "
     model   vdw
     2.286 3.120
  nonbonded pdb=" O   TYR A 902 "
            pdb=" O   HOH A1101 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" OD1 ASP A 501 "
            pdb=" O   HOH A1102 "
     model   vdw
     2.300 3.040
  ... (remaining 57914 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.37 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             2.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.060
  Find NCS groups from input model:        0.030
  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:             0.010
  Load rotamer database and sin/cos tables:7.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7170  Z= 0.230
  Angle     :  0.811  14.254   9840  Z= 0.488
  Chirality :  0.057   0.532   1172
  Planarity :  0.007   0.144   1171
  Dihedral  : 19.065 106.296   2778
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.02 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 26.18 %
    Favored  : 70.15 %
  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:  1.31 (0.30), residues: 849
  helix:  1.74 (0.26), residues: 441
  sheet:  1.24 (0.54), residues: 90
  loop : -0.45 (0.36), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A  93 
 TYR   0.016   0.001   TYR A 778 
 PHE   0.010   0.001   PHE A 205 
 TRP   0.013   0.001   TRP A 445 
 HIS   0.007   0.001   HIS A 507 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 7170)
  covalent geometry    : angle       0.81113 ( 9840)
  hydrogen bonds       : bond        0.15218 (  372)
  hydrogen bonds       : angle       5.27095 ( 1068)

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

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

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 65
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
  outliers start: 25
  outliers final: 16
  residues processed: 89
  average time/residue: 0.5893
  time to fit residues: 55.1141
Evaluate side-chains
  65 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 49
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 HIS
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain A residue  183 ASP
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  368 SER
Chi-restraints excluded: chain A residue  457 SER
Chi-restraints excluded: chain A residue  509 LEU
Chi-restraints excluded: chain A residue  536 THR
Chi-restraints excluded: chain A residue  546 VAL
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  713 LEU
Chi-restraints excluded: chain A residue  859 VAL
Chi-restraints excluded: chain A residue  889 ILE
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  963 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0570
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    0.3980
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.5698

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

Flipped N/Q/H residues before XYZ refinement:
A  97 GLN
A 203 GLN
A 612 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.090474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.062780 restraints weight = 27653.726|
|-----------------------------------------------------------------------------|
r_work (start): 0.2956 rms_B_bonded: 3.96
r_work: 0.2771 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2784
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2784 r_free = 0.2784    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2784 r_free = 0.2784    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2784
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.1263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7170  Z= 0.120
  Angle     :  0.547   6.835   9840  Z= 0.291
  Chirality :  0.042   0.175   1172
  Planarity :  0.004   0.052   1171
  Dihedral  : 14.908 105.679   1304
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.84 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 25.88 %
    Favored  : 70.59 %
  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:  1.64 (0.30), residues: 849
  helix:  1.98 (0.25), residues: 445
  sheet:  1.05 (0.49), residues: 114
  loop : -0.26 (0.38), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 746 
 TYR   0.008   0.001   TYR A 910 
 PHE   0.014   0.001   PHE A 205 
 TRP   0.008   0.001   TRP A 935 
 HIS   0.003   0.001   HIS A 527 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 7170)
  covalent geometry    : angle       0.54717 ( 9840)
  hydrogen bonds       : bond        0.03657 (  372)
  hydrogen bonds       : angle       3.83495 ( 1068)

