Starting phenix.real_space_refine on Thu Mar 5 07:46:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6orq_20178/03_2026/6orq_20178.cif Found real_map, /net/cci-nas-00/data/ceres_data/6orq_20178/03_2026/6orq_20178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6orq_20178/03_2026/6orq_20178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6orq_20178/03_2026/6orq_20178.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6orq_20178/03_2026/6orq_20178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6orq_20178/03_2026/6orq_20178.map" } resolution = 4.4 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= -0.000 sd= 0.144 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 132 5.16 5 C 12626 2.51 5 N 3364 2.21 5 O 4054 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s 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: 20176 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "B" Number of atoms: 3573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3573 Classifications: {'peptide': 453} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Chain: "C" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "D" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "E" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 847 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "F" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "G" Number of atoms: 3573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3573 Classifications: {'peptide': 453} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "I" Number of atoms: 3573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3573 Classifications: {'peptide': 453} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Chain: "J" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "K" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 847 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "L" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 847 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "M" 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: "N" 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: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" 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: "R" 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: "S" 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "W" 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: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" 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: "Z" 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: "a" 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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "e" 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: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" 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: "h" 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: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 4.25, per 1000 atoms: 0.21 Number of scatterers: 20176 At special positions: 0 Unit cell: (146.472, 145.036, 162.268, 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 132 16.00 O 4054 8.00 N 3364 7.00 C 12626 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.05 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.07 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.04 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.04 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.05 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.06 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.04 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.04 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.04 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.05 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.06 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.04 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA d 3 " - " MAN d 4 " ALPHA1-6 " BMA O 3 " - " MAN O 5 " " BMA d 3 " - " MAN d 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 618 " " NAG A 703 " - " ASN A 637 " " NAG B 601 " - " ASN B 88 " " NAG B 602 " - " ASN B 160 " " NAG B 615 " - " ASN B 295 " " NAG B 616 " - " ASN B 301 " " NAG B 619 " - " ASN B 339 " " NAG B 620 " - " ASN B 355 " " NAG B 623 " - " ASN B 392 " " NAG B 624 " - " ASN B 448 " " NAG C 701 " - " ASN C 611 " " NAG C 702 " - " ASN C 618 " " NAG C 703 " - " ASN C 637 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 637 " " NAG G 601 " - " ASN G 88 " " NAG G 611 " - " ASN G 295 " " NAG G 617 " - " ASN G 339 " " NAG G 618 " - " ASN G 355 " " NAG G 621 " - " ASN G 392 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 160 " " NAG I 614 " - " ASN I 295 " " NAG I 615 " - " ASN I 301 " " NAG I 619 " - " ASN I 339 " " NAG I 620 " - " ASN I 355 " " NAG I 623 " - " ASN I 392 " " NAG M 1 " - " ASN B 197 " " NAG N 1 " - " ASN B 234 " " NAG O 1 " - " ASN B 262 " " NAG P 1 " - " ASN B 279 " " NAG Q 1 " - " ASN B 332 " " NAG R 1 " - " ASN B 386 " " NAG S 1 " - " ASN G 160 " " NAG T 1 " - " ASN G 234 " " NAG U 1 " - " ASN G 262 " " NAG V 1 " - " ASN G 279 " " NAG W 1 " - " ASN G 301 " " NAG X 1 " - " ASN G 332 " " NAG Y 1 " - " ASN G 386 " " NAG Z 1 " - " ASN G 448 " " NAG a 1 " - " ASN G 197 " " NAG b 1 " - " ASN I 197 " " NAG c 1 " - " ASN I 234 " " NAG d 1 " - " ASN I 262 " " NAG e 1 " - " ASN I 279 " " NAG f 1 " - " ASN I 332 " " NAG g 1 " - " ASN I 386 " " NAG h 1 " - " ASN I 448 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 838.6 milliseconds 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4512 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 51 sheets defined 20.0% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 529 through 535 removed outlier: 3.743A pdb=" N MET A 535 " --> pdb=" O GLY A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 543 Processing helix chain 'A' and resid 572 through 595 removed outlier: 3.965A pdb=" N ASP A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN A 590 " --> pdb=" O TYR A 586 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN A 591 " --> pdb=" O LEU A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 624 Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.998A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 652 removed outlier: 3.737A pdb=" N GLY A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A 648 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 649 " --> pdb=" O LEU A 645 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 657 Processing helix chain 'A' and resid 657 through 662 Processing helix chain 'B' and resid 59 through 64 removed outlier: 3.757A pdb=" N THR B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 99 through 117 removed outlier: 3.876A pdb=" N ILE B 108 " --> pdb=" O MET B 104 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 109 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 139 removed outlier: 3.536A pdb=" N ASN B 137 " --> pdb=" O TYR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 334 through 351 removed outlier: 3.513A pdb=" N LYS B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 354 No H-bonds generated for 'chain 'B' and resid 352 through 354' Processing helix chain 'B' and resid 368 through 372 removed outlier: 3.997A pdb=" N VAL B 371 " --> pdb=" O ASP B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.668A pdb=" N GLN B 428 " --> pdb=" O ASN B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 483 removed outlier: 3.771A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 535 removed outlier: 3.743A pdb=" N MET C 535 " --> pdb=" O GLY C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 543 Processing helix chain 'C' and resid 572 through 595 removed outlier: 3.966A pdb=" N ASP C 589 " --> pdb=" O HIS C 585 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN C 590 " --> pdb=" O TYR C 586 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN C 591 " --> pdb=" O LEU C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 624 Processing helix chain 'C' and resid 627 through 635 removed outlier: 3.998A pdb=" N LYS C 633 " --> pdb=" O LEU C 629 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU C 634 " --> pdb=" O GLN C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 652 removed outlier: 3.737A pdb=" N GLY C 644 " --> pdb=" O GLN C 640 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU C 648 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 649 " --> pdb=" O LEU C 645 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 657 Processing helix chain 'C' and resid 657 through 662 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.816A pdb=" N ALA E 83 " --> pdb=" O GLU E 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 535 removed outlier: 3.742A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 543 Processing helix chain 'F' and resid 572 through 595 removed outlier: 3.966A pdb=" N ASP F 589 " --> pdb=" O HIS F 585 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN F 590 " --> pdb=" O TYR F 586 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN F 591 " --> pdb=" O LEU F 587 " (cutoff:3.500A) Processing helix chain 'F' and resid 620 through 624 Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.998A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 652 removed outlier: 3.737A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER F 649 " --> pdb=" O LEU F 645 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN F 650 " --> pdb=" O LEU F 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 652 through 657 Processing helix chain 'F' and resid 657 through 662 Processing helix chain 'G' and resid 59 through 64 removed outlier: 3.908A pdb=" N THR G 63 " --> pdb=" O LYS G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 67 No H-bonds generated for 'chain 'G' and resid 65 through 67' Processing helix chain 'G' and resid 99 through 117 removed outlier: 3.616A pdb=" N ILE G 108 " --> pdb=" O MET G 104 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 139 removed outlier: 3.554A pdb=" N ASN G 137 " --> pdb=" O TYR G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 334 through 350 removed outlier: 3.522A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 354 removed outlier: 4.280A pdb=" N GLY G 354 " --> pdb=" O LYS G 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 351 through 354' Processing helix chain 'G' and resid 368 through 373 removed outlier: 4.087A pdb=" N THR G 372 " --> pdb=" O ASP G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.570A pdb=" N GLN G 428 " --> pdb=" O ASN G 425 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 425 through 429' Processing helix chain 'G' and resid 475 through 483 removed outlier: 3.940A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 64 removed outlier: 3.796A pdb=" N THR I 63 " --> pdb=" O LYS I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 67 No H-bonds generated for 'chain 'I' and resid 65 through 67' Processing helix chain 'I' and resid 99 through 117 removed outlier: 3.777A pdb=" N ILE I 108 " --> pdb=" O MET I 104 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE I 109 " --> pdb=" O HIS I 105 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN I 114 " --> pdb=" O SER I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 139 removed outlier: 3.552A pdb=" N ASN I 137 " --> pdb=" O TYR I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 179 No H-bonds generated for 'chain 'I' and resid 177 through 179' Processing helix chain 'I' and resid 334 through 350 removed outlier: 3.503A pdb=" N LYS I 347 " --> pdb=" O GLY I 343 " (cutoff:3.500A) Processing helix chain 'I' and resid 351 through 354 removed outlier: 4.259A pdb=" N GLY I 354 " --> pdb=" O LYS I 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 351 through 354' Processing helix chain 'I' and resid 368 through 372 removed outlier: 4.028A pdb=" N VAL I 371 " --> pdb=" O ASP I 368 " (cutoff:3.500A) Processing helix chain 'I' and resid 387 through 390 Processing helix chain 'I' and resid 425 through 429 removed outlier: 3.726A pdb=" N GLN I 428 " --> pdb=" O ASN I 425 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG I 429 " --> pdb=" O MET I 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 425 through 429' Processing helix chain 'I' and resid 475 through 481 removed outlier: 3.974A pdb=" N TRP I 479 " --> pdb=" O MET I 475 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.816A pdb=" N ALA K 83 " --> pdb=" O GLU K 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.817A pdb=" N ALA L 83 " --> pdb=" O GLU L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 603 through 609 removed outlier: 3.877A pdb=" N CYS A 604 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 38 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR A 606 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL B 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP B 35 " --> pdb=" O THR B 499 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 46 removed outlier: 3.818A pdb=" N LYS B 490 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS B 487 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'B' and resid 92 through 93 Processing sheet with id=AA5, first strand: chain 'B' and resid 130 through 131 removed outlier: 4.046A pdb=" N GLN B 130 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER B 158 " --> pdb=" O GLN B 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 160 through 162 Processing sheet with id=AA7, first strand: chain 'B' and resid 182 through 183 Processing sheet with id=AA8, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.582A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 259 through 261 removed outlier: 4.097A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 452 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B 286 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 259 through 