Starting phenix.real_space_refine on Thu Mar 5 17:27:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bpe_16150/03_2026/8bpe_16150.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bpe_16150/03_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_16150/03_2026/8bpe_16150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bpe_16150/03_2026/8bpe_16150.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bpe_16150/03_2026/8bpe_16150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bpe_16150/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.06, per 1000 atoms: 0.25 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: 1.91 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: 1.09 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: 4.40 Time building geometry restraints manager: 2.56 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: 14004 17.97 - 35.93: 1023 35.93 - 53.90: 168 53.90 - 71.86: 71 71.86 - 89.83: 15 Dihedral angle restraints: 15281 sinusoidal: 6248 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 15278 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: 4.290 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: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.780 Find NCS groups from input model: 0.590 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: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 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 : 13.164 89.830 9302 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 covalent geometry : bond 0.00898 (24728) covalent geometry : angle 1.07441 (33724) SS BOND : bond 0.09310 ( 43) SS BOND : angle 5.05121 ( 86) hydrogen bonds : bond 0.25796 ( 603) hydrogen bonds : angle 8.90087 ( 1824) link_BETA1-4 : bond 0.01877 ( 3) link_BETA1-4 : angle 3.74486 ( 9) link_NAG-ASN : bond 0.01482 ( 11) link_NAG-ASN : angle 5.47554 ( 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 : 0.963 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: 0.2234 time to fit residues: 215.1263 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 : 0.939 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 D 545 ASN P 43 HIS ** P 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 393 HIS F 465 ASN F 510 GLN 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** Q 43 HIS 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.096608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.066656 restraints weight = 88364.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.067444 restraints weight = 61624.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.067364 restraints weight = 48971.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.068009 restraints weight = 43732.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.068049 restraints weight = 38128.822| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 24785 Z= 0.238 Angle : 0.784 13.379 33852 Z= 0.403 Chirality : 0.050 0.230 4007 Planarity : 0.005 0.062 4295 Dihedral : 5.012 37.487 3633 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.30 % Allowed : 12.43 % Favored : 85.27 % 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: -1.39 (0.15), residues: 3064 helix: -2.30 (0.24), residues: 292 sheet: 0.48 (0.15), residues: 1124 loop : -1.74 (0.14), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 443 TYR 0.033 0.002 TYR H 562 PHE 0.033 0.003 PHE G 479 TRP 0.021 0.002 TRP C 528 HIS 0.011 0.002 HIS B 400 Details of bonding type rmsd covalent geometry : bond 0.00558 (24728) covalent geometry : angle 0.77844 (33724) SS BOND : bond 0.01019 ( 43) SS BOND : angle 1.51855 ( 86) hydrogen bonds : bond 0.04706 ( 603) hydrogen bonds : angle 6.51963 ( 1824) link_BETA1-4 : bond 0.00700 ( 3) link_BETA1-4 : angle 1.11589 ( 9) link_NAG-ASN : bond 0.00501 ( 11) link_NAG-ASN : angle 2.04663 ( 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 405 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 342 time to evaluate : 0.970 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: K 568 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7368 (mtp) REVERT: M 52 MET cc_start: 0.8319 (tpp) cc_final: 0.7809 (mtm) REVERT: M 72 TYR cc_start: 0.8294 (m-80) cc_final: 0.8032 (m-10) REVERT: D 405 PHE cc_start: 0.6906 (t80) cc_final: 0.6553 (t80) REVERT: D 506 MET cc_start: 0.7821 (mtt) cc_final: 0.7358 (mtt) REVERT: D 568 MET cc_start: 0.5068 (tmm) cc_final: 0.4637 (ttp) REVERT: F 386 ASN cc_start: 0.8640 (t0) cc_final: 0.8314 (t0) REVERT: F 483 ASP cc_start: 0.6742 (t0) cc_final: 0.6367 (t0) REVERT: G 568 MET cc_start: 0.7460 (ptp) cc_final: 0.6878 (mtm) REVERT: E 553 ASP cc_start: 0.7507 (t0) cc_final: 0.6734 (p0) REVERT: O 94 LEU cc_start: 0.7394 (tp) cc_final: 0.6976 (tt) REVERT: S 45 ARG cc_start: 0.6916 (tpt-90) cc_final: 0.6273 (tpt-90) REVERT: S 87 PHE cc_start: 0.4315 (p90) cc_final: 0.3784 (p90) REVERT: B 358 PHE cc_start: 0.8778 (t80) cc_final: 0.8416 (t80) REVERT: B 376 ASP cc_start: 0.8086 (p0) cc_final: 0.7708 (p0) REVERT: A 465 ASN cc_start: 0.8649 (m-40) cc_final: 0.8407 (m-40) REVERT: I 22 GLU cc_start: 0.8806 (mp0) cc_final: 0.8414 (mp0) REVERT: I 26 GLU cc_start: 0.6559 (mm-30) cc_final: 0.6144 (mm-30) REVERT: L 483 ASP cc_start: 0.7823 (m-30) cc_final: 0.7387 (m-30) REVERT: L 488 TRP cc_start: 0.6806 (m100) cc_final: 0.6377 (m100) outliers start: 63 outliers final: 39 residues processed: 391 average time/residue: 0.1955 time to fit residues: 112.6360 Evaluate side-chains 295 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 255 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 348 PHE 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 518 HIS Chi-restraints excluded: chain K residue 528 TRP Chi-restraints excluded: chain K residue 568 MET Chi-restraints excluded: chain M residue 97 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: 10.0000 chunk 162 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 56 optimal weight: 0.0070 chunk 138 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 252 optimal weight: 7.9990 chunk 256 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 76 optimal weight: 0.0870 chunk 159 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** D 439 GLN D 529 ASN ** P 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 393 HIS 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** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN L 510 GLN ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.099431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.067743 restraints weight = 89339.