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

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

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 52
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
REVERT: A  509 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8636 (tt)
REVERT: A  774 ARG cc_start: 0.9090 (ttm-80) cc_final: 0.8568 (ttp80)
REVERT: A  785 GLU cc_start: 0.8569 (tp30) cc_final: 0.8255 (tm-30)
  outliers start: 24
  outliers final: 10
  residues processed: 73
  average time/residue: 0.5667
  time to fit residues: 43.6362
Evaluate side-chains
  57 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 HIS
Chi-restraints excluded: chain A residue  231 SER
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  509 LEU
Chi-restraints excluded: chain A residue  546 VAL
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  713 LEU
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue  993 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 72 optimal weight:    0.8980
   chunk 25 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0070
   chunk 77 optimal weight:    0.6980
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
A 326 HIS
A 851 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.089838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.061758 restraints weight = 34928.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.2939 rms_B_bonded: 4.37
r_work: 0.2742 rms_B_bonded: 4.78 restraints_weight: 0.5000
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2765
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2765 r_free = 0.2765    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2765 r_free = 0.2765    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2765
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.1495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7170  Z= 0.117
  Angle     :  0.517   6.459   9840  Z= 0.273
  Chirality :  0.041   0.160   1172
  Planarity :  0.004   0.051   1171
  Dihedral  : 14.619 103.134   1291
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.19 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 24.26 %
    Favored  : 71.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.86 (0.30), residues: 849
  helix:  2.20 (0.25), residues: 444
  sheet:  1.03 (0.49), residues: 114
  loop : -0.17 (0.38), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  93 
 TYR   0.017   0.001   TYR A 358 
 PHE   0.011   0.001   PHE A 205 
 TRP   0.007   0.001   TRP A 935 
 HIS   0.004   0.001   HIS A 527 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 7170)
  covalent geometry    : angle       0.51723 ( 9840)
  hydrogen bonds       : bond        0.03319 (  372)
  hydrogen bonds       : angle       3.65444 ( 1068)

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

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

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 46
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
REVERT: A  255 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8080 (mtmm)
REVERT: A  774 ARG cc_start: 0.9126 (ttm-80) cc_final: 0.8593 (ttp80)
REVERT: A  956 ASP cc_start: 0.8593 (m-30) cc_final: 0.8392 (m-30)
  outliers start: 27
  outliers final: 8
  residues processed: 69
  average time/residue: 0.6143
  time to fit residues: 44.6270
Evaluate side-chains
  54 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 HIS
Chi-restraints excluded: chain A residue  255 LYS
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  546 VAL
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  716 CYS
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue  993 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 48 optimal weight:    0.0980
   chunk 33 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 8 optimal weight:    4.9990
   chunk 73 optimal weight:    0.4980
   chunk 13 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   chunk 32 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.089487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.060683 restraints weight = 34335.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.2910 rms_B_bonded: 4.45
r_work: 0.2697 rms_B_bonded: 4.85 restraints_weight: 0.5000
r_work (final): 0.2697
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2706
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2706 r_free = 0.2706    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2706 r_free = 0.2706    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2706
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.1693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7170  Z= 0.113
  Angle     :  0.506   7.813   9840  Z= 0.266
  Chirality :  0.041   0.142   1172
  Planarity :  0.004   0.051   1171
  Dihedral  : 14.327 101.138   1287
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 25.00 %
    Favored  : 72.65 %
  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:  1.95 (0.30), residues: 849
  helix:  2.30 (0.25), residues: 444
  sheet:  0.98 (0.49), residues: 114
  loop : -0.14 (0.39), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  93 
 TYR   0.008   0.001   TYR A 842 
 PHE   0.009   0.001   PHE A 205 
 TRP   0.006   0.001   TRP A 935 
 HIS   0.003   0.001   HIS A 527 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 7170)
  covalent geometry    : angle       0.50621 ( 9840)
  hydrogen bonds       : bond        0.03034 (  372)
  hydrogen bonds       : angle       3.54425 ( 1068)

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

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

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 46
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
REVERT: A  255 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8039 (mtmm)
REVERT: A  774 ARG cc_start: 0.9119 (ttm-80) cc_final: 0.8607 (ttp80)
  outliers start: 16
  outliers final: 6
  residues processed: 59
  average time/residue: 0.6314
  time to fit residues: 39.2417
Evaluate side-chains
  51 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 HIS
Chi-restraints excluded: chain A residue  255 LYS
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  546 VAL
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue  993 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 61 optimal weight:    0.0470
   chunk 74 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   chunk 33 optimal weight:    0.8980
   chunk 54 optimal weight:    5.9990
   chunk 68 optimal weight:    0.0970
   chunk 85 optimal weight:   20.0000
   overall best weight:    0.5676

