Starting phenix.real_space_refine on Sat Jul 4 23:20:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bpe_16150/07_2026/8bpe_16150.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bpe_16150/07_2026/8bpe_16150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8bpe_16150/07_2026/8bpe_16150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bpe_16150/07_2026/8bpe_16150.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8bpe_16150/07_2026/8bpe_16150.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bpe_16150/07_2026/8bpe_16150.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bpe_16150/07_2026/8bpe_16150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bpe_16150/07_2026/8bpe_16150.map" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 142 5.16 5 C 15196 2.51 5 N 4122 2.21 5 O 4735 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24195 Number of models: 1 Model: "" Number of chains: 30 Chain: "C" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1740 Classifications: {'peptide': 224} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1757 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 207} Chain: "K" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1772 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 210} Chain: "M" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 797 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "P" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 797 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "G" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "E" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1743 Classifications: {'peptide': 224} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 205} Chain: "O" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 797 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "R" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 797 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "N" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 797 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "Q" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 797 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "S" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 797 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "B" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1756 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 207} Chain: "A" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1790 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 212} Chain: "I" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 805 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "J" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 827 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 6, 'TRANS': 96} Chain breaks: 1 Chain: "L" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1001 Classifications: {'peptide': 128} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 115} Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.56, per 1000 atoms: 0.23 Number of scatterers: 24195 At special positions: 0 Unit cell: (191.16, 119.88, 170.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 142 16.00 O 4735 8.00 N 4122 7.00 C 15196 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 426 " distance=2.03 Simple disulfide: pdb=" SG CYS C 414 " - pdb=" SG CYS B 414 " distance=2.06 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 536 " distance=2.04 Simple disulfide: pdb=" SG CYS H 367 " - pdb=" SG CYS H 426 " distance=2.03 Simple disulfide: pdb=" SG CYS H 414 " - pdb=" SG CYS K 414 " distance=1.69 Simple disulfide: pdb=" SG CYS H 474 " - pdb=" SG CYS H 536 " distance=2.04 Simple disulfide: pdb=" SG CYS K 367 " - pdb=" SG CYS K 426 " distance=2.03 Simple disulfide: pdb=" SG CYS K 474 " - pdb=" SG CYS K 536 " distance=2.04 Simple disulfide: pdb=" SG CYS M 37 " - pdb=" SG CYS M 104 " distance=2.03 Simple disulfide: pdb=" SG CYS M 49 " - pdb=" SG CYS M 58 " distance=2.03 Simple disulfide: pdb=" SG CYS D 367 " - pdb=" SG CYS D 426 " distance=2.03 Simple disulfide: pdb=" SG CYS D 414 " - pdb=" SG CYS E 414 " distance=2.21 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 536 " distance=2.03 Simple disulfide: pdb=" SG CYS P 37 " - pdb=" SG CYS P 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 49 " - pdb=" SG CYS P 58 " distance=2.03 Simple disulfide: pdb=" SG CYS F 367 " - pdb=" SG CYS F 426 " distance=2.05 Simple disulfide: pdb=" SG CYS F 414 " - pdb=" SG CYS G 414 " distance=2.03 Simple disulfide: pdb=" SG CYS F 474 " - pdb=" SG CYS F 536 " distance=2.04 Simple disulfide: pdb=" SG CYS G 367 " - pdb=" SG CYS G 426 " distance=2.03 Simple disulfide: pdb=" SG CYS G 474 " - pdb=" SG CYS G 536 " distance=2.03 Simple disulfide: pdb=" SG CYS E 367 " - pdb=" SG CYS E 426 " distance=2.05 Simple disulfide: pdb=" SG CYS E 474 " - pdb=" SG CYS E 536 " distance=2.04 Simple disulfide: pdb=" SG CYS O 37 " - pdb=" SG CYS O 104 " distance=2.03 Simple disulfide: pdb=" SG CYS O 49 " - pdb=" SG CYS O 58 " distance=2.03 Simple disulfide: pdb=" SG CYS R 37 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 49 " - pdb=" SG CYS R 58 " distance=2.03 Simple disulfide: pdb=" SG CYS N 37 " - pdb=" SG CYS N 104 " distance=2.03 Simple disulfide: pdb=" SG CYS N 49 " - pdb=" SG CYS N 58 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 37 " - pdb=" SG CYS Q 104 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 49 " - pdb=" SG CYS Q 58 " distance=2.03 Simple disulfide: pdb=" SG CYS S 37 " - pdb=" SG CYS S 104 " distance=2.03 Simple disulfide: pdb=" SG CYS S 49 " - pdb=" SG CYS S 58 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 536 " distance=2.04 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 536 " distance=2.03 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS J 68 " distance=2.16 Simple disulfide: pdb=" SG CYS I 37 " - pdb=" SG CYS I 104 " distance=2.03 Simple disulfide: pdb=" SG CYS I 49 " - pdb=" SG CYS I 58 " distance=1.58 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 100 " distance=2.03 Simple disulfide: pdb=" SG CYS J 14 " - pdb=" SG CYS L 575 " distance=2.03 Simple disulfide: pdb=" SG CYS J 108 " - pdb=" SG CYS J 133 " distance=2.03 Simple disulfide: pdb=" SG CYS L 474 " - pdb=" SG CYS L 536 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A 601 " - " ASN A 563 " " NAG B 601 " - " ASN B 563 " " NAG C 601 " - " ASN C 563 " " NAG D 601 " - " ASN D 563 " " NAG G 601 " - " ASN G 563 " " NAG H 601 " - " ASN H 563 " " NAG K 601 " - " ASN K 563 " " NAG L 601 " - " ASN L 563 " " NAG T 1 " - " ASN F 563 " " NAG U 1 " - " ASN E 563 " " NAG V 1 " - " ASN J 48 " Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 1.1 seconds 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5850 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 72 sheets defined 10.2% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 460 through 465 Processing helix chain 'C' and resid 496 through 498 No H-bonds generated for 'chain 'C' and resid 496 through 498' Processing helix chain 'C' and resid 524 through 529 Processing helix chain 'H' and resid 353 through 360 Processing helix chain 'H' and resid 414 through 419 Processing helix chain 'H' and resid 524 through 529 Processing helix chain 'K' and resid 353 through 360 removed outlier: 3.538A pdb=" N LEU K 359 " --> pdb=" O ALA K 355 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR K 360 " --> pdb=" O SER K 356 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 421 removed outlier: 3.807A pdb=" N TRP K 418 " --> pdb=" O CYS K 414 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY K 421 " --> pdb=" O ASP K 417 " (cutoff:3.500A) Processing helix chain 'K' and resid 460 through 465 Processing helix chain 'K' and resid 496 through 498 No H-bonds generated for 'chain 'K' and resid 496 through 498' Processing helix chain 'K' and resid 524 through 531 Processing helix chain 'M' and resid 69 through 73 Processing helix chain 'D' and resid 353 through 361 Processing helix chain 'D' and resid 414 through 420 removed outlier: 3.603A pdb=" N TRP D 418 " --> pdb=" O CYS D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 466 Processing helix chain 'D' and resid 525 through 530 Processing helix chain 'P' and resid 69 through 73 Processing helix chain 'F' and resid 353 through 361 Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 462 through 466 removed outlier: 3.765A pdb=" N ASN F 465 " --> pdb=" O GLU F 462 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU F 466 " --> pdb=" O GLN F 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 462 through 466' Processing helix chain 'F' and resid 496 through 498 No H-bonds generated for 'chain 'F' and resid 496 through 498' Processing helix chain 'F' and resid 524 through 530 Processing helix chain 'G' and resid 353 through 361 Processing helix chain 'G' and resid 414 through 420 removed outlier: 3.901A pdb=" N TRP G 418 " --> pdb=" O CYS G 414 " (cutoff:3.500A) Processing helix chain 'G' and resid 460 through 466 removed outlier: 3.537A pdb=" N LEU G 466 " --> pdb=" O GLU G 462 " (cutoff:3.500A) Processing helix chain 'G' and resid 525 through 530 Processing helix chain 'E' and resid 353 through 361 Processing helix chain 'E' and resid 414 through 421 removed outlier: 3.815A pdb=" N TRP E 418 " --> pdb=" O CYS E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 466 removed outlier: 3.765A pdb=" N ASN E 465 " --> pdb=" O GLU E 462 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU E 466 " --> pdb=" O GLN E 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 462 