Starting phenix.real_space_refine
on Wed Feb  4 04:27:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9v4o_64781/02_2026/9v4o_64781.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9v4o_64781/02_2026/9v4o_64781.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9v4o_64781/02_2026/9v4o_64781.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9v4o_64781/02_2026/9v4o_64781.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9v4o_64781/02_2026/9v4o_64781.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9v4o_64781/02_2026/9v4o_64781.cif"
  }
  resolution = 2.92
  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=  -0.052 sd=   0.459
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: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      46      5.16       5
     C    5419      2.51       5
     N    1462      2.21       5
     O    1570      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8498
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1064, 8471
          Classifications: {'peptide': 1064}
          Link IDs: {'PTRANS': 58, 'TRANS': 1005}
          Chain breaks: 6
    Chain: "A"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 27
          Unusual residues: {' ZN': 1}
          Classifications: {'peptide': 1, 'undetermined': 1}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   3133  SG  CYS A 800      31.126  66.065  29.043  1.00 42.29           S
  ATOM   3784  SG  CYS A 880      33.663  66.004  26.272  1.00 44.86           S
  ATOM   3803  SG  CYS A 883      30.540  63.851  25.910  1.00 44.76           S

  Time building chain proxies: 1.79, per 1000 atoms: 0.21
  Number of scatterers: 8498
  At special positions: 0
  Unit cell: (91.8, 108.8, 133.45, 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)
     Zn      1     29.99
     S      46     16.00
     O    1570      8.00
     N    1462      7.00
     C    5419      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: 0.68
  Conformation dependent library (CDL) restraints added in 309.5 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1602 "
        pdb="ZN    ZN A1602 " - pdb=" NE2 HIS A 773 "
        pdb="ZN    ZN A1602 " - pdb=" SG  CYS A 880 "
        pdb="ZN    ZN A1602 " - pdb=" SG  CYS A 800 "
        pdb="ZN    ZN A1602 " - pdb=" SG  CYS A 883 "
      Number of angles added : 3