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.090297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.061902 restraints weight = 32639.370|
|-----------------------------------------------------------------------------|
r_work (start): 0.2920 rms_B_bonded: 4.32
r_work: 0.2715 rms_B_bonded: 4.74 restraints_weight: 0.5000
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2726
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2726 r_free = 0.2726    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2726 r_free = 0.2726    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2726
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.1823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7170  Z= 0.108
  Angle     :  0.510   8.199   9840  Z= 0.266
  Chirality :  0.040   0.134   1172
  Planarity :  0.004   0.049   1171
  Dihedral  : 14.258 100.075   1287
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 25.00 %
    Favored  : 72.65 %
  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:  2.03 (0.30), residues: 849
  helix:  2.36 (0.25), residues: 444
  sheet:  0.96 (0.49), residues: 116
  loop : -0.08 (0.39), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  93 
 TYR   0.011   0.001   TYR A 358 
 PHE   0.008   0.001   PHE A 205 
 TRP   0.007   0.001   TRP A 935 
 HIS   0.004   0.000   HIS A 527 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 7170)
  covalent geometry    : angle       0.50970 ( 9840)
  hydrogen bonds       : bond        0.02966 (  372)
  hydrogen bonds       : angle       3.50108 ( 1068)

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

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

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 48
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
REVERT: A  255 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8028 (mtmm)
REVERT: A  774 ARG cc_start: 0.9133 (ttm-80) cc_final: 0.8577 (ttp80)
  outliers start: 16
  outliers final: 8
  residues processed: 60
  average time/residue: 0.6208
  time to fit residues: 39.2518
Evaluate side-chains
  55 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 HIS
Chi-restraints excluded: chain A residue  255 LYS
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  533 VAL
Chi-restraints excluded: chain A residue  546 VAL
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  716 CYS
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue  993 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   chunk 76 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9990
   overall best weight:    0.9180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.088385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.060234 restraints weight = 32954.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.2894 rms_B_bonded: 4.26
r_work: 0.2688 rms_B_bonded: 4.71 restraints_weight: 0.5000
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2695
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2695 r_free = 0.2695    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2695 r_free = 0.2695    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2695
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.1825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7170  Z= 0.134
  Angle     :  0.518   8.863   9840  Z= 0.272
  Chirality :  0.041   0.133   1172
  Planarity :  0.004   0.048   1171
  Dihedral  : 14.179  98.311   1287
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 26.32 %
    Favored  : 71.91 %
  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:  1.99 (0.30), residues: 849
  helix:  2.35 (0.25), residues: 443
  sheet:  0.96 (0.50), residues: 114
  loop : -0.12 (0.39), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  93 
 TYR   0.009   0.001   TYR A 842 
 PHE   0.009   0.001   PHE A 376 
 TRP   0.006   0.001   TRP A 935 
 HIS   0.005   0.001   HIS A 527 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 7170)
  covalent geometry    : angle       0.51797 ( 9840)
  hydrogen bonds       : bond        0.03194 (  372)
  hydrogen bonds       : angle       3.52290 ( 1068)

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

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

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 47
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 GLN cc_start: 0.8462 (tm-30) cc_final: 0.8220 (pp30)
REVERT: A  255 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8093 (mtmm)
REVERT: A  961 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7791 (tp30)
  outliers start: 12
  outliers final: 7
  residues processed: 57
  average time/residue: 0.6013
  time to fit residues: 36.0486
Evaluate side-chains
  55 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 HIS
Chi-restraints excluded: chain A residue  255 LYS
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  546 VAL
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  716 CYS
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  961 GLU
Chi-restraints excluded: chain A residue  988 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 59 optimal weight:    0.4980
   chunk 20 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0370
   chunk 16 optimal weight:    1.9990
   chunk 44 optimal weight:    5.9990
   chunk 11 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 62 optimal weight:    0.7980
   overall best weight:    0.6058

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.089320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.061540 restraints weight = 32802.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.2918 rms_B_bonded: 4.23
r_work: 0.2713 rms_B_bonded: 4.70 restraints_weight: 0.5000
r_work (final): 0.2713
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2720
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2720 r_free = 0.2720    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2720 r_free = 0.2720    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2720
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.1909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7170  Z= 0.110
  Angle     :  0.514   9.406   9840  Z= 0.267
  Chirality :  0.040   0.132   1172
  Planarity :  0.004   0.048   1171
  Dihedral  : 14.133  97.891   1287
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 25.74 %
    Favored  : 72.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.08 (0.30), residues: 849
  helix:  2.42 (0.25), residues: 444
  sheet:  0.93 (0.49), residues: 116
  loop : -0.05 (0.39), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  93 
 TYR   0.009   0.001   TYR A 358 
 PHE   0.008   0.001   PHE A 376 
 TRP   0.007   0.001   TRP A 935 
 HIS   0.004   0.001   HIS A 527 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 7170)
  covalent geometry    : angle       0.51395 ( 9840)
  hydrogen bonds       : bond        0.02914 (  372)
  hydrogen bonds       : angle       3.48601 ( 1068)