through 466' Processing helix chain 'E' and resid 496 through 498 No H-bonds generated for 'chain 'E' and resid 496 through 498' Processing helix chain 'E' and resid 524 through 530 Processing helix chain 'O' and resid 69 through 73 Processing helix chain 'R' and resid 69 through 73 Processing helix chain 'N' and resid 69 through 73 Processing helix chain 'Q' and resid 69 through 73 Processing helix chain 'S' and resid 69 through 73 Processing helix chain 'B' and resid 353 through 361 removed outlier: 3.689A pdb=" N LEU B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 421 removed outlier: 3.855A pdb=" N TRP B 418 " --> pdb=" O CYS B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 465 Processing helix chain 'B' and resid 525 through 531 removed outlier: 3.577A pdb=" N GLY B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 360 Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 460 through 466 removed outlier: 3.610A pdb=" N LEU A 466 " --> pdb=" O GLU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 525 through 529 Processing helix chain 'J' and resid 64 through 68 Processing helix chain 'J' and resid 116 through 120 Processing helix chain 'L' and resid 526 through 530 removed outlier: 3.946A pdb=" N ASN L 529 " --> pdb=" O GLU L 526 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 347 through 350 removed outlier: 4.292A pdb=" N ASP C 371 " --> pdb=" O PHE C 405 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE C 405 " --> pdb=" O ASP C 371 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 379 through 383 removed outlier: 3.611A pdb=" N THR C 379 " --> pdb=" O THR C 429 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE C 424 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL C 428 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU C 437 " --> pdb=" O VAL C 428 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N HIS C 430 " --> pdb=" O SER C 435 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N SER C 435 " --> pdb=" O HIS C 430 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 455 through 457 removed outlier: 3.680A pdb=" N THR C 473 " --> pdb=" O LEU C 457 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER C 519 " --> pdb=" O CYS C 474 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE C 520 " --> pdb=" O VAL C 501 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 455 through 457 removed outlier: 3.680A pdb=" N THR C 473 " --> pdb=" O LEU C 457 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 476 " --> pdb=" O ALA C 517 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N TYR C 515 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 493 through 494 removed outlier: 3.566A pdb=" N MET C 489 " --> pdb=" O THR C 535 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 347 through 350 removed outlier: 3.533A pdb=" N THR H 366 " --> pdb=" O ILE H 350 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR H 370 " --> pdb=" O ALA H 407 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ALA H 407 " --> pdb=" O THR H 370 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU H 372 " --> pdb=" O PHE H 405 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 379 through 383 removed outlier: 4.352A pdb=" N THR H 379 " --> pdb=" O THR H 429 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR H 429 " --> pdb=" O THR H 379 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS H 426 " --> pdb=" O GLN H 439 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN H 439 " --> pdb=" O CYS H 426 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 453 through 457 removed outlier: 3.653A pdb=" N THR H 473 " --> pdb=" O LEU H 457 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER H 519 " --> pdb=" O CYS H 474 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL H 501 " --> pdb=" O ILE H 520 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 453 through 457 removed outlier: 3.653A pdb=" N THR H 473 " --> pdb=" O LEU H 457 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N TYR H 515 " --> pdb=" O GLY H 478 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 493 through 494 Processing sheet with id=AB2, first strand: chain 'K' and resid 347 through 350 removed outlier: 4.376A pdb=" N THR K 366 " --> pdb=" O ILE K 350 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU K 365 " --> pdb=" O ALA K 411 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA K 411 " --> pdb=" O LEU K 365 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 379 through 383 removed outlier: 3.574A pdb=" N THR K 379 " --> pdb=" O THR K 429 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR K 425 " --> pdb=" O THR K 383 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 453 through 457 removed outlier: 3.524A pdb=" N TYR K 455 " --> pdb=" O LEU K 475 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR K 473 " --> pdb=" O LEU K 457 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER K 519 " --> pdb=" O CYS K 474 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 493 through 494 Processing sheet with id=AB6, first strand: chain 'K' and resid 561 through 562 removed outlier: 7.185A pdb=" N LEU K 561 " --> pdb=" O TYR L 562 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL L 564 " --> pdb=" O LEU K 561 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL J 33 " --> pdb=" O LEU L 561 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ASN L 563 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG J 35 " --> pdb=" O ASN L 563 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG J 20 " --> pdb=" O GLU J 34 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ALA J 15 " --> pdb=" O ASP J 9 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP J 9 " --> pdb=" O ALA J 15 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE J 17 " --> pdb=" O LEU J 7 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 32 through 38 removed outlier: 3.507A pdb=" N CYS M 37 " --> pdb=" O PHE M 87 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU M 86 " --> pdb=" O TYR M 81 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR M 81 " --> pdb=" O LEU M 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 46 through 48 Processing sheet with id=AB9, first strand: chain 'D' and resid 346 through 350 removed outlier: 3.767A pdb=" N ARG D 346 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR D 366 " --> pdb=" O ILE D 350 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 379 through 383 removed outlier: 3.866A pdb=" N THR D 379 " --> pdb=" O THR D 429 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE D 424 " --> pdb=" O ILE D 441 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE D 441 " --> pdb=" O PHE D 424 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 453 through 457 removed outlier: 5.142A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 453 through 457 removed outlier: 5.142A pdb=" N TYR D 515 " --> pdb=" O GLY D 478 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 485 through 489 removed outlier: 3.744A pdb=" N THR D 535 " --> pdb=" O MET D 489 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 32 through 38 removed outlier: 3.507A pdb=" N CYS P 37 " --> pdb=" O PHE P 87 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU P 86 " --> pdb=" O TYR P 81 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR P 81 " --> pdb=" O LEU P 86 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'P' and resid 46 through 48 Processing sheet with id=AC7, first strand: chain 'F' and resid 346 through 350 removed outlier: 3.552A pdb=" N ARG F 346 " --> pdb=" O THR F 370 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR F 366 " --> pdb=" O ILE F 350 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 380 through 384 removed outlier: 3.529A pdb=" N CYS F 426 " --> pdb=" O GLN F 439 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN F 439 " --> pdb=" O CYS F 426 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL F 428 " --> pdb=" O LEU F 437 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 399 through 400 removed outlier: 3.755A pdb=" N THR F 404 " --> pdb=" O HIS F 400 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 453 through 457 removed outlier: 6.104A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 453 through 457 removed outlier: 6.104A pdb=" N TYR F 515 " --> pdb=" O GLY F 478 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 493 through 494 Processing sheet with id=AD4, first strand: chain 'F' and resid 565 through 567 Processing sheet with id=AD5, first strand: chain 'G' and resid 346 through 350 removed outlier: 3.767A pdb=" N ARG G 346 " --> pdb=" O THR G 370 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR G 366 " --> pdb=" O ILE G 350 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 379 through 383 removed outlier: 3.866A pdb=" N THR G 379 " --> pdb=" O THR G 429 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE G 424 " --> pdb=" O ILE G 441 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE G 441 " --> pdb=" O PHE G 424 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 453 through 457 removed outlier: 5.142A pdb=" N TYR G 515 " --> pdb=" O GLY G 478 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 453 through 457 removed outlier: 5.142A pdb=" N TYR G 515 " --> pdb=" O GLY G 478 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 485 through 489 removed outlier: 3.604A pdb=" N THR G 535 " --> pdb=" O MET G 489 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 346 through 350 removed outlier: 3.552A pdb=" N ARG E 346 " --> pdb=" O