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.069592 restraints weight = 52815.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.070697 restraints weight = 39429.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.071331 restraints weight = 33621.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.071610 restraints weight = 30888.832| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24785 Z= 0.134 Angle : 0.676 12.879 33852 Z= 0.342 Chirality : 0.046 0.212 4007 Planarity : 0.004 0.047 4295 Dihedral : 4.502 30.187 3633 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.01 % Favored : 93.96 % Rotamer: Outliers : 2.15 % Allowed : 14.87 % Favored : 82.97 % 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: -1.13 (0.15), residues: 3064 helix: -2.10 (0.25), residues: 282 sheet: 0.64 (0.15), residues: 1135 loop : -1.56 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 467 TYR 0.027 0.002 TYR K 515 PHE 0.027 0.002 PHE L 479 TRP 0.012 0.001 TRP C 528 HIS 0.012 0.001 HIS E 430 Details of bonding type rmsd covalent geometry : bond 0.00308 (24728) covalent geometry : angle 0.67311 (33724) SS BOND : bond 0.00476 ( 43) SS BOND : angle 0.98770 ( 86) hydrogen bonds : bond 0.03967 ( 603) hydrogen bonds : angle 5.94977 ( 1824) link_BETA1-4 : bond 0.00425 ( 3) link_BETA1-4 : angle 1.37895 ( 9) link_NAG-ASN : bond 0.00176 ( 11) link_NAG-ASN : angle 1.54317 ( 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 355 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 296 time to evaluate : 0.999 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: C 506 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.7320 (mtm) REVERT: K 568 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.6893 (mtp) REVERT: M 39 LEU cc_start: 0.8523 (tt) cc_final: 0.8125 (mt) REVERT: M 72 TYR cc_start: 0.8205 (m-80) cc_final: 0.7854 (m-10) REVERT: D 405 PHE cc_start: 0.6755 (t80) cc_final: 0.6296 (t80) REVERT: D 506 MET cc_start: 0.7749 (mtt) cc_final: 0.7276 (mtt) REVERT: P 84 LYS cc_start: 0.8218 (pttt) cc_final: 0.7976 (mmtm) REVERT: F 384 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7594 (mtt180) REVERT: G 568 MET cc_start: 0.7239 (ptp) cc_final: 0.6784 (mtm) REVERT: E 553 ASP cc_start: 0.7354 (t0) cc_final: 0.6918 (p0) REVERT: O 94 LEU cc_start: 0.7549 (tp) cc_final: 0.7145 (tt) REVERT: R 88 LEU cc_start: 0.6820 (tp) cc_final: 0.6421 (tp) REVERT: R 108 MET cc_start: 0.6036 (mmt) cc_final: 0.5777 (mmt) REVERT: N 73 LYS cc_start: 0.8792 (tptp) cc_final: 0.8262 (mmmm) REVERT: S 73 LYS cc_start: 0.8235 (mmmt) cc_final: 0.7991 (mmmt) REVERT: B 358 PHE cc_start: 0.8684 (t80) cc_final: 0.8371 (t80) REVERT: B 376 ASP cc_start: 0.8517 (p0) cc_final: 0.8211 (p0) REVERT: A 545 ASN cc_start: 0.7669 (t0) cc_final: 0.6846 (t0) REVERT: I 22 GLU cc_start: 0.8870 (mp0) cc_final: 0.8446 (mp0) REVERT: I 79 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7966 (mmtm) REVERT: I 114 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7210 (mtmm) REVERT: I 117 LYS cc_start: 0.8448 (mmmt) cc_final: 0.8210 (mmmt) REVERT: L 463 GLN cc_start: 0.7748 (tp40) cc_final: 0.7525 (tp40) REVERT: L 483 ASP cc_start: 0.7533 (m-30) cc_final: 0.7207 (m-30) outliers start: 59 outliers final: 27 residues processed: 339 average time/residue: 0.1981 time to fit residues: 100.1421 Evaluate side-chains 285 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 253 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 C residue 520 ILE Chi-restraints excluded: chain H residue 520 ILE Chi-restraints excluded: chain H residue 533 THR Chi-restraints excluded: chain K residue 568 MET Chi-restraints excluded: chain M residue 97 SER 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 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 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: 10.0000 chunk 220 optimal weight: 3.9990 chunk 295 optimal weight: 3.9990 chunk 4 optimal weight: 0.0870 chunk 188 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 279 optimal weight: 3.9990 chunk 192 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 ASN ** 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 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 545 ASN P 123 HIS E 487 GLN E 493 GLN ** S 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 HIS J 36 ASN ** L 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.107966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.077853 restraints weight = 88656.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.078626 restraints weight = 58690.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.078988 restraints weight = 45422.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.079225 restraints weight = 44265.