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

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

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 46
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  255 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.8013 (mtmm)
  outliers start: 14
  outliers final: 9
  residues processed: 57
  average time/residue: 0.6180
  time to fit residues: 37.2297
Evaluate side-chains
  56 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 HIS
Chi-restraints excluded: chain A residue  255 LYS
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  533 VAL
Chi-restraints excluded: chain A residue  546 VAL
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  716 CYS
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue  993 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 40 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9980
   chunk 62 optimal weight:    0.6980
   chunk 43 optimal weight:    0.8980
   chunk 59 optimal weight:    0.4980
   chunk 55 optimal weight:    0.0070
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
A 851 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.090143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.062553 restraints weight = 24109.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.2933 rms_B_bonded: 3.76
r_work: 0.2745 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2756
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2756 r_free = 0.2756    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2756 r_free = 0.2756    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2756
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.1998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   7170  Z= 0.108
  Angle     :  0.522   9.717   9840  Z= 0.271
  Chirality :  0.040   0.130   1172
  Planarity :  0.004   0.050   1171
  Dihedral  : 14.060  97.273   1287
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 25.59 %
    Favored  : 72.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.14 (0.30), residues: 849
  helix:  2.47 (0.25), residues: 444
  sheet:  0.97 (0.50), residues: 116
  loop : -0.03 (0.39), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  93 
 TYR   0.007   0.001   TYR A 294 
 PHE   0.008   0.001   PHE A 376 
 TRP   0.006   0.001   TRP A 935 
 HIS   0.004   0.001   HIS A 527 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 7170)
  covalent geometry    : angle       0.52161 ( 9840)
  hydrogen bonds       : bond        0.02885 (  372)
  hydrogen bonds       : angle       3.47188 ( 1068)

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

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

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 47
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 GLN cc_start: 0.8437 (tm-30) cc_final: 0.8170 (pp30)
REVERT: A  214 MET cc_start: 0.9039 (mtp) cc_final: 0.8683 (ttm)
  outliers start: 13
  outliers final: 9
  residues processed: 58
  average time/residue: 0.6212
  time to fit residues: 38.0306
Evaluate side-chains
  55 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 HIS
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  533 VAL
Chi-restraints excluded: chain A residue  546 VAL
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  716 CYS
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue  993 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 83 optimal weight:    0.3980
   chunk 28 optimal weight:    0.0470
   chunk 52 optimal weight:    0.1980
   chunk 4 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   chunk 81 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 15 optimal weight:    4.9990
   overall best weight:    0.4878

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.089815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.061120 restraints weight = 35449.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.2920 rms_B_bonded: 4.51
r_work: 0.2714 rms_B_bonded: 4.89 restraints_weight: 0.5000
r_work (final): 0.2714
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2725
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2725 r_free = 0.2725    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2725 r_free = 0.2725    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2725
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   7170  Z= 0.105
  Angle     :  0.528  10.077   9840  Z= 0.273
  Chirality :  0.040   0.129   1172
  Planarity :  0.004   0.050   1171
  Dihedral  : 14.025  96.900   1287
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 25.88 %
    Favored  : 72.65 %
  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:  2.20 (0.30), residues: 849
  helix:  2.52 (0.25), residues: 444
  sheet:  0.99 (0.50), residues: 116
  loop : -0.00 (0.39), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  93 
 TYR   0.008   0.001   TYR A 842 
 PHE   0.007   0.001   PHE A 376 
 TRP   0.006   0.001   TRP A 935 
 HIS   0.003   0.000   HIS A 527 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 7170)
  covalent geometry    : angle       0.52833 ( 9840)
  hydrogen bonds       : bond        0.02835 (  372)
  hydrogen bonds       : angle       3.45944 ( 1068)