THR E 370 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR E 366 " --> pdb=" O ILE E 350 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 380 through 384 removed outlier: 3.529A pdb=" N CYS E 426 " --> pdb=" O GLN E 439 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN E 439 " --> pdb=" O CYS E 426 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL E 428 " --> pdb=" O LEU E 437 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 399 through 400 removed outlier: 3.755A pdb=" N THR E 404 " --> pdb=" O HIS E 400 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 453 through 457 removed outlier: 6.126A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 453 through 457 removed outlier: 6.126A pdb=" N TYR E 515 " --> pdb=" O GLY E 478 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 493 through 494 Processing sheet with id=AE7, first strand: chain 'O' and resid 32 through 38 removed outlier: 3.507A pdb=" N CYS O 37 " --> pdb=" O PHE O 87 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU O 86 " --> pdb=" O TYR O 81 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR O 81 " --> pdb=" O LEU O 86 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 46 through 48 Processing sheet with id=AE9, first strand: chain 'O' and resid 50 through 51 Processing sheet with id=AF1, first strand: chain 'R' and resid 32 through 38 removed outlier: 3.508A pdb=" N CYS R 37 " --> pdb=" O PHE R 87 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU R 86 " --> pdb=" O TYR R 81 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR R 81 " --> pdb=" O LEU R 86 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 46 through 48 Processing sheet with id=AF3, first strand: chain 'N' and resid 32 through 38 removed outlier: 3.506A pdb=" N CYS N 37 " --> pdb=" O PHE N 87 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU N 86 " --> pdb=" O TYR N 81 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR N 81 " --> pdb=" O LEU N 86 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 46 through 48 Processing sheet with id=AF5, first strand: chain 'Q' and resid 32 through 38 removed outlier: 3.507A pdb=" N CYS Q 37 " --> pdb=" O PHE Q 87 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU Q 86 " --> pdb=" O TYR Q 81 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR Q 81 " --> pdb=" O LEU Q 86 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 46 through 48 Processing sheet with id=AF7, first strand: chain 'S' and resid 32 through 38 removed outlier: 3.507A pdb=" N CYS S 37 " --> pdb=" O PHE S 87 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU S 86 " --> pdb=" O TYR S 81 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR S 81 " --> pdb=" O LEU S 86 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'S' and resid 46 through 48 Processing sheet with id=AF9, first strand: chain 'B' and resid 379 through 383 Processing sheet with id=AG1, first strand: chain 'B' and resid 453 through 457 removed outlier: 3.503A pdb=" N THR B 473 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 453 through 457 removed outlier: 3.503A pdb=" N THR B 473 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N TYR B 515 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 493 through 494 removed outlier: 3.821A pdb=" N TYR B 534 " --> pdb=" O VAL B 552 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL B 552 " --> pdb=" O TYR B 534 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 561 through 563 Processing sheet with id=AG5, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AG6, first strand: chain 'A' and resid 380 through 384 Processing sheet with id=AG7, first strand: chain 'A' and resid 453 through 457 Processing sheet with id=AG8, first strand: chain 'A' and resid 453 through 457 removed outlier: 5.142A pdb=" N THR A 477 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ALA A 517 " --> pdb=" O THR A 477 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'A' and resid 493 through 494 removed outlier: 3.687A pdb=" N MET A 489 " --> pdb=" O THR A 535 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'A' and resid 493 through 494 removed outlier: 3.687A pdb=" N MET A 489 " --> pdb=" O THR A 535 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A 534 " --> pdb=" O VAL A 552 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'A' and resid 565 through 569 removed outlier: 3.584A pdb=" N PHE J 60 " --> pdb=" O SER A 565 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 32 through 38 removed outlier: 3.681A pdb=" N CYS I 37 " --> pdb=" O PHE I 87 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'I' and resid 100 through 105 removed outlier: 3.589A pdb=" N CYS I 104 " --> pdb=" O GLN I 116 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN I 116 " --> pdb=" O CYS I 104 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'J' and resid 40 through 42 Processing sheet with id=AH6, first strand: chain 'J' and resid 110 through 115 Processing sheet with id=AH7, first strand: chain 'L' and resid 454 through 457 removed outlier: 3.923A pdb=" N ILE L 520 " --> pdb=" O VAL L 501 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 454 through 457 Processing sheet with id=AH9, first strand: chain 'L' and resid 489 through 490 712 hydrogen bonds defined for protein. 1824 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: 4.33 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5680 1.33 - 1.45: 5084 1.45 - 1.58: 13767 1.58 - 1.70: 0 1.70 - 1.82: 197 Bond restraints: 24728 Sorted by residual: bond pdb=" N GLY K 557 " pdb=" CA GLY K 557 " ideal model delta sigma weight residual 1.443 1.477 -0.034 8.60e-03 1.35e+04 1.58e+01 bond pdb=" C MET B 568 " pdb=" N SER B 569 " ideal model delta sigma weight residual 1.331 1.380 -0.049 1.33e-02 5.65e+03 1.36e+01 bond pdb=" N VAL D 547 " pdb=" CA VAL D 547 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.14e-02 7.69e+03 1.31e+01 bond pdb=" N VAL G 547 " pdb=" CA VAL G 547 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.14e-02 7.69e+03 1.26e+01 bond pdb=" N VAL A 552 " pdb=" CA VAL A 552 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.11e-02 8.12e+03 1.25e+01 ... (remaining 24723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 28827 1.58 - 3.17: 4399 3.17 - 4.75: 472 4.75 - 6.34: 23 6.34 - 7.92: 3 Bond angle restraints: 33724 Sorted by residual: angle pdb=" CA GLY M 107 " pdb=" C GLY M 107 " pdb=" O GLY M 107 " ideal model delta sigma weight residual 122.29 118.20 4.09 8.10e-01 1.52e+00 2.55e+01 angle pdb=" CA GLY N 107 " pdb=" C GLY N 107 " pdb=" O GLY N 107 " ideal model delta sigma weight residual 122.29 118.20 4.09 8.10e-01 1.52e+00 2.54e+01 angle pdb=" CA GLY O 107 " pdb=" C GLY O 107 " pdb=" O GLY O 107 " ideal model delta sigma weight residual 122.29 118.24 4.05 8.10e-01 1.52e+00 2.50e+01 angle pdb=" CA GLY Q 107 " pdb=" C GLY Q 107 " pdb=" O GLY Q 107 " ideal model delta sigma weight residual 122.29 118.26 4.03 8.10e-01 1.52e+00 2.48e+01 angle pdb=" CA GLY P 107 " pdb=" C GLY P 107 " pdb=" O GLY P 107 " ideal model delta sigma weight residual 122.29 118.30 3.99 8.10e-01 1.52e+00 2.42e+01 ... (remaining 33719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 13726 17.97 - 35.93: 1007 35.93 - 53.90: 168 53.90 - 71.86: 71 71.86 - 89.83: 15 Dihedral angle restraints: 14987 sinusoidal: 5954 harmonic: 9033 Sorted by residual: dihedral pdb=" CB CYS A 367 " pdb=" SG CYS A 367 " pdb=" SG CYS A 426 " pdb=" CB CYS A 426 " ideal model delta sinusoidal sigma weight residual -86.00 -173.30 87.30 1 1.00e+01 1.00e-02 9.15e+01 dihedral pdb=" CB CYS J 14 " pdb=" SG CYS J 14 " pdb=" SG CYS L 575 " pdb=" CB CYS L 575 " ideal model delta sinusoidal sigma weight residual -86.00 -160.89 74.89 1 1.00e+01 1.00e-02 7.10e+01 dihedral pdb=" CB CYS J 12 " pdb=" SG CYS J 12 " pdb=" SG CYS J 100 " pdb=" CB CYS J 100 " ideal model delta sinusoidal sigma weight residual 93.00 155.46 -62.46 1 1.00e+01 1.00e-02 5.16e+01 ... (remaining 14984 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.167: 3889 0.167 - 0.333: 114 0.333 - 0.500: 2 0.500 - 0.666: 0 0.666 - 0.833: 2 Chirality restraints: 4007 Sorted by residual: chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN E 563 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.57 -0.83 2.00e-01 2.50e+01 1.73e+01 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN F 563 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.57 -0.83 2.00e-01 2.50e+01 1.70e+01 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.23e+01 ... (remaining 4004 not shown) Planarity restraints: 4306 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN K 563 " -0.039 2.00e-02 2.50e+03 4.17e-02 2.18e+01 pdb=" CG ASN K 563 " 0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN K 563 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN K 563 " 0.066 2.00e-02 2.50e+03 pdb=" C1 NAG K 601 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 546 " -0.278 9.50e-02 1.11e+02 1.24e-01 9.51e+00 pdb=" NE ARG A 546 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 546 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 546 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 546 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 75 " -0.274 9.50e-02 1.11e+02 1.23e-01 9.31e+00 pdb=" NE ARG I 75 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG I 75 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG I 75 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG I 75 " -0.009 2.00e-02 2.50e+03 ... (remaining 4303 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 5783 2.81 - 3.33: 21942 3.33 - 3.85: 37188 3.85 - 4.38: 42360 4.38 - 4.90: 73171 Nonbonded interactions: 180444 Sorted by model distance: nonbonded pdb=" O LEU H 372 " pdb=" OG1 THR H 404 " model vdw 2.283 3.040 nonbonded pdb=" OG SER L 469 " pdb=" O VAL L 523 " model vdw 2.287 3.040 nonbonded pdb=" OG1 THR K 379 " pdb=" OG1 THR K 429 " model vdw 2.305 3.040 nonbonded pdb=" O ILE J 5 " pdb=" OG1 THR J 18 " model vdw 2.308 3.040 nonbonded pdb=" O ASP K 417 " pdb=" OG SER K 420 " model vdw 2.319 3.040 ... (remaining 180439 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 346 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 568)) selection = (chain 'B' and (resid 346 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 568)) selection = (chain 'C' and resid 346 through 568) selection = (chain 'D' and (resid 346 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 568)) selection = (chain 'E' and (resid 346 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 568)) selection = (chain 'F' and (resid 346 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 568)) selection = (chain 'G' and (resid 346 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 568)) selection = (chain 'H' and (resid 346 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 568)) selection = (chain 'K' and (resid 346 through 512 or (resid 513 and (name N or name CA or na \ me C )) or resid 514 through 568)) } ncs_group { reference = (chain 'I' and resid 20 through 124) selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } ncs_group { reference = chain 'T' selection = chain 'U' selection = chain 'V' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.630 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 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 : 0.010 0.452 24785 Z= 0.692 Angle : 1.117 30.861 33852 Z= 0.782 Chirality : 0.076 0.833 4007 Planarity : 0.008 0.124 4295 Dihedral : 13.291 89.830 9008 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % 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 (0.15), residues: 3064 helix: -1.54 (0.29), residues: 250 sheet: 0.26 (0.16), residues: 1147 loop : -1.82 (0.14), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 467 TYR 0.011 0.001 TYR E 500 PHE 0.019 0.002 PHE L 479 TRP 0.020 0.001 TRP C 418 HIS 0.008 0.001 HIS A 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00898 / 0.67 (24728) covalent geometry : angle 1.07441 / 0.77 (33724) SS BOND : bond 0.09310 / 8.03 ( 43) SS BOND : angle 5.05121 / 3.29 ( 86) hydrogen bonds : bond 0.25796 / 16.70 ( 603) hydrogen bonds : angle 8.90087 / 6.25 ( 1824) link_BETA1-4 : bond 0.01877 / 0.94 ( 3) link_BETA1-4 : angle 3.74486 / 2.66 ( 9) link_NAG-ASN : bond 0.01482 / 0.79 ( 11) link_NAG-ASN : angle 5.47554 / 3.91 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 678 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 384 ARG cc_start: 0.6392 (mmm160) cc_final: 0.5637 (tpp-160) REVERT: S 78 LEU cc_start: 0.4230 (tt) cc_final: 0.3481 (pp) REVERT: B 376 ASP cc_start: 0.7816 (p0) cc_final: 0.7437 (p0) REVERT: I 22 GLU cc_start: 0.8881 (mp0) cc_final: 0.8503 (mp0) REVERT: I 72 TYR cc_start: 0.7935 (m-80) cc_final: 0.7546 (m-80) REVERT: I 120 LEU cc_start: 0.8715 (tp) cc_final: 0.8508 (tp) REVERT: L 483 ASP cc_start: 0.7683 (m-30) cc_final: 0.7161 (m-30) outliers start: 0 outliers final: 0 residues processed: 678 average time/residue: 0.2135 time to fit residues: 207.6617 Evaluate side-chains 298 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 545 ASN K 430 HIS ** K 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 ASN D 419 ASN ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 GLN ** D 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 ASN P 43 HIS ** P 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 393 HIS F 465 ASN ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 529 ASN F 540 HIS ** G 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 393 HIS E 465 ASN ** E 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 HIS ** O 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 HIS ** N 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 66 ASN ** S 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.096714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.066799 restraints weight = 88327.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.067562 restraints weight = 61293.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.067544 restraints weight = 47089.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.068091 restraints weight = 43656.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.068140 restraints weight = 38680.792| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 24785 Z= 0.237 Angle : 0.778 11.783 33852 Z= 0.402 Chirality : 0.049 0.218 4007 Planarity : 0.005 0.064 4295 Dihedral : 4.525 36.791 3339 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.26 % Allowed : 12.36 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.38 (0.15), residues: 3064 helix: -2.23 (0.24), residues: 292 sheet: 0.49 (0.15), residues: 1117 loop : -1.74 (0.14), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 443 TYR 0.030 0.002 TYR H 562 PHE 0.032 0.002 PHE G 479 TRP 0.019 0.002 TRP E 528 HIS 0.011 0.002 HIS B 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.24 (24728) covalent geometry : angle 0.77270 / 0.40 (33724) SS BOND : bond 0.00630 / 0.44 ( 43) SS BOND : angle 1.50791 / 1.02 ( 86) hydrogen bonds : bond 0.04968 / 3.30 ( 603) hydrogen bonds : angle 6.56064 / 4.54 ( 1824) link_BETA1-4 : bond 0.00632 / 0.32 ( 3) link_BETA1-4 : angle 1.04092 / 0.73 ( 9) link_NAG-ASN : bond 0.00433 / 0.27 ( 11) link_NAG-ASN : angle 2.10320 / 1.49 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 338 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 52 MET cc_start: 0.8457 (tpp) cc_final: 0.7858 (mtm) REVERT: M 72 TYR cc_start: 0.8297 (m-80) cc_final: 0.7939 (m-10) REVERT: D 405 PHE cc_start: 0.6897 (t80) cc_final: 0.6524 (t80) REVERT: D 506 MET cc_start: 0.7817 (mtt) cc_final: 0.7359 (mtt) REVERT: D 568 MET cc_start: 0.5093 (tmm) cc_final: 0.4477 (tmm) REVERT: F 386 ASN cc_start: 0.8638 (t0) cc_final: 0.8313 (t0) REVERT: F 483 ASP cc_start: 0.6628 (t0) cc_final: 0.6296 (t0) REVERT: G 568 MET cc_start: 0.7511 (ptp) cc_final: 0.6940 (mtm) REVERT: E 553 ASP cc_start: 0.7508 (t0) cc_final: 0.6744 (p0) REVERT: O 94 LEU cc_start: 0.7416 (tp) cc_final: 0.6847 (tt) REVERT: S 45 ARG cc_start: 0.6884 (tpt-90) cc_final: 0.5981 (tpt-90) REVERT: S 87 PHE cc_start: 0.4420 (p90) cc_final: 0.3874 (p90) REVERT: B 358 PHE cc_start: 0.8778 (t80) cc_final: 0.8407 (t80) REVERT: B 376 ASP cc_start: 0.8130 (p0) cc_final: 0.7764 (p0) REVERT: B 443 ARG cc_start: 0.8792 (tpt170) cc_final: 0.8553 (ttm-80) REVERT: A 465 ASN cc_start: 0.8663 (m-40) cc_final: 0.8439 (m-40) REVERT: I 22 GLU cc_start: 0.8806 (mp0) cc_final: 0.8414 (mp0) REVERT: I 26 GLU cc_start: 0.6650 (mm-30) cc_final: 0.6225 (mm-30) REVERT: J 29 ASN cc_start: 0.9080 (m-40) cc_final: 0.8739 (m-40) REVERT: L 483 ASP cc_start: 0.7824 (m-30) cc_final: 0.7383 (m-30) REVERT: L 488 TRP cc_start: 0.6803 (m100) cc_final: 0.6368 (m100) outliers start: 62 outliers final: 40 residues processed: 386 average time/residue: 0.1949 time to fit residues: 111.3775 Evaluate side-chains 301 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 261 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 502 THR Chi-restraints excluded: chain K residue 528 TRP Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 98 ASP Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 364 LYS Chi-restraints excluded: chain F residue 384 ARG Chi-restraints excluded: chain F residue 393 HIS Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain E residue 348 PHE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 393 HIS Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 79 LYS Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 527 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 212 optimal weight: 9.9990 chunk 162 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 252 optimal weight: 6.9990 chunk 256 optimal weight: 0.0770 chunk 124 optimal weight: 0.0270 chunk 76 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 GLN D 493 GLN D 529 ASN ** P 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 393 HIS F 510 GLN G 510 GLN E 393 HIS E 510 GLN O 43 HIS ** O 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN L 510 GLN L 518 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.097597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.067806 restraints weight = 88858.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.068917 restraints weight = 59502.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.069378 restraints weight = 43386.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.070043 restraints weight = 37678.