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.079520 restraints weight = 39346.742| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 24785 Z= 0.263 Angle : 0.750 12.146 33852 Z= 0.387 Chirality : 0.049 0.210 4007 Planarity : 0.005 0.047 4295 Dihedral : 4.959 28.516 3633 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.00 % Favored : 91.97 % Rotamer: Outliers : 3.54 % Allowed : 15.64 % Favored : 80.82 % 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: -1.40 (0.15), residues: 3064 helix: -2.40 (0.23), residues: 283 sheet: 0.38 (0.16), residues: 1089 loop : -1.61 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 467 TYR 0.031 0.002 TYR K 515 PHE 0.031 0.002 PHE G 479 TRP 0.020 0.002 TRP K 488 HIS 0.010 0.002 HIS E 430 Details of bonding type rmsd covalent geometry : bond 0.00622 (24728) covalent geometry : angle 0.74475 (33724) SS BOND : bond 0.00621 ( 43) SS BOND : angle 1.33082 ( 86) hydrogen bonds : bond 0.04647 ( 603) hydrogen bonds : angle 6.11026 ( 1824) link_BETA1-4 : bond 0.00628 ( 3) link_BETA1-4 : angle 1.47194 ( 9) link_NAG-ASN : bond 0.00539 ( 11) link_NAG-ASN : angle 2.05925 ( 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 379 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 282 time to evaluate : 0.958 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: C 506 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7568 (mtm) REVERT: M 80 GLN cc_start: 0.7822 (pm20) cc_final: 0.7582 (mm-40) REVERT: M 84 LYS cc_start: 0.8305 (tmtt) cc_final: 0.7621 (mmmm) REVERT: D 405 PHE cc_start: 0.7003 (t80) cc_final: 0.6517 (t80) REVERT: D 506 MET cc_start: 0.7843 (mtt) cc_final: 0.7400 (mtt) REVERT: P 84 LYS cc_start: 0.8184 (pttt) cc_final: 0.7831 (mmtm) REVERT: P 108 MET cc_start: 0.8494 (mmm) cc_final: 0.8171 (mmt) REVERT: F 413 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8483 (pt) REVERT: O 94 LEU cc_start: 0.7693 (tp) cc_final: 0.7334 (tt) REVERT: Q 66 ASN cc_start: 0.7584 (m110) cc_final: 0.7191 (m110) REVERT: S 45 ARG cc_start: 0.6512 (tpt-90) cc_final: 0.6268 (tpt-90) REVERT: S 73 LYS cc_start: 0.8166 (mmmt) cc_final: 0.7869 (mmmt) REVERT: S 117 LYS cc_start: 0.7667 (mptt) cc_final: 0.7402 (mptt) REVERT: B 376 ASP cc_start: 0.7973 (p0) cc_final: 0.7636 (p0) REVERT: I 22 GLU cc_start: 0.8815 (mp0) cc_final: 0.8418 (mp0) REVERT: I 47 TYR cc_start: 0.7948 (p90) cc_final: 0.7498 (p90) REVERT: I 79 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8286 (mmtm) REVERT: J 22 ILE cc_start: 0.8467 (pt) cc_final: 0.8110 (pt) REVERT: L 483 ASP cc_start: 0.7915 (m-30) cc_final: 0.7592 (m-30) REVERT: L 488 TRP cc_start: 0.6923 (m100) cc_final: 0.6547 (m100) REVERT: L 515 TYR cc_start: 0.7619 (m-80) cc_final: 0.6990 (m-80) outliers start: 97 outliers final: 57 residues processed: 359 average time/residue: 0.1881 time to fit residues: 102.2349 Evaluate side-chains 295 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 235 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 388 GLU Chi-restraints excluded: chain C residue 417 ASP 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 D residue 537 VAL Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 384 ARG Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain F residue 456 LEU 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 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 383 THR 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 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 51 GLU Chi-restraints excluded: chain S residue 66 ASN 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 473 THR Chi-restraints excluded: chain A residue 357 ILE 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 218 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 300 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 161 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 GLN ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 439 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 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 GLN G 463 GLN ** 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** L 518 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.095684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.063751 restraints weight = 89171.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.065474 restraints weight = 53860.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.066371 restraints weight = 40760.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.067049 restraints weight = 35321.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.067273 restraints weight = 32481.284| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 24785 Z= 0.189 Angle : 0.692 13.512 33852 Z= 0.353 Chirality : 0.047 0.206 4007 Planarity : 0.004 0.067 4295 Dihedral : 4.760 26.676 3633 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.95 % Favored : 93.02 % Rotamer: Outliers : 3.28 % Allowed : 17.43 % Favored : 79.29 % 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: -1.34 (0.15), residues: 3064 helix: -2.18 (0.25), residues: 281 sheet: 0.28 (0.15), residues: 1132 loop : -1.53 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 546 TYR 0.029 0.002 TYR K 515 PHE 0.023 0.002 PHE R 87 TRP 0.013 0.002 TRP K 488 HIS 0.009 0.002 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00448 (24728) covalent geometry : angle 0.68952 (33724) SS BOND : bond 0.00505 ( 43) SS BOND : angle 1.03633 ( 86) hydrogen bonds : bond 0.03949 ( 603) hydrogen bonds : angle 5.79571 ( 1824) link_BETA1-4 : bond 0.00264 ( 3) link_BETA1-4 : angle 1.40734 ( 9) link_NAG-ASN : bond 0.00219 ( 11) link_NAG-ASN : angle 1.57829 ( 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 354 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 264 time to evaluate : 0.917 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: C 506 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.7365 (mtm) REVERT: M 42 MET cc_start: 0.2508 (tpt) cc_final: 0.1709 (tpp) REVERT: M 75 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7177 (mtp180) REVERT: M 80 GLN cc_start: 0.7800 (pm20) cc_final: 0.7425 (mm-40) REVERT: D 405 PHE cc_start: 0.6953 (t80) cc_final: 0.6488 (t80) REVERT: D 506 MET cc_start: 0.7698 (mtt) cc_final: 0.7253 (mtt) REVERT: P 84 LYS cc_start: 0.8190 (pttt) cc_final: 0.7849 (mmtm) REVERT: P 108 MET cc_start: 0.8319 (mmm) cc_final: 0.8079 (mmt) REVERT: F 384 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7726 (mtt180) REVERT: O 42 MET cc_start: 0.3536 (tpt) cc_final: 0.3115 (mmm) REVERT: O 51 GLU cc_start: 0.8676 (tp30) cc_final: 0.8281 (mp0) REVERT: O 84 LYS cc_start: 0.8693 (ptmm) cc_final: 0.8484 (ptmm) REVERT: O 94 LEU cc_start: 0.7576 (tp) cc_final: 0.7343 (tp) REVERT: R 88 LEU cc_start: 0.6829 (tp) cc_final: 0.6519 (tp) REVERT: Q 66 ASN