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

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

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8242 (pp30)
REVERT: A  214 MET cc_start: 0.9055 (mtp) cc_final: 0.8710 (ttm)
  outliers start: 10
  outliers final: 9
  residues processed: 54
  average time/residue: 0.5778
  time to fit residues: 32.8555
Evaluate side-chains
  55 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 HIS
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  533 VAL
Chi-restraints excluded: chain A residue  546 VAL
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  716 CYS
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue  993 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 23 optimal weight:    0.0070
   chunk 78 optimal weight:    5.9990
   chunk 38 optimal weight:    0.0030
   chunk 68 optimal weight:    0.0070
   chunk 75 optimal weight:    2.9990
   chunk 41 optimal weight:    0.1980
   chunk 30 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 37 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.1826

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.091541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.064128 restraints weight = 30570.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.2979 rms_B_bonded: 4.14
r_work: 0.2780 rms_B_bonded: 4.67 restraints_weight: 0.5000
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2789
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2789
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.2313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048   7170  Z= 0.095
  Angle     :  0.528  10.380   9840  Z= 0.272
  Chirality :  0.039   0.132   1172
  Planarity :  0.004   0.049   1171
  Dihedral  : 13.974  96.812   1287
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 26.18 %
    Favored  : 72.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.38 (0.31), residues: 849
  helix:  2.66 (0.25), residues: 437
  sheet:  1.01 (0.51), residues: 117
  loop :  0.19 (0.40), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  93 
 TYR   0.007   0.001   TYR A 294 
 PHE   0.006   0.001   PHE A 205 
 TRP   0.005   0.001   TRP A 935 
 HIS   0.003   0.000   HIS A 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 ( 7170)
  covalent geometry    : angle       0.52827 ( 9840)
  hydrogen bonds       : bond        0.02591 (  372)
  hydrogen bonds       : angle       3.42893 ( 1068)

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

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

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1698 Ramachandran restraints generated.
    849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 GLN cc_start: 0.8488 (tm-30) cc_final: 0.8265 (pp30)
REVERT: A  214 MET cc_start: 0.9029 (mtp) cc_final: 0.8718 (ttm)
REVERT: A  433 GLU cc_start: 0.7982 (pm20) cc_final: 0.7637 (mp0)
REVERT: A  961 GLU cc_start: 0.8188 (tp30) cc_final: 0.7968 (mp0)
  outliers start: 9
  outliers final: 8
  residues processed: 54
  average time/residue: 0.6302
  time to fit residues: 35.7255
Evaluate side-chains
  54 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  533 VAL
Chi-restraints excluded: chain A residue  546 VAL
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  716 CYS
Chi-restraints excluded: chain A residue  907 VAL
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue  993 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 82 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 0 optimal weight:   70.0000
   chunk 15 optimal weight:    3.9990
   chunk 74 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 85 optimal weight:   20.0000
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.8580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.089448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.060447 restraints weight = 36712.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.2909 rms_B_bonded: 4.59
r_work: 0.2699 rms_B_bonded: 4.99 restraints_weight: 0.5000
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2709
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2709 r_free = 0.2709    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2709 r_free = 0.2709    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2709
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.2200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7170  Z= 0.133
  Angle     :  0.555  10.280   9840  Z= 0.285
  Chirality :  0.040   0.130   1172
  Planarity :  0.004   0.048   1171
  Dihedral  : 13.879  95.564   1285
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 26.47 %
    Favored  : 72.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.24 (0.30), residues: 849
  helix:  2.55 (0.25), residues: 443
  sheet:  1.07 (0.51), residues: 116
  loop :  0.00 (0.39), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  93 
 TYR   0.013   0.001   TYR A 842 
 PHE   0.008   0.001   PHE A 376 
 TRP   0.006   0.001   TRP A 935 
 HIS   0.005   0.001   HIS A 527 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 7170)
  covalent geometry    : angle       0.55475 ( 9840)
  hydrogen bonds       : bond        0.03052 (  372)
  hydrogen bonds       : angle       3.46337 ( 1068)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2695.64 seconds
wall clock time: 46 minutes 37.95 seconds (2797.95 seconds total)