  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1984

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 15 sheets defined
      30.5% alpha, 25.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 350 through 355
      removed outlier: 3.618A  pdb=" N   ILE A 354 " --> pdb=" O   ASN A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 358
      No H-bonds generated for 'chain 'A' and resid 356 through 358'
    Processing helix  chain 'A' and resid 374 through 376
      No H-bonds generated for 'chain 'A' and resid 374 through 376'
    Processing helix  chain 'A' and resid 407 through 411
      removed outlier: 3.902A  pdb=" N   LEU A 410 " --> pdb=" O   SER A 407 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LEU A 411 " --> pdb=" O   LEU A 408 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 407 through 411'
    Processing helix  chain 'A' and resid 494 through 497
    Processing helix  chain 'A' and resid 498 through 517
      removed outlier: 3.595A  pdb=" N   LEU A 502 " --> pdb=" O   TRP A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 525 through 535
    Processing helix  chain 'A' and resid 547 through 558
    Processing helix  chain 'A' and resid 558 through 566
      removed outlier: 3.966A  pdb=" N   ILE A 562 " --> pdb=" O   HIS A 558 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 586
    Processing helix  chain 'A' and resid 631 through 644
      removed outlier: 3.787A  pdb=" N   PHE A 640 " --> pdb=" O   ILE A 636 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   TYR A 641 " --> pdb=" O   TRP A 637 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 781 through 783
      No H-bonds generated for 'chain 'A' and resid 781 through 783'
    Processing helix  chain 'A' and resid 785 through 789
      removed outlier: 3.765A  pdb=" N   ALA A 789 " --> pdb=" O   GLY A 786 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 822 through 824
      No H-bonds generated for 'chain 'A' and resid 822 through 824'
    Processing helix  chain 'A' and resid 825 through 847
      removed outlier: 3.691A  pdb=" N   ILE A 830 " --> pdb=" O   ARG A 826 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 880 through 892
    Processing helix  chain 'A' and resid 921 through 924
      removed outlier: 3.676A  pdb=" N   ILE A 924 " --> pdb=" O   PRO A 921 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 921 through 924'
    Processing helix  chain 'A' and resid 976 through 980
    Processing helix  chain 'A' and resid 981 through 988
      removed outlier: 3.546A  pdb=" N   ALA A 985 " --> pdb=" O   SER A 981 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1003 through 1005
      No H-bonds generated for 'chain 'A' and resid 1003 through 1005'
    Processing helix  chain 'A' and resid 1015 through 1019
    Processing helix  chain 'A' and resid 1103 through 1112
      removed outlier: 3.547A  pdb=" N   GLY A1108 " --> pdb=" O   GLY A1104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1124 through 1135
      removed outlier: 3.561A  pdb=" N   ASN A1134 " --> pdb=" O   ALA A1130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1144 through 1155
      removed outlier: 3.546A  pdb=" N   ARG A1150 " --> pdb=" O   ASN A1146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1165 through 1174
    Processing helix  chain 'A' and resid 1176 through 1182
      removed outlier: 3.659A  pdb=" N   THR A1182 " --> pdb=" O   GLU A1178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1218 through 1231
      removed outlier: 4.315A  pdb=" N   ALA A1222 " --> pdb=" O   GLU A1218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1242 through 1248
      removed outlier: 3.754A  pdb=" N   PHE A1246 " --> pdb=" O   PHE A1243 " (cutoff:3.500A)
      removed outlier: 7.288A  pdb=" N   ASN A1247 " --> pdb=" O   VAL A1244 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   LYS A1248 " --> pdb=" O   SER A1245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1249 through 1263
      removed outlier: 3.615A  pdb=" N   MET A1262 " --> pdb=" O   SER A1258 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   GLY A1263 " --> pdb=" O   LEU A1259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1274 through 1277
      removed outlier: 3.689A  pdb=" N   GLY A1277 " --> pdb=" O   GLY A1274 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1274 through 1277'
    Processing helix  chain 'A' and resid 1338 through 1343
    Processing helix  chain 'A' and resid 1365 through 1373
      removed outlier: 3.816A  pdb=" N   ARG A1372 " --> pdb=" O   GLN A1368 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   GLY A1373 " --> pdb=" O   LYS A1369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1387 through 1396
    Processing helix  chain 'A' and resid 1404 through 1408
    Processing helix  chain 'A' and resid 1477 through 1484
    Processing helix  chain 'A' and resid 1496 through 1506
    Processing helix  chain 'A' and resid 1509 through 1524
    Processing sheet with id=AA1, first strand: chain 'A' and resid 345 through 349
    Processing sheet with id=AA2, first strand: chain 'A' and resid 371 through 372
      removed outlier: 3.774A  pdb=" N   ALA A 397 " --> pdb=" O   SER A 426 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 430 through 431
      removed outlier: 3.944A  pdb=" N   MET A 392 " --> pdb=" O   THR A 430 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   ARG A 391 " --> pdb=" O   ARG A 486 " (cutoff:3.500A)
      removed outlier: 5.397A  pdb=" N   ILE A 476 " --> pdb=" O   LEU A 487 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 430 through 431
      removed outlier: 3.944A  pdb=" N   MET A 392 " --> pdb=" O   THR A 430 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   ARG A 391 " --> pdb=" O   ARG A 486 " (cutoff:3.500A)
      removed outlier: 5.397A  pdb=" N   ILE A 476 " --> pdb=" O   LEU A 487 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   GLU A 463 " --> pdb=" O   ARG A 479 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 629 through 630
    Processing sheet with id=AA6, first strand: chain 'A' and resid 710 through 712
    Processing sheet with id=AA7, first strand: chain 'A' and resid 718 through 719
      removed outlier: 3.731A  pdb=" N   GLY A 718 " --> pdb=" O   LEU A 726 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   MET A 762 " --> pdb=" O   TYR A 727 " (cutoff:3.500A)