cc_start: 0.7599 (m110) cc_final: 0.7205 (m110) REVERT: Q 83 ARG cc_start: 0.8867 (mmm160) cc_final: 0.8569 (mmp80) REVERT: S 73 LYS cc_start: 0.8263 (mmmt) cc_final: 0.7862 (mmmt) REVERT: B 364 LYS cc_start: 0.8538 (ptpp) cc_final: 0.8326 (ptpp) REVERT: B 376 ASP cc_start: 0.8524 (p0) cc_final: 0.8195 (p0) REVERT: A 561 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8392 (pt) REVERT: I 22 GLU cc_start: 0.8822 (mp0) cc_final: 0.8414 (mp0) REVERT: I 47 TYR cc_start: 0.7828 (p90) cc_final: 0.6904 (p90) REVERT: I 72 TYR cc_start: 0.8259 (m-80) cc_final: 0.8008 (m-80) REVERT: I 79 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8313 (mmtm) REVERT: J 22 ILE cc_start: 0.8364 (pt) cc_final: 0.8076 (pt) REVERT: L 483 ASP cc_start: 0.7519 (m-30) cc_final: 0.7256 (m-30) outliers start: 90 outliers final: 58 residues processed: 335 average time/residue: 0.1799 time to fit residues: 92.2666 Evaluate side-chains 302 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 239 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 388 GLU Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 506 MET 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 H residue 538 VAL Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 502 THR Chi-restraints excluded: chain K residue 506 MET 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 537 VAL 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 537 VAL Chi-restraints excluded: chain G residue 538 VAL Chi-restraints excluded: chain G residue 552 VAL Chi-restraints excluded: chain E residue 426 CYS 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 N residue 114 LYS Chi-restraints excluded: chain Q residue 81 TYR Chi-restraints excluded: chain Q residue 108 MET Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 64 THR 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 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 556 THR Chi-restraints excluded: chain A residue 561 LEU 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 J residue 126 THR Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 552 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 148 optimal weight: 0.9980 chunk 190 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 257 optimal weight: 0.3980 chunk 176 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 226 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** H 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 GLN D 463 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** J 45 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.096268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.064447 restraints weight = 89177.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.066182 restraints weight = 53807.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.067231 restraints weight = 40550.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.067822 restraints weight = 34777.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.068030 restraints weight = 32050.033| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24785 Z= 0.142 Angle : 0.656 14.191 33852 Z= 0.332 Chirality : 0.046 0.205 4007 Planarity : 0.004 0.054 4295 Dihedral : 4.495 24.422 3633 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.21 % Favored : 92.75 % Rotamer: Outliers : 3.21 % Allowed : 18.19 % Favored : 78.60 % 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: -1.25 (0.15), residues: 3064 helix: -2.02 (0.25), residues: 295 sheet: 0.34 (0.15), residues: 1139 loop : -1.48 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 346 TYR 0.024 0.002 TYR K 515 PHE 0.021 0.001 PHE L 479 TRP 0.012 0.001 TRP E 528 HIS 0.011 0.001 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00334 (24728) covalent geometry : angle 0.65400 (33724) SS BOND : bond 0.00512 ( 43) SS BOND : angle 0.81488 ( 86) hydrogen bonds : bond 0.03560 ( 603) hydrogen bonds : angle 5.54929 ( 1824) link_BETA1-4 : bond 0.00156 ( 3) link_BETA1-4 : angle 1.28769 ( 9) link_NAG-ASN : bond 0.00115 ( 11) link_NAG-ASN : angle 1.51030 ( 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 355 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 267 time to evaluate : 1.146 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: H 483 ASP cc_start: 0.8330 (m-30) cc_final: 0.7679 (t0) REVERT: M 39 LEU cc_start: 0.8466 (tt) cc_final: 0.7681 (tt) REVERT: M 42 MET cc_start: 0.2499 (tpt) cc_final: 0.1737 (tpp) REVERT: M 75 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7151 (mtp180) REVERT: M 80 GLN cc_start: 0.7834 (pm20) cc_final: 0.7443 (mm-40) REVERT: D 405 PHE cc_start: 0.6944 (t80) cc_final: 0.6509 (t80) REVERT: D 506 MET cc_start: 0.7657 (mtt) cc_final: 0.7215 (mtt) REVERT: P 84 LYS cc_start: 0.8103 (pttt) cc_final: 0.7779 (mmtm) REVERT: P 118 VAL cc_start: 0.7290 (OUTLIER) cc_final: 0.6888 (p) REVERT: F 384 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7685 (mtt180) REVERT: O 42 MET cc_start: 0.3992 (tpt) cc_final: 0.3628 (mmm) REVERT: O 51 GLU cc_start: 0.8668 (tp30) cc_final: 0.8232 (mp0) REVERT: O 94 LEU cc_start: 0.7550 (tp) cc_final: 0.7318 (tp) REVERT: R 79 LYS cc_start: 0.8477 (tptt) cc_final: 0.8276 (tptp) REVERT: R 88 LEU cc_start: 0.6816 (tp) cc_final: 0.6523 (tp) REVERT: Q 66 ASN cc_start: 0.7577 (m110) cc_final: 0.7184 (m110) REVERT: S 73 LYS cc_start: 0.8317 (mmmt) cc_final: 0.7974 (mmmt) REVERT: S 87 PHE cc_start: 0.4886 (p90) cc_final: 0.4440 (p90) REVERT: S 117 LYS cc_start: 0.7657 (mptt) cc_final: 0.7403 (mptt) REVERT: B 364 LYS cc_start: 0.8598 (ptpp) cc_final: 0.8143 (ptpp) REVERT: B 376 ASP cc_start: 0.8556 (p0) cc_final: 0.8237 (p0) REVERT: A 561 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8458 (pt) REVERT: I 22 GLU cc_start: 0.8789 (mp0) cc_final: 0.8389 (mp0) REVERT: I 47 TYR cc_start: 0.7700 (p90) cc_final: 0.7241 (p90) REVERT: I 72 TYR cc_start: 0.8216 (m-80) cc_final: 0.7981 (m-80) REVERT: I 79 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8341 (mmtm) REVERT: I 114 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7168 (mtmm) REVERT: J 129 THR cc_start: 0.8412 (m) cc_final: 0.8160 (p) REVERT: L 483 ASP cc_start: 0.7537 (m-30) cc_final: 0.7272 (m-30) REVERT: L 488 TRP cc_start: 0.6731 (m100) cc_final: 0.6397 (m100) outliers start: 88 outliers final: 53 residues processed: 340 average time/residue: 0.1789 time to fit residues: 93.4720 Evaluate side-chains 297 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 238 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 533 THR Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 561 LEU 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 537 VAL Chi-restraints excluded: chain D residue 552 VAL 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 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 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 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 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 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 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 561 LEU Chi-restraints excluded: chain A residue 571 THR 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 L residue 457 LEU Chi-restraints excluded: chain L residue 552 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 22 optimal weight: 5.9990 chunk 174 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 229 optimal weight: 40.0000 chunk 165 optimal weight: 0.5980 chunk 211 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 175 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 217 optimal weight: 8.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 385 GLN ** 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** ** H 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 487 GLN ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 GLN D 545 ASN O 80 GLN ** O 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 490 GLN ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.095203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.063270 restraints weight = 88983.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.065000 restraints weight = 53831.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.066036 restraints weight = 40793.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.066510 restraints weight = 35071.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.066726 restraints weight = 32511.087| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.5825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24785 Z= 0.185 Angle : 0.692 14.827 33852 Z= 0.351 Chirality : 0.046 0.196 4007 Planarity : 0.005 0.103 4295 Dihedral : 4.594 23.892 3633 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.60 % Favored : 92.36 % Rotamer: Outliers : 2.99 % Allowed : 19.58 % 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: -1.32 (0.15), residues: 3064 helix: -2.08 (0.25), residues: 288 sheet: 0.21 (0.15), residues: 1136 loop : -1.45 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 461 TYR 0.020 0.002 TYR K 515 PHE 0.020 0.002 PHE L 479 TRP 0.012 0.002 TRP E 488 HIS 0.006 0.001 HIS C 430 Details of bonding type rmsd covalent geometry : bond 0.00441 (24728) covalent geometry : angle 0.68915 (33724) SS BOND : bond 0.00499 ( 43) SS BOND : angle 1.05012 ( 86) hydrogen bonds : bond 0.03803 ( 603) hydrogen bonds : angle 5.59872 ( 1824) link_BETA1-4 : bond 0.00185 ( 3) link_BETA1-4 : angle 1.32999 ( 9) link_NAG-ASN : bond 0.00236 ( 11) link_NAG-ASN : angle 1.67570 ( 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 335 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 253 time to evaluate : 0.930 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: H 483 ASP cc_start: 0.8425 (m-30) cc_final: 0.7753 (t0) REVERT: M 39 LEU cc_start: 0.8441 (tt) cc_final: 0.7937 (tp) REVERT: M 42 MET cc_start: 0.2704 (tpt) cc_final: 0.1805 (tpp) REVERT: M 75 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7118 (mtp180) REVERT: D 506 MET cc_start: 0.7673 (mtt) cc_final: 0.7316 (mtt) REVERT: P 84 LYS cc_start: 0.8136 (pttt) cc_final: 0.7765 (mmtm) REVERT: F 384 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7679 (mtt180) REVERT: E 385 GLN cc_start: 0.7104 (mt0) cc_final: 0.6603 (mt0) REVERT: O 51 GLU cc_start: 0.8664 (tp30) cc_final: 0.8233 (mp0) REVERT: O 80 GLN cc_start: 0.7251 (tm130) cc_final: 0.6816 (tm-30) REVERT: O 94 LEU cc_start: 0.7528 (tp) cc_final: 0.7282 (tp) REVERT: R 88 LEU cc_start: 0.6855 (tp) cc_final: 0.6550 (tp) REVERT: N 42 MET cc_start: 0.2709 (tpp) cc_final: 0.2281 (tpp) REVERT: Q 66 ASN cc_start: 0.7597 (m110) cc_final: 0.7208 (m110) REVERT: S 73 LYS cc_start: 0.8446 (mmmt) cc_final: 0.8104 (mmmt) REVERT: B 364 LYS cc_start: 0.8652 (ptpp) cc_final: 0.8355 (ptpp) REVERT: B 376 ASP cc_start: 0.8593 (p0) cc_final: 0.8265 (p0) REVERT: A 561 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8415 (pt) REVERT: I 22 GLU cc_start: 0.8725 (mp0) cc_final: 0.8335 (mp0) REVERT: I 41 GLU cc_start: 0.7398 (tp30) cc_final: 0.7177 (tp30) REVERT: I 72 TYR cc_start: 0.8276 (m-80) cc_final: 0.8058 (m-80) REVERT: I 79 LYS cc_start: 0.8636 (mmtp) cc_final: 0.8387 (mmtm) REVERT: I 114 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7783 (mtmm) REVERT: J 129 THR cc_start: 0.8473 (m) cc_final: 0.8242 (p) REVERT: L 483 ASP cc_start: 0.7552 (m-30) cc_final: 0.7301 (m-30) REVERT: L 488 TRP cc_start: 0.6804 (m100) cc_final: 0.6565 (m100) outliers start: 82 outliers final: 64 residues processed: 323 average time/residue: 0.1740 time to fit residues: 86.7541 Evaluate side-chains 307 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 239 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 388 GLU 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 H residue 538 VAL Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 518 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 537 VAL Chi-restraints excluded: chain D residue 552 VAL 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 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 520 ILE 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 392 THR 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 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 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 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 386 ASN 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 538 VAL Chi-restraints excluded: chain A residue 561 LEU 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 L residue 456 LEU Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 552 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 132 optimal weight: 0.9980 chunk 229 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 231 optimal weight: 4.9990 chunk 24 optimal weight: 20.0000 chunk 140 optimal weight: 0.0470 chunk 228 optimal weight: 6.9990 overall best weight: 2.