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.070108 restraints weight = 33842.390| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24785 Z= 0.132 Angle : 0.677 13.072 33852 Z= 0.343 Chirality : 0.046 0.181 4007 Planarity : 0.004 0.050 4295 Dihedral : 4.230 19.807 3339 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.97 % Favored : 93.99 % Rotamer: Outliers : 1.97 % Allowed : 14.84 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.15), residues: 3064 helix: -2.10 (0.24), residues: 282 sheet: 0.67 (0.15), residues: 1135 loop : -1.55 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 83 TYR 0.026 0.002 TYR K 515 PHE 0.027 0.002 PHE L 479 TRP 0.013 0.001 TRP C 528 HIS 0.012 0.001 HIS E 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (24728) covalent geometry : angle 0.67476 / 0.34 (33724) SS BOND : bond 0.00506 / 0.35 ( 43) SS BOND : angle 0.98886 / 0.66 ( 86) hydrogen bonds : bond 0.03977 / 2.65 ( 603) hydrogen bonds : angle 5.96082 / 4.12 ( 1824) link_BETA1-4 : bond 0.00431 / 0.21 ( 3) link_BETA1-4 : angle 1.50894 / 1.11 ( 9) link_NAG-ASN : bond 0.00163 / 0.09 ( 11) link_NAG-ASN : angle 1.53340 / 1.04 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 305 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 506 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.7310 (mtm) REVERT: K 568 MET cc_start: 0.7589 (mtm) cc_final: 0.7120 (mtp) REVERT: M 72 TYR cc_start: 0.8160 (m-80) cc_final: 0.7814 (m-10) REVERT: D 405 PHE cc_start: 0.6929 (t80) cc_final: 0.6482 (t80) REVERT: D 506 MET cc_start: 0.7751 (mtt) cc_final: 0.7281 (mtt) REVERT: P 84 LYS cc_start: 0.8474 (pttt) cc_final: 0.8061 (mmtm) REVERT: P 108 MET cc_start: 0.8386 (mmm) cc_final: 0.8125 (mmt) REVERT: F 384 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7561 (mtt180) REVERT: G 568 MET cc_start: 0.7396 (ptp) cc_final: 0.6993 (mtm) REVERT: E 553 ASP cc_start: 0.7381 (t0) cc_final: 0.6941 (p0) REVERT: O 94 LEU cc_start: 0.7548 (tp) cc_final: 0.7134 (tt) REVERT: R 83 ARG cc_start: 0.8790 (mmp80) cc_final: 0.8521 (mmp80) REVERT: R 88 LEU cc_start: 0.6876 (tp) cc_final: 0.6492 (tp) REVERT: R 108 MET cc_start: 0.5903 (mmt) cc_final: 0.5637 (mmt) REVERT: N 73 LYS cc_start: 0.8792 (tptp) cc_final: 0.8300 (mmmm) REVERT: S 73 LYS cc_start: 0.8159 (mmmt) cc_final: 0.7792 (mmmt) REVERT: B 376 ASP cc_start: 0.7996 (p0) cc_final: 0.7669 (p0) REVERT: A 545 ASN cc_start: 0.7580 (t0) cc_final: 0.6800 (t0) REVERT: I 22 GLU cc_start: 0.8861 (mp0) cc_final: 0.8446 (mp0) REVERT: I 79 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8051 (mmtm) REVERT: I 114 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7181 (mtmm) REVERT: I 117 LYS cc_start: 0.8432 (mmmt) cc_final: 0.8232 (mmmt) REVERT: L 463 GLN cc_start: 0.7828 (tp40) cc_final: 0.7611 (tp40) REVERT: L 483 ASP cc_start: 0.7771 (m-30) cc_final: 0.7368 (m-30) outliers start: 54 outliers final: 29 residues processed: 343 average time/residue: 0.1885 time to fit residues: 96.7723 Evaluate side-chains 286 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 253 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain K residue 518 HIS Chi-restraints excluded: chain K residue 561 LEU Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain P residue 98 ASP Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain F residue 364 LYS Chi-restraints excluded: chain F residue 384 ARG Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain E residue 392 THR Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain Q residue 81 TYR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain I residue 79 LYS Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 527 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 194 optimal weight: 0.2980 chunk 220 optimal weight: 4.9990 chunk 295 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 188 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 279 optimal weight: 3.9990 chunk 192 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 154 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 43 HIS ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.096996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.064937 restraints weight = 89026.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.066730 restraints weight = 53566.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.067788 restraints weight = 40434.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.068288 restraints weight = 34645.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.068694 restraints weight = 32072.533| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 24785 Z= 0.200 Angle : 0.694 11.979 33852 Z= 0.354 Chirality : 0.047 0.182 4007 Planarity : 0.005 0.046 4295 Dihedral : 4.413 20.015 3339 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.34 % Favored : 92.62 % Rotamer: Outliers : 2.95 % Allowed : 15.60 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % 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: -1.26 (0.15), residues: 3064 helix: -2.23 (0.24), residues: 283 sheet: 0.40 (0.15), residues: 1115 loop : -1.49 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 346 TYR 0.027 0.002 TYR K 515 PHE 0.032 0.002 PHE S 87 TRP 0.016 0.002 TRP K 488 HIS 0.009 0.002 HIS O 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (24728) covalent geometry : angle 0.69054 / 0.35 (33724) SS BOND : bond 0.00540 / 0.39 ( 43) SS BOND : angle 1.14233 / 0.77 ( 86) hydrogen bonds : bond 0.04195 / 2.76 ( 603) hydrogen bonds : angle 5.87531 / 4.05 ( 1824) link_BETA1-4 : bond 0.00367 / 0.19 ( 3) link_BETA1-4 : angle 1.17502 / 0.82 ( 9) link_NAG-ASN : bond 0.00357 / 0.22 ( 11) link_NAG-ASN : angle 1.76796 / 1.16 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 274 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 506 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7523 (mtm) REVERT: K 568 MET cc_start: 0.7444 (mtm) cc_final: 0.6956 (mtp) REVERT: D 405 PHE cc_start: 0.6808 (t80) cc_final: 0.6412 (t80) REVERT: D 506 MET cc_start: 0.7787 (mtt) cc_final: 0.7322 (mtt) REVERT: P 84 LYS cc_start: 0.8286 (pttt) cc_final: 0.7889 (mmtm) REVERT: F 384 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7649 (mtt180) REVERT: E 553 ASP cc_start: 0.7419 (t0) cc_final: 0.6737 (p0) REVERT: O 94 LEU cc_start: 0.7623 (tp) cc_final: 0.7242 (tt) REVERT: Q 66 ASN cc_start: 0.7535 (m110) cc_final: 0.7121 (m110) REVERT: S 73 LYS cc_start: 0.8181 (mmmt) cc_final: 0.7753 (mmmt) REVERT: S 87 PHE cc_start: 0.4908 (p90) cc_final: 0.4479 (p90) REVERT: S 117 LYS cc_start: 0.7549 (mptt) cc_final: 0.7286 (mptt) REVERT: B 376 ASP cc_start: 0.8541 (p0) cc_final: 0.8230 (p0) REVERT: A 489 MET cc_start: 0.8055 (pmm) cc_final: 0.7724 (ptp) REVERT: A 545 ASN cc_start: 0.8159 (t0) cc_final: 0.7498 (t0) REVERT: I 22 GLU cc_start: 0.8849 (mp0) cc_final: 0.8407 (mp0) REVERT: I 47 TYR cc_start: 0.7773 (p90) cc_final: 0.7521 (p90) REVERT: I 72 TYR cc_start: 0.8243 (m-80) cc_final: 0.8022 (m-80) REVERT: I 79 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8181 (mmtm) REVERT: L 483 ASP cc_start: 0.7741 (m-30) cc_final: 0.7445 (m-30) REVERT: L 488 TRP cc_start: 0.6645 (m100) cc_final: 0.6401 (m100) REVERT: L 489 MET cc_start: 0.6419 (pmm) cc_final: 0.6142 (pmm) REVERT: L 515 TYR cc_start: 0.7474 (m-80) cc_final: 0.6936 (m-80) outliers start: 81 outliers final: 48 residues processed: 338 average time/residue: 0.1850 time to fit residues: 95.2212 Evaluate side-chains 286 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 235 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 506 MET Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain H residue 445 LYS Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 502 THR Chi-restraints excluded: chain K residue 506 MET Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 384 ARG Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 379 THR Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain E residue 348 PHE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain Q residue 81 TYR Chi-restraints excluded: chain S residue 67 PHE Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 79 LYS Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain L residue 457 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 218 optimal weight: 0.2980 chunk 80 optimal weight: 1.9990 chunk 261 optimal weight: 0.4980 chunk 61 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 300 optimal weight: 0.0970 chunk 32 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 GLN D 463 GLN ** P 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 487 GLN ** O 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 123 HIS ** S 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.096363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.066451 restraints weight = 87474.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.067607 restraints weight = 56460.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.067929 restraints weight = 41192.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.068391 restraints weight = 38245.