      removed outlier: 7.391A  pdb=" N   ALA A 742 " --> pdb=" O   VAL A 811 " (cutoff:3.500A)
      removed outlier: 5.061A  pdb=" N   VAL A 811 " --> pdb=" O   ALA A 742 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   THR A 744 " --> pdb=" O   LYS A 809 " (cutoff:3.500A)
      removed outlier: 9.484A  pdb=" N   TYR A 852 " --> pdb=" O   VAL A 811 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   SER A 813 " --> pdb=" O   TYR A 852 " (cutoff:3.500A)
      removed outlier: 8.079A  pdb=" N   CYS A 854 " --> pdb=" O   SER A 813 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   GLU A 815 " --> pdb=" O   CYS A 854 " (cutoff:3.500A)
      removed outlier: 8.607A  pdb=" N   SER A 856 " --> pdb=" O   GLU A 815 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   ILE A1192 " --> pdb=" O   LEU A1236 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   GLU A1238 " --> pdb=" O   ILE A1192 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   GLY A1194 " --> pdb=" O   GLU A1238 " (cutoff:3.500A)
      removed outlier: 8.731A  pdb=" N   VAL A1240 " --> pdb=" O   GLY A1194 " (cutoff:3.500A)
      removed outlier: 5.732A  pdb=" N   LEU A1093 " --> pdb=" O   SER A1115 " (cutoff:3.500A)
      removed outlier: 5.835A  pdb=" N   ALA A1117 " --> pdb=" O   LEU A1093 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   THR A1095 " --> pdb=" O   ALA A1117 " (cutoff:3.500A)
      removed outlier: 8.167A  pdb=" N   THR A1139 " --> pdb=" O   ASP A1116 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   LYS A1118 " --> pdb=" O   THR A1139 " (cutoff:3.500A)
      removed outlier: 7.778A  pdb=" N   PHE A1141 " --> pdb=" O   LYS A1118 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   ALA A1120 " --> pdb=" O   PHE A1141 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 718 through 719
      removed outlier: 3.731A  pdb=" N   GLY A 718 " --> pdb=" O   LEU A 726 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   MET A 762 " --> pdb=" O   TYR A 727 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   ILE A 756 " --> pdb=" O   LEU A 777 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   HIS A 773 " --> pdb=" O   GLU A 760 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   MET A 762 " --> pdb=" O   MET A 771 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   MET A 771 " --> pdb=" O   MET A 762 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   LYS A 770 " --> pdb=" O   THR A 803 " (cutoff:3.500A)
      removed outlier: 7.001A  pdb=" N   THR A 803 " --> pdb=" O   LYS A 770 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   LEU A 772 " --> pdb=" O   MET A 801 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   MET A 801 " --> pdb=" O   LEU A 772 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   GLY A 774 " --> pdb=" O   GLU A 799 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   GLU A 799 " --> pdb=" O   GLY A 774 " (cutoff:3.500A)
      removed outlier: 4.770A  pdb=" N   PHE A 776 " --> pdb=" O   THR A 797 " (cutoff:3.500A)
      removed outlier: 7.757A  pdb=" N   LEU A 794 " --> pdb=" O   SER A 856 " (cutoff:3.500A)
      removed outlier: 7.526A  pdb=" N   TYR A 858 " --> pdb=" O   LEU A 794 " (cutoff:3.500A)
      removed outlier: 5.929A  pdb=" N   LEU A 796 " --> pdb=" O   TYR A 858 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   ILE A1192 " --> pdb=" O   LEU A1236 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   GLU A1238 " --> pdb=" O   ILE A1192 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   GLY A1194 " --> pdb=" O   GLU A1238 " (cutoff:3.500A)
      removed outlier: 8.731A  pdb=" N   VAL A1240 " --> pdb=" O   GLY A1194 " (cutoff:3.500A)
      removed outlier: 5.732A  pdb=" N   LEU A1093 " --> pdb=" O   SER A1115 " (cutoff:3.500A)
      removed outlier: 5.835A  pdb=" N   ALA A1117 " --> pdb=" O   LEU A1093 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   THR A1095 " --> pdb=" O   ALA A1117 " (cutoff:3.500A)
      removed outlier: 8.167A  pdb=" N   THR A1139 " --> pdb=" O   ASP A1116 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   LYS A1118 " --> pdb=" O   THR A1139 " (cutoff:3.500A)
      removed outlier: 7.778A  pdb=" N   PHE A1141 " --> pdb=" O   LYS A1118 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   ALA A1120 " --> pdb=" O   PHE A1141 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 904 through 906
    Processing sheet with id=AB1, first strand: chain 'A' and resid 992 through 995
      removed outlier: 7.618A  pdb=" N   LEU A 993 " --> pdb=" O   LEU A1036 " (cutoff:3.500A)
      removed outlier: 7.523A  pdb=" N   PHE A1038 " --> pdb=" O   LEU A 993 " (cutoff:3.500A)
      removed outlier: 6.009A  pdb=" N   PHE A 995 " --> pdb=" O   PHE A1038 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   TYR A 918 " --> pdb=" O   GLU A1008 " (cutoff:3.500A)
      removed outlier: 4.661A  pdb=" N   LYS A1010 " --> pdb=" O   PHE A 916 " (cutoff:3.500A)
      removed outlier: 7.492A  pdb=" N   PHE A 916 " --> pdb=" O   LYS A1010 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   LYS A 970 " --> pdb=" O   LEU A 952 " (cutoff:3.500A)
      removed outlier: 4.928A  pdb=" N   ILE A 954 " --> pdb=" O   ASP A 968 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   ASP A 968 " --> pdb=" O   ILE A 954 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 992 through 995
      removed outlier: 7.618A  pdb=" N   LEU A 993 " --> pdb=" O   LEU A1036 " (cutoff:3.500A)
      removed outlier: 7.523A  pdb=" N   PHE A1038 " --> pdb=" O   LEU A 993 " (cutoff:3.500A)
      removed outlier: 6.009A  pdb=" N   PHE A 995 " --> pdb=" O   PHE A1038 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   SER A1044 " --> pdb=" O   ASP A1039 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1313 through 1315
      removed outlier: 3.686A  pdb=" N   LEU A1319 " --> pdb=" O   LEU A1315 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 1356 through 1357
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1412 through 1414
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1443 through 1444
      removed outlier: 7.332A  pdb=" N   GLY A1443 " --> pdb=" O   PHE A1468 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6