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 43 HIS ** D 393 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** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.092214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.063334 restraints weight = 88729.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.063674 restraints weight = 57187.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.063373 restraints weight = 52297.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.064006 restraints weight = 45855.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.064031 restraints weight = 39371.409| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.6200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 24785 Z= 0.227 Angle : 0.743 15.289 33852 Z= 0.378 Chirality : 0.047 0.197 4007 Planarity : 0.005 0.053 4295 Dihedral : 4.930 25.288 3633 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.39 % Favored : 91.58 % Rotamer: Outliers : 3.14 % Allowed : 20.31 % Favored : 76.56 % 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: -1.47 (0.15), residues: 3064 helix: -2.13 (0.25), residues: 289 sheet: -0.01 (0.15), residues: 1148 loop : -1.47 (0.15), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 461 TYR 0.022 0.002 TYR K 515 PHE 0.021 0.002 PHE G 479 TRP 0.014 0.002 TRP K 488 HIS 0.006 0.002 HIS F 518 Details of bonding type rmsd covalent geometry : bond 0.00542 (24728) covalent geometry : angle 0.73840 (33724) SS BOND : bond 0.00544 ( 43) SS BOND : angle 1.28472 ( 86) hydrogen bonds : bond 0.04111 ( 603) hydrogen bonds : angle 5.78619 ( 1824) link_BETA1-4 : bond 0.00132 ( 3) link_BETA1-4 : angle 1.41152 ( 9) link_NAG-ASN : bond 0.00355 ( 11) link_NAG-ASN : angle 1.88755 ( 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 333 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 247 time to evaluate : 1.135 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: C 372 LEU cc_start: 0.7758 (mt) cc_final: 0.7388 (mt) REVERT: M 39 LEU cc_start: 0.8420 (tt) cc_final: 0.8069 (tt) REVERT: M 42 MET cc_start: 0.2903 (tpt) cc_final: 0.1843 (tpp) REVERT: M 43 HIS cc_start: 0.5249 (OUTLIER) cc_final: 0.5047 (m-70) REVERT: M 52 MET cc_start: 0.7828 (mmp) cc_final: 0.7364 (mtm) REVERT: M 75 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.6947 (mtp180) REVERT: M 80 GLN cc_start: 0.8054 (pm20) cc_final: 0.7641 (mm-40) REVERT: D 405 PHE cc_start: 0.7052 (t80) cc_final: 0.6115 (t80) REVERT: P 84 LYS cc_start: 0.8344 (pttt) cc_final: 0.7884 (mmtm) REVERT: O 51 GLU cc_start: 0.8733 (tp30) cc_final: 0.8246 (mp0) REVERT: O 94 LEU cc_start: 0.7633 (tp) cc_final: 0.7398 (tp) REVERT: R 88 LEU cc_start: 0.6789 (tp) cc_final: 0.6436 (tp) REVERT: Q 66 ASN cc_start: 0.7644 (m110) cc_final: 0.7333 (m-40) REVERT: S 73 LYS cc_start: 0.8438 (mmmt) cc_final: 0.8128 (mmmt) REVERT: S 117 LYS cc_start: 0.7839 (mptt) cc_final: 0.7574 (mptt) REVERT: B 364 LYS cc_start: 0.8743 (ptpp) cc_final: 0.8455 (ptpp) REVERT: B 376 ASP cc_start: 0.8094 (p0) cc_final: 0.7724 (p0) REVERT: B 386 ASN cc_start: 0.8832 (p0) cc_final: 0.8068 (p0) REVERT: A 553 ASP cc_start: 0.7930 (t0) cc_final: 0.7500 (t70) REVERT: A 561 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8260 (pt) REVERT: I 22 GLU cc_start: 0.8658 (mp0) cc_final: 0.8293 (mp0) REVERT: I 79 LYS cc_start: 0.8735 (mmtp) cc_final: 0.8482 (mmtm) REVERT: J 22 ILE cc_start: 0.8467 (pt) cc_final: 0.8194 (pt) REVERT: J 129 THR cc_start: 0.8518 (m) cc_final: 0.8289 (p) REVERT: L 483 ASP cc_start: 0.7877 (m-30) cc_final: 0.7545 (m-30) REVERT: L 488 TRP cc_start: 0.6799 (m100) cc_final: 0.6454 (m100) outliers start: 86 outliers final: 73 residues processed: 320 average time/residue: 0.1761 time to fit residues: 86.8941 Evaluate side-chains 296 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 220 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 456 LEU Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 518 HIS 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 537 VAL Chi-restraints excluded: chain D residue 552 VAL 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 P residue 123 HIS Chi-restraints excluded: chain F residue 363 THR Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 384 ARG Chi-restraints excluded: chain F residue 456 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 383 THR Chi-restraints excluded: chain G residue 520 ILE 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 520 ILE Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain N residue 24 LYS 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 62 VAL Chi-restraints excluded: chain Q residue 81 TYR Chi-restraints excluded: chain Q residue 108 MET Chi-restraints excluded: chain S residue 64 THR Chi-restraints excluded: chain S residue 66 ASN 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 520 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 561 LEU 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 L residue 456 LEU Chi-restraints excluded: chain L residue 457 LEU Chi-restraints excluded: chain L residue 545 ASN Chi-restraints excluded: chain L residue 552 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 137 optimal weight: 1.9990 chunk 290 optimal weight: 0.0000 chunk 21 optimal weight: 2.9990 chunk 146 optimal weight: 0.0770 chunk 125 optimal weight: 0.7980 chunk 81 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 4 optimal weight: 0.2980 chunk 218 optimal weight: 0.0010 chunk 187 optimal weight: 0.3980 chunk 171 optimal weight: 2.9990 overall best weight: 0.1548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** H 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 43 HIS D 439 GLN ** E 540 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 ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.094399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.066152 restraints weight = 88224.