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.068447 restraints weight = 34844.673| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24785 Z= 0.121 Angle : 0.649 13.144 33852 Z= 0.329 Chirality : 0.045 0.173 4007 Planarity : 0.004 0.044 4295 Dihedral : 4.229 20.418 3339 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.33 % Favored : 93.64 % Rotamer: Outliers : 2.48 % Allowed : 17.39 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % 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 (0.15), residues: 3064 helix: -1.90 (0.25), residues: 295 sheet: 0.50 (0.15), residues: 1137 loop : -1.40 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 83 TYR 0.026 0.001 TYR K 515 PHE 0.022 0.001 PHE L 479 TRP 0.010 0.001 TRP C 528 HIS 0.011 0.001 HIS A 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (24728) covalent geometry : angle 0.64684 / 0.33 (33724) SS BOND : bond 0.00462 / 0.34 ( 43) SS BOND : angle 0.85275 / 0.59 ( 86) hydrogen bonds : bond 0.03436 / 2.26 ( 603) hydrogen bonds : angle 5.49230 / 3.79 ( 1824) link_BETA1-4 : bond 0.00279 / 0.14 ( 3) link_BETA1-4 : angle 1.20410 / 0.91 ( 9) link_NAG-ASN : bond 0.00169 / 0.09 ( 11) link_NAG-ASN : angle 1.30609 / 0.86 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 287 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 371 ASP cc_start: 0.6832 (p0) cc_final: 0.6626 (p0) REVERT: M 42 MET cc_start: 0.2315 (tpp) cc_final: 0.1339 (tpt) REVERT: D 405 PHE cc_start: 0.7010 (t80) cc_final: 0.6522 (t80) REVERT: D 506 MET cc_start: 0.7702 (mtt) cc_final: 0.7214 (mtt) REVERT: P 84 LYS cc_start: 0.8489 (pttt) cc_final: 0.8000 (mmtm) REVERT: P 108 MET cc_start: 0.8314 (mmm) cc_final: 0.7955 (mmt) REVERT: E 553 ASP cc_start: 0.7338 (t0) cc_final: 0.6742 (p0) REVERT: O 94 LEU cc_start: 0.7482 (tp) cc_final: 0.7099 (tt) REVERT: R 88 LEU cc_start: 0.6811 (tp) cc_final: 0.6476 (tp) REVERT: Q 66 ASN cc_start: 0.7538 (m110) cc_final: 0.7104 (m110) REVERT: S 73 LYS cc_start: 0.8237 (mmmt) cc_final: 0.7881 (mmmt) REVERT: B 358 PHE cc_start: 0.8717 (t80) cc_final: 0.8376 (t80) REVERT: B 376 ASP cc_start: 0.7993 (p0) cc_final: 0.7647 (p0) REVERT: I 22 GLU cc_start: 0.8806 (mp0) cc_final: 0.8431 (mp0) REVERT: I 47 TYR cc_start: 0.7488 (p90) cc_final: 0.7263 (p90) REVERT: I 72 TYR cc_start: 0.8258 (m-80) cc_final: 0.8052 (m-80) REVERT: I 79 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8314 (mmtm) REVERT: I 114 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7197 (mtmm) REVERT: L 483 ASP cc_start: 0.7787 (m-30) cc_final: 0.7429 (m-30) REVERT: L 488 TRP cc_start: 0.6697 (m100) cc_final: 0.6311 (m100) REVERT: L 489 MET cc_start: 0.6504 (pmm) cc_final: 0.6208 (pmm) outliers start: 68 outliers final: 40 residues processed: 344 average time/residue: 0.1791 time to fit residues: 94.0072 Evaluate side-chains 289 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 247 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 348 PHE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 445 LYS Chi-restraints excluded: chain H residue 516 PHE Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 506 MET Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 429 THR Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain E residue 348 PHE Chi-restraints excluded: chain E residue 426 CYS Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain Q residue 81 TYR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain I residue 79 LYS Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain L residue 457 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 148 optimal weight: 3.9990 chunk 190 optimal weight: 9.9990 chunk 175 optimal weight: 4.9990 chunk 126 optimal weight: 0.0870 chunk 14 optimal weight: 3.9990 chunk 257 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 226 optimal weight: 6.9990 chunk 33 optimal weight: 0.2980 overall best weight: 1.2762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 GLN ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 395 ASN H 545 ASN ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN ** O 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.094947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.065312 restraints weight = 88473.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.066233 restraints weight = 60212.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.066268 restraints weight = 43431.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.066574 restraints weight = 43170.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.066750 restraints weight = 38627.281| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.5255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24785 Z= 0.158 Angle : 0.668 12.921 33852 Z= 0.338 Chirality : 0.046 0.187 4007 Planarity : 0.004 0.105 4295 Dihedral : 4.275 20.355 3339 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.28 % Favored : 92.69 % Rotamer: Outliers : 2.62 % Allowed : 18.30 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % 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: -1.14 (0.15), residues: 3064 helix: -1.88 (0.25), residues: 295 sheet: 0.38 (0.15), residues: 1133 loop : -1.39 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 443 TYR 0.024 0.002 TYR K 515 PHE 0.021 0.002 PHE L 479 TRP 0.012 0.001 TRP K 488 HIS 0.007 0.001 HIS A 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (24728) covalent geometry : angle 0.66547 / 0.34 (33724) SS BOND : bond 0.00447 / 0.33 ( 43) SS BOND : angle 0.87963 / 0.62 ( 86) hydrogen bonds : bond 0.03667 / 2.41 ( 603) hydrogen bonds : angle 5.50445 / 3.80 ( 1824) link_BETA1-4 : bond 0.00456 / 0.23 ( 3) link_BETA1-4 : angle 1.20129 / 0.90 ( 9) link_NAG-ASN : bond 0.00225 / 0.14 ( 11) link_NAG-ASN : angle 1.56328 / 1.05 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 263 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 483 ASP cc_start: 0.8349 (m-30) cc_final: 0.7783 (t0) REVERT: M 42 MET cc_start: 0.2693 (tpp) cc_final: 0.2282 (tpp) REVERT: M 72 TYR cc_start: 0.8171 (m-10) cc_final: 0.7931 (m-10) REVERT: M 75 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7164 (mtp180) REVERT: M 84 LYS cc_start: 0.8380 (tmtt) cc_final: 0.7978 (mmmm) REVERT: D 405 PHE cc_start: 0.7169 (t80) cc_final: 0.6753 (t80) REVERT: D 506 MET cc_start: 0.7711 (mtt) cc_final: 0.7267 (mtt) REVERT: P 84 LYS cc_start: 0.8512 (pttt) cc_final: 0.8082 (mmtm) REVERT: P 108 MET cc_start: 0.8286 (mmm) cc_final: 0.8008 (mmt) REVERT: F 483 ASP cc_start: 0.6735 (t0) cc_final: 0.6497 (t0) REVERT: E 553 ASP cc_start: 0.7351 (t0) cc_final: 0.6673 (p0) REVERT: O 80 GLN cc_start: 0.7154 (tm130) cc_final: 0.6828 (tm-30) REVERT: O 94 LEU cc_start: 0.7501 (tp) cc_final: 0.7296 (tp) REVERT: R 83 ARG cc_start: 0.8845 (mmp80) cc_final: 0.8416 (mmp80) REVERT: R 88 LEU cc_start: 0.6909 (tp) cc_final: 0.6587 (tp) REVERT: Q 66 ASN cc_start: 0.7597 (m110) cc_final: 0.7172 (m110) REVERT: S 73 LYS cc_start: 0.8325 (mmmt) cc_final: 0.7973 (mmmt) REVERT: S 117 LYS cc_start: 0.7605 (mptt) cc_final: 0.7334 (mptt) REVERT: B 358 PHE cc_start: 0.8753 (t80) cc_final: 0.8400 (t80) REVERT: B 376 ASP cc_start: 0.8077 (p0) cc_final: 0.7729 (p0) REVERT: I 22 GLU cc_start: 0.8759 (mp0) cc_final: 0.8380 (mp0) REVERT: I 47 TYR cc_start: 0.7642 (p90) cc_final: 0.7426 (p90) REVERT: I 72 TYR cc_start: 0.8334 (m-80) cc_final: 0.8124 (m-80) REVERT: I 79 LYS cc_start: 0.8621 (mmtp) cc_final: 0.8374 (mmtm) REVERT: I 114 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7796 (mtmm) REVERT: L 483 ASP cc_start: 0.7952 (m-30) cc_final: 0.7571 (m-30) outliers start: 72 outliers final: 55 residues processed: 321 average time/residue: 0.1835 time to fit residues: 90.2904 Evaluate side-chains 308 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 251 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 395 ASN Chi-restraints excluded: chain H residue 445 LYS Chi-restraints excluded: chain H residue 516 PHE Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 506 MET Chi-restraints excluded: chain M residue 43 HIS Chi-restraints excluded: chain M residue 75 ARG Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain E residue 348 PHE Chi-restraints excluded: chain E residue 426 CYS Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain Q residue 81 TYR Chi-restraints excluded: chain S residue 67 PHE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain L residue 457 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 22 optimal weight: 0.0070 chunk 174 optimal weight: 9.9990 chunk 86 optimal weight: 0.0980 chunk 229 optimal weight: 40.0000 chunk 165 optimal weight: 0.5980 chunk 211 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 217 optimal weight: 10.0000 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 395 ASN ** P 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.095390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.065675 restraints weight = 87311.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.066711 restraints weight = 57009.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.067182 restraints weight = 41256.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.067741 restraints weight = 38056.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.067755 restraints weight = 35290.756| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.5402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24785 Z= 0.125 Angle : 0.643 14.679 33852 Z= 0.324 Chirality : 0.045 0.236 4007 Planarity : 0.004 0.056 4295 Dihedral : 4.157 20.295 3339 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.10 % Favored : 93.86 % Rotamer: Outliers : 2.41 % Allowed : 19.25 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % 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: -1.07 (0.15), residues: 3064 helix: -1.79 (0.25), residues: 295 sheet: 0.45 (0.15), residues: 1131 loop : -1.36 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 443 TYR 0.023 0.001 TYR R 81 PHE 0.021 0.001 PHE L 479 TRP 0.012 0.001 TRP L 488 HIS 0.006 0.001 HIS A 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (24728) covalent geometry : angle 0.64102 / 0.32 (33724) SS BOND : bond 0.00639 / 0.36 ( 43) SS BOND : angle 0.78308 / 0.54 ( 86) hydrogen bonds : bond 0.03300 / 2.15 ( 603) hydrogen bonds : angle 5.25873 / 3.64 ( 1824) link_BETA1-4 : bond 0.00354 / 0.17 ( 3) link_BETA1-4 : angle 1.19132 / 0.92 ( 9) link_NAG-ASN : bond 0.00117 / 0.07 ( 11) link_NAG-ASN : angle 1.28346 / 0.87 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 274 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 428 VAL cc_start: 0.5288 (OUTLIER) cc_final: 0.5066 (p) REVERT: H 483 ASP cc_start: 0.8308 (m-30) cc_final: 0.7594 (t0) REVERT: M 72 TYR cc_start: 0.8079 (m-10) cc_final: 0.7869 (m-10) REVERT: M 75 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7195 (mtp180) REVERT: D 405 PHE cc_start: 0.7010 (t80) cc_final: 0.6630 (t80) REVERT: D 506 MET cc_start: 