    298 hydrogen bonds defined for protein.
    816 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: 1.60

  Time building geometry restraints manager: 0.94 seconds

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

  Histogram of bond lengths:
        1.15 -     1.28: 1409
        1.28 -     1.42: 2253
        1.42 -     1.55: 4964
        1.55 -     1.68: 3
        1.68 -     1.82: 71
  Bond restraints: 8700
  Sorted by residual:
  bond pdb=" C   SAH A1601 "
       pdb=" OXT SAH A1601 "
    ideal  model  delta    sigma   weight residual
    1.246  1.152  0.094 2.00e-02 2.50e+03 2.20e+01
  bond pdb=" N   SAH A1601 "
       pdb=" CA  SAH A1601 "
    ideal  model  delta    sigma   weight residual
    1.458  1.376  0.082 1.90e-02 2.77e+03 1.87e+01
  bond pdb=" CG  SAH A1601 "
       pdb=" SD  SAH A1601 "
    ideal  model  delta    sigma   weight residual
    1.819  1.735  0.084 2.00e-02 2.50e+03 1.77e+01
  bond pdb=" CA  GLU A1124 "
       pdb=" C   GLU A1124 "
    ideal  model  delta    sigma   weight residual
    1.523  1.574 -0.052 1.28e-02 6.10e+03 1.62e+01
  bond pdb=" C   GLU A1124 "
       pdb=" O   GLU A1124 "
    ideal  model  delta    sigma   weight residual
    1.234  1.187  0.047 1.22e-02 6.72e+03 1.50e+01
  ... (remaining 8695 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.34: 11605
        3.34 -     6.68: 143
        6.68 -    10.03: 13
       10.03 -    13.37: 2
       13.37 -    16.71: 1
  Bond angle restraints: 11764
  Sorted by residual:
  angle pdb=" N   SAH A1601 "
        pdb=" CA  SAH A1601 "
        pdb=" C   SAH A1601 "
      ideal   model   delta    sigma   weight residual
     111.00   94.29   16.71 2.80e+00 1.28e-01 3.56e+01
  angle pdb=" C   SAH A1601 "
        pdb=" CA  SAH A1601 "
        pdb=" CB  SAH A1601 "
      ideal   model   delta    sigma   weight residual
     110.10  119.64   -9.54 1.90e+00 2.77e-01 2.52e+01
  angle pdb=" N   PHE A1333 "
        pdb=" CA  PHE A1333 "
        pdb=" C   PHE A1333 "
      ideal   model   delta    sigma   weight residual
     109.69  116.15   -6.46 1.44e+00 4.82e-01 2.01e+01
  angle pdb=" N   ILE A1121 "
        pdb=" CA  ILE A1121 "
        pdb=" C   ILE A1121 "
      ideal   model   delta    sigma   weight residual
     106.42  112.94   -6.52 1.51e+00 4.39e-01 1.86e+01
  angle pdb=" N   GLU A 518 "
        pdb=" CA  GLU A 518 "
        pdb=" C   GLU A 518 "
      ideal   model   delta    sigma   weight residual
     112.54  107.35    5.19 1.22e+00 6.72e-01 1.81e+01
  ... (remaining 11759 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.92: 4698
       16.92 -    33.83: 433
       33.83 -    50.75: 76
       50.75 -    67.66: 12
       67.66 -    84.58: 9
  Dihedral angle restraints: 5228
    sinusoidal: 2150
      harmonic: 3078
  Sorted by residual:
  dihedral pdb=" CA  LYS A 601 "
           pdb=" C   LYS A 601 "
           pdb=" N   ILE A 602 "
           pdb=" CA  ILE A 602 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.87  -27.13     0      5.00e+00 4.00e-02 2.94e+01
  dihedral pdb=" CA  SER A1057 "
           pdb=" C   SER A1057 "
           pdb=" N   THR A1058 "
           pdb=" CA  THR A1058 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.71  -26.29     0      5.00e+00 4.00e-02 2.76e+01
  dihedral pdb=" CA  TYR A1264 "
           pdb=" C   TYR A1264 "
           pdb=" N   GLN A1265 "
           pdb=" CA  GLN A1265 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.04   24.96     0      5.00e+00 4.00e-02 2.49e+01
  ... (remaining 5225 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1060
       0.068 -    0.136: 195
       0.136 -    0.204: 9
       0.204 -    0.271: 2
       0.271 -    0.339: 1
  Chirality restraints: 1267
  Sorted by residual:
  chirality pdb=" CG  LEU A1428 "
            pdb=" CB  LEU A1428 "
            pdb=" CD1 LEU A1428 "
            pdb=" CD2 LEU A1428 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.25   -0.34 2.00e-01 2.50e+01 2.88e+00
  chirality pdb=" CA  PRO A1309 "
            pdb=" N   PRO A1309 "
            pdb=" C   PRO A1309 "
            pdb=" CB  PRO A1309 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.51    0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CA  TYR A1123 "
            pdb=" N   TYR A1123 "
            pdb=" C   TYR A1123 "
            pdb=" CB  TYR A1123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.11e+00
  ... (remaining 1264 not shown)

  Planarity restraints: 1516
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 577 "    0.045 5.00e-02 4.00e+02   6.80e-02 7.40e+00
        pdb=" N   PRO A 578 "   -0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO A 578 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 578 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A1459 "   -0.039 5.00e-02 4.00e+02   5.86e-02 5.50e+00
        pdb=" N   PRO A1460 "    0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO A1460 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A1460 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A1308 "   -0.038 5.00e-02 4.00e+02   5.69e-02 5.19e+00
        pdb=" N   PRO A1309 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO A1309 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A1309 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 1513 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 355
        2.71 -     3.26: 7820
        3.26 -     3.80: 12464
        3.80 -     4.35: 16407
        4.35 -     4.90: 28314
  Nonbonded interactions: 65360
  Sorted by model distance:
  nonbonded pdb=" N   SAH A1601 "
            pdb=" OXT SAH A1601 "
     model   vdw
     2.161 2.496
  nonbonded pdb=" OH  TYR A 358 "
            pdb=" OE2 GLU A 409 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" NH2 ARG A 708 "
            pdb=" O   ILE A 808 "
     model   vdw
     2.216 3.120
  nonbonded pdb=" OH  TYR A 975 "
            pdb=" OD2 ASP A 998 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   VAL A1308 "
            pdb=" OG  SER A1326 "
     model   vdw
     2.301 3.040
  ... (remaining 65355 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.830
  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:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     9.890
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:6.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8657
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      :  0.007   0.094   8704  Z= 0.326
  Angle     :  0.948  16.710  11767  Z= 0.520
  Chirality :  0.051   0.339   1267
  Planarity :  0.007   0.068   1516
  Dihedral  : 13.475  84.578   3244
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  :  8.86 %
    Favored  : 90.48 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  0.54 %
    Favored  : 98.48 %
  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 are not related in a simple way.
  whole: -2.11 (0.24), residues: 1050
  helix: -0.80 (0.31), residues: 274
  sheet: -0.47 (0.40), residues: 159
  loop : -2.01 (0.23), residues: 617

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 479 
 TYR   0.024   0.003   TYR A 399 
 PHE   0.027   0.003   PHE A1201 
 TRP   0.019   0.003   TRP A1438 
 HIS   0.009   0.002   HIS A1381 

Details of bonding type rmsd
  covalent geometry    : bond        0.00724 ( 8700)
  covalent geometry    : angle       0.94704 (11764)
  hydrogen bonds       : bond        0.21145 (  266)
  hydrogen bonds       : angle       7.25024 (  816)
  metal coordination   : bond        0.01143 (    4)
  metal coordination   : angle       2.54896 (    3)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 115
  time to evaluate  : 0.347 
Fit side-chains
  outliers start: 9
  outliers final: 3
  residues processed: 120
  average time/residue: 0.6297
  time to fit residues: 79.9569
Evaluate side-chains
  95 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 92
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1052 MET
Chi-restraints excluded: chain A residue 1201 PHE
Chi-restraints excluded: chain A residue 1428 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.0770
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.6938