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.066062 restraints weight = 55249.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.066431 restraints weight = 44977.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.066783 restraints weight = 43460.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.066955 restraints weight = 36794.152| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.6183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24785 Z= 0.123 Angle : 0.696 16.007 33852 Z= 0.349 Chirality : 0.046 0.201 4007 Planarity : 0.004 0.046 4295 Dihedral : 4.394 21.079 3633 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.74 % Favored : 94.22 % Rotamer: Outliers : 2.04 % Allowed : 21.55 % Favored : 76.41 % 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: -1.20 (0.15), residues: 3064 helix: -1.92 (0.25), residues: 288 sheet: 0.24 (0.15), residues: 1156 loop : -1.36 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 75 TYR 0.026 0.001 TYR F 375 PHE 0.022 0.001 PHE L 479 TRP 0.012 0.001 TRP E 418 HIS 0.011 0.001 HIS M 43 Details of bonding type rmsd covalent geometry : bond 0.00277 (24728) covalent geometry : angle 0.69470 (33724) SS BOND : bond 0.00337 ( 43) SS BOND : angle 0.66579 ( 86) hydrogen bonds : bond 0.03164 ( 603) hydrogen bonds : angle 5.19923 ( 1824) link_BETA1-4 : bond 0.00324 ( 3) link_BETA1-4 : angle 1.19587 ( 9) link_NAG-ASN : bond 0.00314 ( 11) link_NAG-ASN : angle 1.32223 ( 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 337 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 281 time to evaluate : 1.022 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: M 39 LEU cc_start: 0.8313 (tt) cc_final: 0.7914 (tt) REVERT: M 51 GLU cc_start: 0.7664 (tp30) cc_final: 0.7326 (mm-30) REVERT: M 52 MET cc_start: 0.7636 (mmp) cc_final: 0.7047 (mtm) REVERT: M 75 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7025 (mtp180) REVERT: M 80 GLN cc_start: 0.7887 (pm20) cc_final: 0.7458 (mm-40) REVERT: D 364 LYS cc_start: 0.8206 (mmtt) cc_final: 0.7772 (tptt) REVERT: D 405 PHE cc_start: 0.7026 (t80) cc_final: 0.6340 (t80) REVERT: D 506 MET cc_start: 0.7617 (mtt) cc_final: 0.7267 (mtt) REVERT: P 84 LYS cc_start: 0.8360 (pttt) cc_final: 0.7889 (mmtm) REVERT: F 384 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7697 (mtt180) REVERT: O 80 GLN cc_start: 0.7233 (tm130) cc_final: 0.6974 (tm-30) REVERT: O 84 LYS cc_start: 0.8368 (ptmm) cc_final: 0.8095 (pttp) REVERT: O 94 LEU cc_start: 0.7368 (tp) cc_final: 0.7128 (tp) REVERT: N 42 MET cc_start: 0.1446 (tpp) cc_final: 0.1002 (tpp) REVERT: Q 42 MET cc_start: 0.2965 (tpt) cc_final: 0.2677 (tpp) REVERT: Q 66 ASN cc_start: 0.7670 (m110) cc_final: 0.7262 (m110) REVERT: S 52 MET cc_start: 0.6794 (mmt) cc_final: 0.5767 (tpt) REVERT: S 73 LYS cc_start: 0.8348 (mmmt) cc_final: 0.8089 (mmmt) REVERT: S 117 LYS cc_start: 0.7818 (mptt) cc_final: 0.7555 (mptt) REVERT: B 358 PHE cc_start: 0.8692 (t80) cc_final: 0.8418 (t80) REVERT: B 376 ASP cc_start: 0.8035 (p0) cc_final: 0.7685 (p0) REVERT: I 22 GLU cc_start: 0.8737 (mp0) cc_final: 0.8331 (mp0) REVERT: I 47 TYR cc_start: 0.7502 (p90) cc_final: 0.7232 (p90) REVERT: I 79 LYS cc_start: 0.8671 (mmtp) cc_final: 0.8398 (mmtm) REVERT: J 129 THR cc_start: 0.8413 (m) cc_final: 0.8192 (p) REVERT: L 483 ASP cc_start: 0.7748 (m-30) cc_final: 0.7442 (m-30) REVERT: L 488 TRP cc_start: 0.6799 (m100) cc_final: 0.6522 (m100) outliers start: 56 outliers final: 41 residues processed: 324 average time/residue: 0.1741 time to fit residues: 86.2742 Evaluate side-chains 286 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 243 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 363 THR 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 518 HIS Chi-restraints excluded: chain M residue 43 HIS Chi-restraints excluded: chain M residue 75 ARG Chi-restraints excluded: chain D residue 537 VAL 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 537 VAL 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 426 CYS 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 O residue 122 VAL Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain Q residue 62 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 406 SER Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 108 MET 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 L residue 457 LEU Chi-restraints excluded: chain L residue 523 VAL 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: 0.0470 chunk 48 optimal weight: 8.9990 chunk 167 optimal weight: 3.9990 chunk 173 optimal weight: 0.0470 chunk 278 optimal weight: 4.9990 chunk 217 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 239 optimal weight: 5.9990 chunk 279 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 43 HIS D 439 GLN ** Q 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 ASN ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.094000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.065689 restraints weight = 88633.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.065364 restraints weight = 57523.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.066085 restraints weight = 44443.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.066249 restraints weight = 42784.