0.7657 (mtt) cc_final: 0.7222 (mtt) REVERT: P 84 LYS cc_start: 0.8386 (pttt) cc_final: 0.7923 (mmtm) REVERT: P 108 MET cc_start: 0.8225 (mmm) cc_final: 0.7974 (mmt) REVERT: F 386 ASN cc_start: 0.8693 (t0) cc_final: 0.8385 (t0) REVERT: E 553 ASP cc_start: 0.7304 (t0) cc_final: 0.6694 (p0) REVERT: O 51 GLU cc_start: 0.8776 (tp30) cc_final: 0.8297 (mp0) REVERT: O 80 GLN cc_start: 0.7034 (tm130) cc_final: 0.6718 (tm-30) REVERT: O 94 LEU cc_start: 0.7414 (tp) cc_final: 0.7199 (tp) REVERT: R 83 ARG cc_start: 0.8828 (mmp80) cc_final: 0.8445 (mmp80) REVERT: R 88 LEU cc_start: 0.6908 (tp) cc_final: 0.6605 (tp) REVERT: N 42 MET cc_start: 0.2541 (tpp) cc_final: 0.2172 (tpp) REVERT: Q 66 ASN cc_start: 0.7576 (m110) cc_final: 0.7164 (m110) REVERT: S 73 LYS cc_start: 0.8328 (mmmt) cc_final: 0.8001 (mmmt) REVERT: B 358 PHE cc_start: 0.8717 (t80) cc_final: 0.8382 (t80) REVERT: B 376 ASP cc_start: 0.8021 (p0) cc_final: 0.7674 (p0) REVERT: I 22 GLU cc_start: 0.8758 (mp0) cc_final: 0.8317 (mp0) REVERT: I 41 GLU cc_start: 0.7392 (tp30) cc_final: 0.7120 (tp30) REVERT: I 72 TYR cc_start: 0.8249 (m-80) cc_final: 0.8035 (m-80) REVERT: I 79 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8380 (mmtm) REVERT: I 114 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7238 (mtmm) REVERT: I 117 LYS cc_start: 0.8647 (mmmt) cc_final: 0.8422 (mmmt) REVERT: L 483 ASP cc_start: 0.7895 (m-30) cc_final: 0.7534 (m-30) REVERT: L 488 TRP cc_start: 0.6621 (m100) cc_final: 0.6408 (m100) REVERT: L 489 MET cc_start: 0.6451 (pmm) cc_final: 0.5895 (pmm) REVERT: L 549 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8025 (tp30) outliers start: 66 outliers final: 51 residues processed: 326 average time/residue: 0.1900 time to fit residues: 94.0877 Evaluate side-chains 305 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 250 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 445 LYS Chi-restraints excluded: chain H residue 516 PHE Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 506 MET Chi-restraints excluded: chain M residue 43 HIS Chi-restraints excluded: chain M residue 75 ARG Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 379 THR Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain E residue 348 PHE Chi-restraints excluded: chain E residue 426 CYS Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 122 VAL Chi-restraints excluded: chain Q residue 81 TYR Chi-restraints excluded: chain S residue 67 PHE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 79 LYS Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 129 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 132 optimal weight: 2.9990 chunk 229 optimal weight: 0.0570 chunk 30 optimal weight: 6.9990 chunk 2 optimal weight: 0.0570 chunk 125 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 231 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 140 optimal weight: 0.1980 chunk 228 optimal weight: 5.9990 overall best weight: 1.0620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 487 GLN ** O 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.094864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.065416 restraints weight = 88421.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.066350 restraints weight = 55943.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.066212 restraints weight = 44975.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.066598 restraints weight = 42197.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.066694 restraints weight = 37768.688| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.5620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24785 Z= 0.141 Angle : 0.658 13.275 33852 Z= 0.332 Chirality : 0.045 0.169 4007 Planarity : 0.004 0.054 4295 Dihedral : 4.159 20.167 3339 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.05 % Favored : 92.92 % Rotamer: Outliers : 2.52 % Allowed : 19.36 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % 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: -1.03 (0.15), residues: 3064 helix: -1.78 (0.26), residues: 296 sheet: 0.51 (0.15), residues: 1137 loop : -1.37 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 491 TYR 0.022 0.001 TYR R 81 PHE 0.020 0.001 PHE L 479 TRP 0.011 0.001 TRP L 488 HIS 0.006 0.001 HIS O 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (24728) covalent geometry : angle 0.65639 / 0.33 (33724) SS BOND : bond 0.00423 / 0.30 ( 43) SS BOND : angle 0.84925 / 0.59 ( 86) hydrogen bonds : bond 0.03402 / 2.23 ( 603) hydrogen bonds : angle 5.24867 / 3.64 ( 1824) link_BETA1-4 : bond 0.00105 / 0.05 ( 3) link_BETA1-4 : angle 1.21677 / 0.91 ( 9) link_NAG-ASN : bond 0.00144 / 0.09 ( 11) link_NAG-ASN : angle 1.42890 / 0.97 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 260 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 483 ASP cc_start: 0.8329 (m-30) cc_final: 0.7824 (t0) REVERT: M 72 TYR cc_start: 0.8202 (m-10) cc_final: 0.8002 (m-10) REVERT: M 75 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7172 (mtp180) REVERT: M 84 LYS cc_start: 0.8325 (tmtt) cc_final: 0.7815 (mmmm) REVERT: D 405 PHE cc_start: 0.7099 (t80) cc_final: 0.6686 (t80) REVERT: D 506 MET cc_start: 0.7706 (mtt) cc_final: 0.7275 (mtt) REVERT: P 84 LYS cc_start: 0.8450 (pttt) cc_final: 0.8021 (mmtm) REVERT: F 386 ASN cc_start: 0.8776 (t0) cc_final: 0.8439 (t0) REVERT: E 553 ASP cc_start: 0.7418 (t0) cc_final: 0.6667 (p0) REVERT: O 51 GLU cc_start: 0.8784 (tp30) cc_final: 0.8265 (mp0) REVERT: O 80 GLN cc_start: 0.7266 (tm130) cc_final: 0.6908 (tm-30) REVERT: R 88 LEU cc_start: 0.6973 (tp) cc_final: 0.6684 (tp) REVERT: N 42 MET cc_start: 0.2815 (tpp) cc_final: 0.2220 (tpp) REVERT: Q 66 ASN cc_start: 0.7634 (m110) cc_final: 0.7209 (m110) REVERT: S 45 ARG cc_start: 0.6234 (tpt90) cc_final: 0.5986 (tpt90) REVERT: S 73 LYS cc_start: 0.8335 (mmmt) cc_final: 0.7959 (mmmt) REVERT: S 117 LYS cc_start: 0.7626 (mptt) cc_final: 0.7403 (mptt) REVERT: B 376 ASP cc_start: 0.8037 (p0) cc_final: 0.7701 (p0) REVERT: I 22 GLU cc_start: 0.8714 (mp0) cc_final: 0.8280 (mp0) REVERT: I 79 LYS cc_start: 0.8675 (mmtp) cc_final: 0.8414 (mmtm) REVERT: I 114 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7227 (mtmm) REVERT: I 117 LYS cc_start: 0.8664 (mmmt) cc_final: 0.8425 (mmmt) REVERT: L 483 ASP cc_start: 0.7949 (m-30) cc_final: 0.7588 (m-30) REVERT: L 488 TRP cc_start: 0.6645 (m100) cc_final: 0.6358 (m100) REVERT: L 489 MET cc_start: 0.6541 (pmm) cc_final: 0.5951 (pmm) REVERT: L 549 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8158 (tp30) outliers start: 69 outliers final: 57 residues processed: 316 average time/residue: 0.1745 time to fit residues: 85.0686 Evaluate side-chains 300 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 241 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain H residue 445 LYS Chi-restraints excluded: chain H residue 516 PHE Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain M residue 43 HIS Chi-restraints excluded: chain M residue 75 ARG Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 379 THR Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain E residue 348 PHE Chi-restraints excluded: chain E residue 426 CYS Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 520 ILE Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 122 VAL Chi-restraints excluded: chain Q residue 81 TYR Chi-restraints excluded: chain S residue 67 PHE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain L residue 456 LEU Chi-restraints excluded: chain L residue 457 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 137 optimal weight: 5.9990 chunk 290 optimal weight: 0.0040 chunk 21 optimal weight: 1.9990 chunk 146 optimal weight: 0.0070 chunk 125 optimal weight: 3.9990 chunk 81 optimal weight: 0.0030 chunk 103 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 218 optimal weight: 0.7980 chunk 187 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 overall best weight: 0.5622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.095378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.065870 restraints weight = 87808.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.066547 restraints weight = 65787.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.066809 restraints weight = 47165.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.067138 restraints weight = 44636.