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

Flipped N/Q/H residues before XYZ refinement:
A 384 GLN
A1501 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.055849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2491 r_free = 0.2491 target = 0.045059 restraints weight = 20751.872|
|-----------------------------------------------------------------------------|
r_work (start): 0.2489 rms_B_bonded: 1.77
r_work: 0.2407 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2306 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.2306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8811
moved from start:          0.1375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8704  Z= 0.138
  Angle     :  0.662  16.043  11767  Z= 0.338
  Chirality :  0.044   0.159   1267
  Planarity :  0.006   0.057   1516
  Dihedral  :  5.792  44.954   1163
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  6.48 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  :  8.03 %
    Favored  : 90.34 %
  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 are not related in a simple way.
  whole: -1.45 (0.25), residues: 1050
  helix:  0.08 (0.32), residues: 274
  sheet: -0.21 (0.40), residues: 166
  loop : -1.74 (0.24), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 631 
 TYR   0.017   0.002   TYR A1123 
 PHE   0.024   0.002   PHE A 514 
 TRP   0.014   0.002   TRP A 484 
 HIS   0.003   0.001   HIS A1381 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 8700)
  covalent geometry    : angle       0.66027 (11764)
  hydrogen bonds       : bond        0.04736 (  266)
  hydrogen bonds       : angle       4.82577 (  816)
  metal coordination   : bond        0.01793 (    4)
  metal coordination   : angle       3.07419 (    3)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.363 
Fit side-chains
REVERT: A 1052 MET cc_start: 0.5979 (OUTLIER) cc_final: 0.5719 (pp-130)
  outliers start: 15
  outliers final: 6
  residues processed: 101
  average time/residue: 0.6549
  time to fit residues: 70.2017
Evaluate side-chains
  96 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  489 LYS
Chi-restraints excluded: chain A residue  771 MET
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1052 MET
Chi-restraints excluded: chain A residue 1123 TYR
Chi-restraints excluded: chain A residue 1428 LEU
Chi-restraints excluded: chain A residue 1461 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 77 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 104 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 41 optimal weight:    0.5980
   chunk 71 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 384 GLN
A 537 GLN
A1265 GLN
A1317 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2753 r_free = 0.2753 target = 0.054674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2462 r_free = 0.2462 target = 0.043931 restraints weight = 20428.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.2460 rms_B_bonded: 1.75
r_work: 0.2376 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2275 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.2275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8834
moved from start:          0.1536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8704  Z= 0.149
  Angle     :  0.665  18.022  11767  Z= 0.335
  Chirality :  0.044   0.163   1267
  Planarity :  0.006   0.050   1516
  Dihedral  :  5.450  45.600   1161
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.33 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 11.18 %
    Favored  : 86.86 %
  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 are not related in a simple way.
  whole: -1.21 (0.26), residues: 1050
  helix:  0.44 (0.32), residues: 274
  sheet: -0.15 (0.40), residues: 166
  loop : -1.64 (0.24), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 631 
 TYR   0.016   0.002   TYR A1123 
 PHE   0.028   0.002   PHE A 514 
 TRP   0.015   0.002   TRP A1405 
 HIS   0.005   0.001   HIS A1381 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 8700)
  covalent geometry    : angle       0.66379 (11764)
  hydrogen bonds       : bond        0.05050 (  266)
  hydrogen bonds       : angle       4.64574 (  816)
  metal coordination   : bond        0.01430 (    4)
  metal coordination   : angle       2.86510 (    3)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
  outliers start: 18
  outliers final: 7
  residues processed: 102
  average time/residue: 0.6286
  time to fit residues: 67.9213
Evaluate side-chains
  99 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain A residue  771 MET
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1123 TYR
Chi-restraints excluded: chain A residue 1316 SER
Chi-restraints excluded: chain A residue 1428 LEU
Chi-restraints excluded: chain A residue 1461 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 86 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9980
   chunk 73 optimal weight:    4.9990
   chunk 97 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 94 optimal weight:    3.9990
   chunk 42 optimal weight:    0.5980
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 384 GLN
A 537 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.054593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2459 r_free = 0.2459 target = 0.043806 restraints weight = 20676.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.2456 rms_B_bonded: 1.77
r_work: 0.2372 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2270 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.2270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8838
moved from start:          0.1699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8704  Z= 0.147
  Angle     :  0.658  19.189  11767  Z= 0.330
  Chirality :  0.044   0.159   1267
  Planarity :  0.006   0.050   1516
  Dihedral  :  5.184  47.810   1158
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.14 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 14.01 %
    Favored  : 84.36 %
  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 are not related in a simple way.
  whole: -1.08 (0.26), residues: 1050
  helix:  0.64 (0.33), residues: 275
  sheet: -0.13 (0.40), residues: 166
  loop : -1.59 (0.25), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1023 
 TYR   0.018   0.002   TYR A1025 
 PHE   0.027   0.002   PHE A 514 
 TRP   0.014   0.002   TRP A1405 
 HIS   0.005   0.001   HIS A1381 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 8700)
  covalent geometry    : angle       0.65623 (11764)
  hydrogen bonds       : bond        0.04768 (  266)
  hydrogen bonds       : angle       4.55371 (  816)
  metal coordination   : bond        0.01161 (    4)