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.066339 restraints weight = 37817.950| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.6266 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= 0.130 Angle : 0.714 15.939 33852 Z= 0.355 Chirality : 0.046 0.215 4007 Planarity : 0.004 0.044 4295 Dihedral : 4.314 21.298 3633 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.66 % Favored : 93.28 % Rotamer: Outliers : 1.53 % Allowed : 22.42 % Favored : 76.05 % 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: -1.19 (0.15), residues: 3064 helix: -1.86 (0.25), residues: 288 sheet: 0.14 (0.15), residues: 1189 loop : -1.30 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 45 TYR 0.036 0.001 TYR R 81 PHE 0.035 0.001 PHE F 405 TRP 0.010 0.001 TRP L 488 HIS 0.012 0.001 HIS M 43 Details of bonding type rmsd covalent geometry : bond 0.00305 (24728) covalent geometry : angle 0.71213 (33724) SS BOND : bond 0.00419 ( 43) SS BOND : angle 0.81589 ( 86) hydrogen bonds : bond 0.03219 ( 603) hydrogen bonds : angle 5.17720 ( 1824) link_BETA1-4 : bond 0.00264 ( 3) link_BETA1-4 : angle 1.17192 ( 9) link_NAG-ASN : bond 0.00121 ( 11) link_NAG-ASN : angle 1.44502 ( 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 291 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 249 time to evaluate : 1.022 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: H 483 ASP cc_start: 0.8410 (m-30) cc_final: 0.7723 (t0) REVERT: M 39 LEU cc_start: 0.8268 (tt) cc_final: 0.7902 (tt) REVERT: M 51 GLU cc_start: 0.7695 (tp30) cc_final: 0.7328 (mm-30) REVERT: M 52 MET cc_start: 0.7713 (mmp) cc_final: 0.7071 (mtm) REVERT: M 75 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.6952 (mtp180) REVERT: M 80 GLN cc_start: 0.7892 (pm20) cc_final: 0.7454 (mm-40) REVERT: D 405 PHE cc_start: 0.7040 (t80) cc_final: 0.6344 (t80) REVERT: D 506 MET cc_start: 0.7649 (mtt) cc_final: 0.7286 (mtt) REVERT: P 84 LYS cc_start: 0.8456 (pttt) cc_final: 0.7868 (mmtm) REVERT: F 384 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7718 (mtt180) REVERT: F 419 ASN cc_start: 0.8917 (t0) cc_final: 0.8691 (p0) REVERT: O 51 GLU cc_start: 0.8801 (tp30) cc_final: 0.8197 (mp0) REVERT: O 94 LEU cc_start: 0.7510 (tp) cc_final: 0.7238 (tp) REVERT: N 42 MET cc_start: 0.1466 (tpp) cc_final: 0.1257 (tpp) REVERT: Q 42 MET cc_start: 0.2825 (tpt) cc_final: 0.2494 (tpp) REVERT: Q 66 ASN cc_start: 0.7683 (m110) cc_final: 0.7273 (m110) REVERT: S 52 MET cc_start: 0.6885 (mmt) cc_final: 0.5804 (tpt) REVERT: S 117 LYS cc_start: 0.7826 (mptt) cc_final: 0.7545 (mptt) REVERT: B 358 PHE cc_start: 0.8703 (t80) cc_final: 0.8436 (t80) REVERT: B 364 LYS cc_start: 0.8859 (ptpp) cc_final: 0.8550 (ptpp) REVERT: B 376 ASP cc_start: 0.7989 (p0) cc_final: 0.7645 (p0) REVERT: I 22 GLU cc_start: 0.8626 (mp0) cc_final: 0.8191 (mp0) REVERT: I 79 LYS cc_start: 0.8650 (mmtp) cc_final: 0.8380 (mmtm) REVERT: J 22 ILE cc_start: 0.8462 (pt) cc_final: 0.8244 (pt) REVERT: J 129 THR cc_start: 0.8483 (m) cc_final: 0.8263 (p) REVERT: L 483 ASP cc_start: 0.7846 (m-30) cc_final: 0.7539 (m-30) REVERT: L 488 TRP cc_start: 0.6694 (m100) cc_final: 0.6422 (m100) REVERT: L 545 ASN cc_start: 0.8694 (p0) cc_final: 0.8371 (t0) outliers start: 42 outliers final: 38 residues processed: 284 average time/residue: 0.1712 time to fit residues: 75.1762 Evaluate side-chains 271 residues out of total 2743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 231 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 363 THR 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 M residue 75 ARG Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 537 VAL 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 537 VAL 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 408 VAL Chi-restraints excluded: chain E residue 426 CYS Chi-restraints excluded: chain E residue 483 ASP 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 62 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 406 SER Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 108 MET 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 L residue 457 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 209 optimal weight: 6.9990 chunk 225 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 173 optimal weight: 0.0870 chunk 51 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** H 540 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** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.094071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.064305 restraints weight = 88091.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.065733 restraints weight = 56978.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.065708 restraints weight = 39295.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.066002 restraints weight = 41116.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.066140 restraints weight = 36588.549| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.6330 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= 0.128 Angle : 0.706 15.967 33852 Z= 0.349 Chirality : 0.045 0.198 4007 Planarity : 0.004 0.043 4295 Dihedral : 4.265 21.862 3633 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.46 % Favored : 93.47 % Rotamer: Outliers : 1.75 % Allowed : 22.27 % Favored : 75.98 % 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: -1.12 (0.15), residues: 3064 helix: -1.79 (0.25), residues: 288 sheet: 0.21 (0.15), residues: 1184 loop : -1.28 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 46 TYR 0.023 0.001 TYR F 375 PHE 0.027 0.001 PHE F 405 TRP 0.009 0.001 TRP L 488 HIS 0.006 0.001 HIS M 43 Details of bonding type rmsd covalent geometry : bond 0.00303 (24728) covalent geometry : angle 0.70421 (33724) SS BOND : bond 0.00372 ( 43) SS BOND : angle 0.81696 ( 86) hydrogen bonds : bond 0.03180 ( 603) hydrogen bonds : angle 5.15023 ( 1824) link_BETA1-4 : bond 0.00239 ( 3) link_BETA1-4 : angle 1.17033 ( 9) link_NAG-ASN : bond 0.00117 ( 11) link_NAG-ASN : angle 1.42745 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5121.41 seconds wall clock time: 89 minutes 11.99 seconds (5351.99 seconds total)