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.067368 restraints weight = 39510.088| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.5720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24785 Z= 0.119 Angle : 0.662 16.165 33852 Z= 0.330 Chirality : 0.045 0.176 4007 Planarity : 0.004 0.094 4295 Dihedral : 4.098 20.691 3339 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.14 % Favored : 93.83 % Rotamer: Outliers : 2.30 % Allowed : 19.83 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % 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 (0.15), residues: 3064 helix: -1.72 (0.26), residues: 297 sheet: 0.52 (0.15), residues: 1149 loop : -1.30 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 83 TYR 0.024 0.001 TYR R 81 PHE 0.020 0.001 PHE L 479 TRP 0.011 0.001 TRP L 488 HIS 0.005 0.001 HIS H 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (24728) covalent geometry : angle 0.66042 / 0.33 (33724) SS BOND : bond 0.00372 / 0.27 ( 43) SS BOND : angle 0.73665 / 0.49 ( 86) hydrogen bonds : bond 0.03130 / 2.03 ( 603) hydrogen bonds : angle 5.07359 / 3.52 ( 1824) link_BETA1-4 : bond 0.00207 / 0.10 ( 3) link_BETA1-4 : angle 1.15784 / 0.90 ( 9) link_NAG-ASN : bond 0.00092 / 0.06 ( 11) link_NAG-ASN : angle 1.24035 / 0.85 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 258 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 483 ASP cc_start: 0.8277 (m-30) cc_final: 0.7636 (t0) REVERT: K 371 ASP cc_start: 0.6758 (p0) cc_final: 0.6412 (p0) REVERT: M 51 GLU cc_start: 0.7739 (tp30) cc_final: 0.7382 (mm-30) REVERT: M 75 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7166 (mtp180) REVERT: D 405 PHE cc_start: 0.7206 (t80) cc_final: 0.6806 (t80) REVERT: D 506 MET cc_start: 0.7670 (mtt) cc_final: 0.7231 (mtt) REVERT: P 84 LYS cc_start: 0.8449 (pttt) cc_final: 0.8020 (mmtm) REVERT: E 553 ASP cc_start: 0.7321 (t0) cc_final: 0.6674 (p0) REVERT: O 51 GLU cc_start: 0.8755 (tp30) cc_final: 0.8241 (mp0) REVERT: O 80 GLN cc_start: 0.7291 (tm130) cc_final: 0.6949 (tm-30) REVERT: R 88 LEU cc_start: 0.7016 (tp) cc_final: 0.6755 (tp) REVERT: N 42 MET cc_start: 0.2996 (tpp) cc_final: 0.2263 (tpp) REVERT: Q 42 MET cc_start: 0.2792 (tpt) cc_final: 0.2536 (tpp) REVERT: Q 66 ASN cc_start: 0.7627 (m110) cc_final: 0.7203 (m110) REVERT: S 73 LYS cc_start: 0.8347 (mmmt) cc_final: 0.8037 (mmmt) REVERT: B 376 ASP cc_start: 0.8089 (p0) cc_final: 0.7753 (p0) REVERT: A 489 MET cc_start: 0.8092 (pmm) cc_final: 0.7554 (ptp) REVERT: A 575 CYS cc_start: 0.3509 (m) cc_final: 0.3185 (m) REVERT: I 22 GLU cc_start: 0.8710 (mp0) cc_final: 0.8276 (mp0) REVERT: I 79 LYS cc_start: 0.8772 (mmtp) cc_final: 0.8518 (mmtm) REVERT: I 117 LYS cc_start: 0.8645 (mmmt) cc_final: 0.8431 (mmmt) REVERT: L 483 ASP cc_start: 0.7903 (m-30) cc_final: 0.7539 (m-30) REVERT: L 488 TRP cc_start: 0.6588 (m100) cc_final: 0.6283 (m100) REVERT: L 489 MET cc_start: 0.6620 (pmm) cc_final: 0.6009 (pmm) REVERT: L 549 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8121 (tp30) outliers start: 63 outliers final: 56 residues processed: 310 average time/residue: 0.1565 time to fit residues: 76.0650 Evaluate side-chains 298 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 241 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 445 LYS Chi-restraints excluded: chain H residue 516 PHE Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain M residue 43 HIS Chi-restraints excluded: chain M residue 75 ARG Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 120 LEU Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 379 THR Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain E residue 348 PHE Chi-restraints excluded: chain E residue 426 CYS Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 122 VAL Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 81 TYR Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain L residue 456 LEU Chi-restraints excluded: chain L residue 552 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 75 optimal weight: 0.9990 chunk 130 optimal weight: 0.0060 chunk 48 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 278 optimal weight: 3.9990 chunk 217 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 239 optimal weight: 1.9990 chunk 279 optimal weight: 3.9990 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.094095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.065112 restraints weight = 88164.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.065502 restraints weight = 54845.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.065682 restraints weight = 43661.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.066096 restraints weight = 41745.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.066339 restraints weight = 36362.983| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.5925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24785 Z= 0.163 Angle : 0.701 19.975 33852 Z= 0.349 Chirality : 0.046 0.202 4007 Planarity : 0.004 0.071 4295 Dihedral : 4.237 21.481 3339 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.44 % Favored : 92.49 % Rotamer: Outliers : 2.37 % Allowed : 20.20 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % 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 (0.15), residues: 3064 helix: -1.75 (0.26), residues: 297 sheet: 0.36 (0.15), residues: 1159 loop : -1.33 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 461 TYR 0.024 0.002 TYR R 81 PHE 0.019 0.002 PHE L 479 TRP 0.012 0.001 TRP K 488 HIS 0.005 0.001 HIS M 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (24728) covalent geometry : angle 0.69898 / 0.35 (33724) SS BOND : bond 0.00444 / 0.31 ( 43) SS BOND : angle 0.94751 / 0.65 ( 86) hydrogen bonds : bond 0.03482 / 2.28 ( 603) hydrogen bonds : angle 5.22441 / 3.62 ( 1824) link_BETA1-4 : bond 0.00133 / 0.07 ( 3) link_BETA1-4 : angle 1.25153 / 0.96 ( 9) link_NAG-ASN : bond 0.00208 / 0.13 ( 11) link_NAG-ASN : angle 1.53669 / 1.04 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 248 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 483 ASP cc_start: 0.8358 (m-30) cc_final: 0.7751 (t0) REVERT: K 371 ASP cc_start: 0.6830 (p0) cc_final: 0.6593 (p0) REVERT: M 51 GLU cc_start: 0.7707 (tp30) cc_final: 0.7421 (mm-30) REVERT: M 75 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7074 (mtp180) REVERT: D 405 PHE cc_start: 0.7110 (t80) cc_final: 0.6650 (t80) REVERT: D 506 MET cc_start: 0.7716 (mtt) cc_final: 0.7295 (mtt) REVERT: P 84 LYS cc_start: 0.8331 (pttt) cc_final: 0.7933 (mmtm) REVERT: P 118 VAL cc_start: 0.7566 (OUTLIER) cc_final: 0.7355 (m) REVERT: E 553 ASP cc_start: 0.7478 (t0) cc_final: 0.6552 (p0) REVERT: O 51 GLU cc_start: 0.8721 (tp30) cc_final: 0.8273 (mp0) REVERT: R 88 LEU cc_start: 0.6998 (tp) cc_final: 0.6684 (tp) REVERT: N 42 MET cc_start: 0.2908 (tpp) cc_final: 0.2326 (tpp) REVERT: N 97 SER cc_start: 0.7459 (t) cc_final: 0.7204 (m) REVERT: Q 66 ASN cc_start: 0.7657 (m110) cc_final: 0.7264 (m110) REVERT: S 73 LYS cc_start: 0.8356 (mmmt) cc_final: 0.8042 (mmmt) REVERT: B 376 ASP cc_start: 0.8001 (p0) cc_final: 0.7668 (p0) REVERT: A 575 CYS cc_start: 0.3510 (m) cc_final: 0.3196 (m) REVERT: I 22 GLU cc_start: 0.8671 (mp0) cc_final: 0.8188 (mp0) REVERT: I 79 LYS cc_start: 0.8674 (mmtp) cc_final: 0.8416 (mmtm) REVERT: L 483 ASP cc_start: 0.7882 (m-30) cc_final: 0.7555 (m-30) REVERT: L 488 TRP cc_start: 0.6683 (m100) cc_final: 0.6370 (m100) REVERT: L 489 MET cc_start: 0.6721 (pmm) cc_final: 0.6111 (pmm) REVERT: L 549 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8186 (tp30) outliers start: 65 outliers final: 59 residues processed: 299 average time/residue: 0.1753 time to fit residues: 82.0402 Evaluate side-chains 301 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 240 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 445 LYS Chi-restraints excluded: chain H residue 516 PHE Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 538 VAL Chi-restraints excluded: chain K residue 417 ASP Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain M residue 43 HIS Chi-restraints excluded: chain M residue 75 ARG Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 118 VAL Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 537 VAL Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 379 THR Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain E residue 348 PHE Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 426 CYS Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 122 VAL Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 81 TYR Chi-restraints excluded: chain Q residue 108 MET Chi-restraints excluded: chain S residue 67 PHE Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain L residue 456 LEU Chi-restraints excluded: chain L residue 466 LEU Chi-restraints excluded: chain L residue 552 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 209 optimal weight: 0.9980 chunk 225 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 66 optimal weight: 0.1980 chunk 173 optimal weight: 0.7980 chunk 51 optimal weight: 10.0000 chunk 4 optimal weight: 0.5980 chunk 116 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.094960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.065029 restraints weight = 87897.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.066207 restraints weight = 60354.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.066069 restraints weight = 45862.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.066396 restraints weight = 42414.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.066738 restraints weight = 39148.209| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.6002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24785 Z= 0.126 Angle : 0.680 15.511 33852 Z= 0.338 Chirality : 0.045 0.207 4007 Planarity : 0.004 0.074 4295 Dihedral : 4.157 21.785 3339 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.87 % Favored : 94.06 % Rotamer: Outliers : 2.30 % Allowed : 20.27 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.72 % 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: -0.99 (0.15), residues: 3064 helix: -1.68 (0.26), residues: 297 sheet: 0.45 (0.15), residues: 1143 loop : -1.29 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 461 TYR 0.024 0.001 TYR R 81 PHE 0.035 0.001 PHE F 405 TRP 0.010 0.001 TRP L 488 HIS 0.004 0.001 HIS H 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (24728) covalent geometry : angle 0.67868 / 0.34 (33724) SS BOND : bond 0.00368 / 0.27 ( 43) SS BOND : angle 0.77338 / 0.53 ( 86) hydrogen bonds : bond 0.03156 / 2.05 ( 603) hydrogen bonds : angle 5.05459 / 3.51 ( 1824) link_BETA1-4 : bond 0.00301 / 0.15 ( 3) link_BETA1-4 : angle 1.22667 / 0.93 ( 9) link_NAG-ASN : bond 0.00083 / 0.05 ( 11) link_NAG-ASN : angle 1.25259 / 0.86 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4686.19 seconds wall clock time: 81 minutes 49.67 seconds (4909.67 seconds total)