  metal coordination   : angle       2.69459 (    3)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.396 
Fit side-chains
REVERT: A  715 GLU cc_start: 0.8839 (pm20) cc_final: 0.8623 (mp0)
REVERT: A 1204 MET cc_start: 0.4697 (pmm) cc_final: 0.3956 (tpp)
  outliers start: 15
  outliers final: 7
  residues processed: 98
  average time/residue: 0.5800
  time to fit residues: 60.3297
Evaluate side-chains
  94 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue  771 MET
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1123 TYR
Chi-restraints excluded: chain A residue 1428 LEU
Chi-restraints excluded: chain A residue 1461 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 84 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 99 optimal weight:    0.0980
   chunk 86 optimal weight:    0.8980
   chunk 96 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 91 optimal weight:    3.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.2752 r_free = 0.2752 target = 0.054816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2456 r_free = 0.2456 target = 0.043822 restraints weight = 21012.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.2453 rms_B_bonded: 1.87
r_work: 0.2365 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2263 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.2263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8845
moved from start:          0.1820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8704  Z= 0.139
  Angle     :  0.644  19.597  11767  Z= 0.322
  Chirality :  0.043   0.150   1267
  Planarity :  0.006   0.049   1516
  Dihedral  :  5.113  48.841   1158
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.95 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 14.22 %
    Favored  : 83.93 %
  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 are not related in a simple way.
  whole: -0.96 (0.26), residues: 1050
  helix:  0.81 (0.33), residues: 273
  sheet: -0.20 (0.39), residues: 172
  loop : -1.50 (0.25), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1023 
 TYR   0.020   0.002   TYR A1025 
 PHE   0.026   0.002   PHE A 514 
 TRP   0.013   0.002   TRP A 484 
 HIS   0.004   0.001   HIS A1381 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 8700)
  covalent geometry    : angle       0.64257 (11764)
  hydrogen bonds       : bond        0.04556 (  266)
  hydrogen bonds       : angle       4.49792 (  816)
  metal coordination   : bond        0.01495 (    4)
  metal coordination   : angle       2.63250 (    3)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 96
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
REVERT: A  481 ASP cc_start: 0.8444 (m-30) cc_final: 0.8143 (m-30)
REVERT: A 1204 MET cc_start: 0.4863 (pmm) cc_final: 0.4341 (tpp)
  outliers start: 17
  outliers final: 11
  residues processed: 106
  average time/residue: 0.6126
  time to fit residues: 69.0246
Evaluate side-chains
  102 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  605 LYS
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue  771 MET
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1123 TYR
Chi-restraints excluded: chain A residue 1242 THR
Chi-restraints excluded: chain A residue 1316 SER
Chi-restraints excluded: chain A residue 1428 LEU
Chi-restraints excluded: chain A residue 1461 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 79 optimal weight:    3.9990
   chunk 83 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   chunk 96 optimal weight:    0.8980
   chunk 9 optimal weight:    0.2980
   chunk 33 optimal weight:    0.9990
   chunk 102 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 57 optimal weight:    0.5980
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A1501 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.055124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2465 r_free = 0.2465 target = 0.044151 restraints weight = 20846.937|
|-----------------------------------------------------------------------------|
r_work (start): 0.2462 rms_B_bonded: 1.87
r_work: 0.2374 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2273 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.2273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8838
moved from start:          0.1962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8704  Z= 0.131
  Angle     :  0.643  19.628  11767  Z= 0.320
  Chirality :  0.043   0.243   1267
  Planarity :  0.005   0.049   1516
  Dihedral  :  5.037  49.565   1158
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.57 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 15.09 %
    Favored  : 83.06 %
  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 are not related in a simple way.
  whole: -0.85 (0.26), residues: 1050
  helix:  0.92 (0.33), residues: 273
  sheet: -0.19 (0.39), residues: 172
  loop : -1.44 (0.25), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1023 
 TYR   0.019   0.002   TYR A1025 
 PHE   0.026   0.002   PHE A 514 
 TRP   0.012   0.002   TRP A1405 
 HIS   0.004   0.001   HIS A 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 8700)
  covalent geometry    : angle       0.64207 (11764)
  hydrogen bonds       : bond        0.04296 (  266)
  hydrogen bonds       : angle       4.44349 (  816)
  metal coordination   : bond        0.01216 (    4)
  metal coordination   : angle       2.43886 (    3)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  481 ASP cc_start: 0.8397 (m-30) cc_final: 0.8094 (m-30)
REVERT: A  764 GLU cc_start: 0.8731 (tt0) cc_final: 0.8463 (mm-30)
REVERT: A 1204 MET cc_start: 0.4893 (OUTLIER) cc_final: 0.4638 (tpp)
  outliers start: 17
  outliers final: 11
  residues processed: 103
  average time/residue: 0.5753
  time to fit residues: 62.8359
Evaluate side-chains
  100 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  605 LYS
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1123 TYR
Chi-restraints excluded: chain A residue 1204 MET
Chi-restraints excluded: chain A residue 1242 THR
Chi-restraints excluded: chain A residue 1311 LEU
Chi-restraints excluded: chain A residue 1428 LEU
Chi-restraints excluded: chain A residue 1453 THR
Chi-restraints excluded: chain A residue 1461 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 25 optimal weight:    0.0040
   chunk 41 optimal weight:    0.8980
   chunk 77 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   chunk 36 optimal weight:    3.9990
   chunk 21 optimal weight:    0.6980
   chunk 68 optimal weight:    0.3980
   chunk 97 optimal weight:    3.9990
   chunk 99 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 104 optimal weight:    0.5980
   overall best weight:    0.4392

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

Flipped N/Q/H residues before XYZ refinement:
A1317 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.056566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2505 r_free = 0.2505 target = 0.045559 restraints weight = 21040.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.2501 rms_B_bonded: 1.88
r_work: 0.2414 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2312 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.2312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8809
moved from start:          0.2162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8704  Z= 0.112
  Angle     :  0.625  19.964  11767  Z= 0.308
  Chirality :  0.042   0.200   1267
  Planarity :  0.005   0.048   1516
  Dihedral  :  4.894  49.967   1158
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.19 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 15.96 %
    Favored  : 82.30 %
  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 are not related in a simple way.
  whole: -0.69 (0.26), residues: 1050
  helix:  1.12 (0.33), residues: 272
  sheet: -0.12 (0.39), residues: 170
  loop : -1.35 (0.25), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1023 
 TYR   0.015   0.001   TYR A1025 
 PHE   0.026   0.001   PHE A 514 
 TRP   0.016   0.002   TRP A 396 
 HIS   0.007   0.001   HIS A 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 8700)
  covalent geometry    : angle       0.62375 (11764)
  hydrogen bonds       : bond        0.03604 (  266)
  hydrogen bonds       : angle       4.28016 (  816)
  metal coordination   : bond        0.01556 (    4)
  metal coordination   : angle       2.55336 (    3)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
REVERT: A  481 ASP cc_start: 0.8280 (m-30) cc_final: 0.7961 (m-30)
REVERT: A  715 GLU cc_start: 0.8802 (pm20) cc_final: 0.8574 (mp0)
REVERT: A  764 GLU cc_start: 0.8697 (tt0) cc_final: 0.8451 (mm-30)
REVERT: A 1461 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8665 (ttp)
  outliers start: 16
  outliers final: 7
  residues processed: 103
  average time/residue: 0.7298
  time to fit residues: 79.2080
Evaluate side-chains
  96 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1123 TYR
Chi-restraints excluded: chain A residue 1242 THR
Chi-restraints excluded: chain A residue 1311 LEU
Chi-restraints excluded: chain A residue 1316 SER
Chi-restraints excluded: chain A residue 1461 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 9 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 60 optimal weight:    0.2980
   chunk 44 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 29 optimal weight:    0.1980
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A1501 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.055907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2485 r_free = 0.2485 target = 0.044819 restraints weight = 21174.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.2482 rms_B_bonded: 1.89
r_work: 0.2394 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2293 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.2293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8823
moved from start:          0.2177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8704  Z= 0.125
  Angle     :  0.647  20.083  11767  Z= 0.320
  Chirality :  0.042   0.168   1267
  Planarity :  0.005   0.049   1516
  Dihedral  :  4.698  19.502   1156
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.29 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 16.07 %
    Favored  : 81.87 %
  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 are not related in a simple way.
  whole: -0.67 (0.26), residues: 1050
  helix:  1.11 (0.33), residues: 274
  sheet: -0.09 (0.39), residues: 171
  loop : -1.33 (0.25), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1023 
 TYR   0.016   0.001   TYR A1025 
 PHE   0.025   0.002   PHE A 514 
 TRP   0.023   0.002   TRP A 396 
 HIS   0.007   0.001   HIS A 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 8700)
  covalent geometry    : angle       0.64577 (11764)
  hydrogen bonds       : bond        0.04026 (  266)
  hydrogen bonds       : angle       4.32644 (  816)
  metal coordination   : bond        0.00980 (    4)
  metal coordination   : angle       2.18462 (    3)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
REVERT: A  481 ASP cc_start: 0.8296 (m-30) cc_final: 0.7990 (m-30)
REVERT: A  715 GLU cc_start: 0.8835 (pm20) cc_final: 0.8607 (mp0)
REVERT: A  764 GLU cc_start: 0.8699 (tt0) cc_final: 0.8447 (mm-30)
REVERT: A 1093 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8202 (mt)
  outliers start: 19
  outliers final: 13
  residues processed: 106
  average time/residue: 0.6566
  time to fit residues: 73.8256
Evaluate side-chains
  101 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  605 LYS
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue  990 ILE
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1093 LEU
Chi-restraints excluded: chain A residue 1123 TYR
Chi-restraints excluded: chain A residue 1159 GLN
Chi-restraints excluded: chain A residue 1242 THR
Chi-restraints excluded: chain A residue 1311 LEU
Chi-restraints excluded: chain A residue 1316 SER
Chi-restraints excluded: chain A residue 1453 THR
Chi-restraints excluded: chain A residue 1461 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 96 optimal weight:    0.0570
   chunk 29 optimal weight:    0.9980
   chunk 55 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 59 optimal weight:    0.0670
   chunk 27 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9990
   chunk 92 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.4636

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

Flipped N/Q/H residues before XYZ refinement:
A1317 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.056553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2501 r_free = 0.2501 target = 0.045391 restraints weight = 21266.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.2498 rms_B_bonded: 1.92
r_work: 0.2412 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2311 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8807
moved from start:          0.2289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8704  Z= 0.115
  Angle     :  0.638  20.272  11767  Z= 0.313
  Chirality :  0.042   0.145   1267
  Planarity :  0.005   0.049   1516
  Dihedral  :  4.598  19.510   1156
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.71 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 16.72 %
    Favored  : 81.43 %
  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 are not related in a simple way.
  whole: -0.57 (0.26), residues: 1050
  helix:  1.20 (0.33), residues: 274
  sheet:  0.06 (0.39), residues: 167
  loop : -1.29 (0.25), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1023 
 TYR   0.015   0.001   TYR A1025 
 PHE   0.026   0.002   PHE A 514 
 TRP   0.029   0.002   TRP A 396 
 HIS   0.005   0.001   HIS A 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 8700)
  covalent geometry    : angle       0.63703 (11764)
  hydrogen bonds       : bond        0.03662 (  266)
  hydrogen bonds       : angle       4.24919 (  816)
  metal coordination   : bond        0.00793 (    4)
  metal coordination   : angle       1.95837 (    3)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
REVERT: A  472 ASP cc_start: 0.8477 (m-30) cc_final: 0.8120 (t0)
REVERT: A  481 ASP cc_start: 0.8194 (m-30) cc_final: 0.7891 (m-30)
REVERT: A  715 GLU cc_start: 0.8798 (pm20) cc_final: 0.8598 (mp0)
REVERT: A  764 GLU cc_start: 0.8692 (tt0) cc_final: 0.8459 (mm-30)
REVERT: A  847 ASP cc_start: 0.7909 (t70) cc_final: 0.7644 (t70)
REVERT: A 1093 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8143 (mt)
  outliers start: 17
  outliers final: 12
  residues processed: 102
  average time/residue: 0.6529
  time to fit residues: 70.7050
Evaluate side-chains
  100 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  605 LYS
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue  990 ILE
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1093 LEU
Chi-restraints excluded: chain A residue 1123 TYR
Chi-restraints excluded: chain A residue 1159 GLN
Chi-restraints excluded: chain A residue 1242 THR
Chi-restraints excluded: chain A residue 1311 LEU
Chi-restraints excluded: chain A residue 1316 SER
Chi-restraints excluded: chain A residue 1453 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 55 optimal weight:    0.2980
   chunk 44 optimal weight:    0.5980
   chunk 46 optimal weight:    2.9990
   chunk 84 optimal weight:    0.0980
   chunk 34 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 26 optimal weight:    0.3980
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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 = 0.2799 r_free = 0.2799 target = 0.056657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2506 r_free = 0.2506 target = 0.045553 restraints weight = 21281.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.2503 rms_B_bonded: 1.91
r_work: 0.2417 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2316 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8803
moved from start:          0.2361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8704  Z= 0.114
  Angle     :  0.635  20.162  11767  Z= 0.313
  Chirality :  0.042   0.133   1267
  Planarity :  0.005   0.047   1516
  Dihedral  :  4.548  19.241   1156
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.19 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 17.05 %
    Favored  : 81.22 %
  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 are not related in a simple way.
  whole: -0.55 (0.26), residues: 1050
  helix:  1.18 (0.33), residues: 275
  sheet:  0.09 (0.39), residues: 164
  loop : -1.27 (0.25), residues: 611

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1023 
 TYR   0.014   0.001   TYR A1025 
 PHE   0.025   0.001   PHE A 514 
 TRP   0.031   0.002   TRP A 396 
 HIS   0.005   0.001   HIS A 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 8700)
  covalent geometry    : angle       0.63451 (11764)
  hydrogen bonds       : bond        0.03626 (  266)
  hydrogen bonds       : angle       4.19441 (  816)
  metal coordination   : bond        0.00725 (    4)
  metal coordination   : angle       1.86729 (    3)

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

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

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2100 Ramachandran restraints generated.
    1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
REVERT: A  472 ASP cc_start: 0.8476 (m-30) cc_final: 0.8116 (t0)
REVERT: A  764 GLU cc_start: 0.8686 (tt0) cc_final: 0.8477 (mm-30)
REVERT: A  879 PHE cc_start: 0.8433 (t80) cc_final: 0.8224 (t80)
REVERT: A 1093 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8123 (mt)
  outliers start: 16
  outliers final: 12
  residues processed: 98
  average time/residue: 0.7210
  time to fit residues: 74.7541
Evaluate side-chains
  99 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  605 LYS
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue  990 ILE
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1093 LEU
Chi-restraints excluded: chain A residue 1123 TYR
Chi-restraints excluded: chain A residue 1159 GLN
Chi-restraints excluded: chain A residue 1242 THR
Chi-restraints excluded: chain A residue 1311 LEU
Chi-restraints excluded: chain A residue 1316 SER
Chi-restraints excluded: chain A residue 1453 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   chunk 90 optimal weight:    0.6980
   chunk 96 optimal weight:    1.9990
   chunk 84 optimal weight:    0.2980
   chunk 64 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9980
   chunk 105 optimal weight:    0.7980
   chunk 23 optimal weight:    0.2980
   chunk 7 optimal weight:    0.3980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A1317 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.056552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2502 r_free = 0.2502 target = 0.045435 restraints weight = 21166.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.2499 rms_B_bonded: 1.92
r_work: 0.2414 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2312 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8805
moved from start:          0.2374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8704  Z= 0.121
  Angle     :  0.655  19.971  11767  Z= 0.322
  Chirality :  0.042   0.162   1267
  Planarity :  0.005   0.049   1516
  Dihedral  :  4.548  19.180   1156
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.90 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 17.16 %
    Favored  : 81.22 %
  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 are not related in a simple way.
  whole: -0.53 (0.26), residues: 1050
  helix:  1.20 (0.33), residues: 273
  sheet:  0.17 (0.39), residues: 166
  loop : -1.29 (0.25), residues: 611

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1023 
 TYR   0.015   0.001   TYR A1025 
 PHE   0.025   0.002   PHE A 514 
 TRP   0.021   0.002   TRP A 396 
 HIS   0.005   0.001   HIS A 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 8700)
  covalent geometry    : angle       0.65477 (11764)
  hydrogen bonds       : bond        0.03734 (  266)
  hydrogen bonds       : angle       4.22301 (  816)
  metal coordination   : bond        0.00582 (    4)
  metal coordination   : angle       1.71640 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2782.33 seconds
wall clock time: 48 minutes 14.54 seconds (2894.54 seconds total)