261 removed outlier: 4.097A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL B 292 " --> pdb=" O ILE B 449 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN B 295 " --> pdb=" O ASN B 332 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR B 297 " --> pdb=" O HIS B 330 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N HIS B 330 " --> pdb=" O THR B 297 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE B 376 " --> pdb=" O PHE B 383 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 305 through 308 removed outlier: 3.533A pdb=" N LYS B 305 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 394 through 395 removed outlier: 3.601A pdb=" N ILE B 359 " --> pdb=" O TRP B 395 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 603 through 609 removed outlier: 3.949A pdb=" N CYS C 604 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL G 38 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR C 606 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL G 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 19 through 21 Processing sheet with id=AB6, first strand: chain 'D' and resid 48 through 49 removed outlier: 3.621A pdb=" N ALA D 93 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 37 " --> pdb=" O TYR D 91 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 45 through 46 Processing sheet with id=AB8, first strand: chain 'E' and resid 48 through 49 Processing sheet with id=AB9, first strand: chain 'E' and resid 63 through 64 removed outlier: 3.973A pdb=" N SER E 63 " --> pdb=" O ASN E 74 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN E 74 " --> pdb=" O SER E 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 603 through 609 removed outlier: 3.908A pdb=" N CYS F 604 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL I 38 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR F 606 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL I 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 45 through 46 removed outlier: 3.524A pdb=" N LYS G 46 " --> pdb=" O LYS G 490 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS G 490 " --> pdb=" O LYS G 46 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS G 487 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AC4, first strand: chain 'G' and resid 92 through 93 Processing sheet with id=AC5, first strand: chain 'G' and resid 130 through 132 removed outlier: 4.057A pdb=" N GLN G 130 " --> pdb=" O SER G 158 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER G 158 " --> pdb=" O GLN G 130 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR G 132 " --> pdb=" O GLN G 156 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 160 through 162 Processing sheet with id=AC7, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AC8, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.706A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 271 through 274 Processing sheet with id=AD1, first strand: chain 'G' and resid 374 through 378 removed outlier: 3.731A pdb=" N PHE G 376 " --> pdb=" O PHE G 383 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N HIS G 330 " --> pdb=" O THR G 297 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR G 297 " --> pdb=" O HIS G 330 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN G 295 " --> pdb=" O ASN G 332 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL G 292 " --> pdb=" O ILE G 449 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 304 through 308 removed outlier: 3.678A pdb=" N LYS G 305 " --> pdb=" O TYR G 319 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 394 through 395 removed outlier: 3.597A pdb=" N ILE G 359 " --> pdb=" O TRP G 395 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 19 through 21 Processing sheet with id=AD5, first strand: chain 'H' and resid 48 through 49 removed outlier: 3.621A pdb=" N ALA H 93 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 45 through 46 removed outlier: 3.737A pdb=" N LYS I 490 " --> pdb=" O LYS I 46 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 53 through 55 removed outlier: 3.790A pdb=" N HIS I 216 " --> pdb=" O ALA I 55 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 91 through 93 removed outlier: 4.087A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 121 through 122 removed outlier: 3.947A pdb=" N LEU I 122 " --> pdb=" O ILE I 201 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ILE I 201 " --> pdb=" O LEU I 122 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 130 through 132 removed outlier: 4.110A pdb=" N GLN I 130 " --> pdb=" O SER I 158 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER I 158 " --> pdb=" O GLN I 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 160 through 162 Processing sheet with id=AE3, first strand: chain 'I' and resid 181 through 183 Processing sheet with id=AE4, first strand: chain 'I' and resid 271 through 274 removed outlier: 3.574A pdb=" N GLN I 287 " --> pdb=" O ILE I 271 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 374 through 378 removed outlier: 3.741A pdb=" N PHE I 376 " --> pdb=" O PHE I 383 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N HIS I 330 " --> pdb=" O THR I 297 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR I 297 " --> pdb=" O HIS I 330 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN I 295 " --> pdb=" O ASN I 332 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL I 292 " --> pdb=" O ILE I 449 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 304 through 308 removed outlier: 3.553A pdb=" N LYS I 305 " --> pdb=" O TYR I 319 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 394 through 395 removed outlier: 3.623A pdb=" N ILE I 359 " --> pdb=" O TRP I 395 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 19 through 21 Processing sheet with id=AE9, first strand: chain 'J' and resid 48 through 49 removed outlier: 3.621A pdb=" N ALA J 93 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL J 37 " --> pdb=" O TYR J 91 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 45 through 46 Processing sheet with id=AF2, first strand: chain 'K' and resid 48 through 49 Processing sheet with id=AF3, first strand: chain 'K' and resid 63 through 64 removed outlier: 3.974A pdb=" N SER K 63 " --> pdb=" O ASN K 74 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN K 74 " --> pdb=" O SER K 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'L' and resid 45 through 46 Processing sheet with id=AF5, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AF6, first strand: chain 'L' and resid 63 through 64 removed outlier: 3.974A pdb=" N SER L 63 " --> pdb=" O ASN L 74 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN L 74 " --> pdb=" O SER L 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 415 hydrogen bonds defined for protein. 1026 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: 3.19 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3261 1.31 - 1.45: 5847 1.45 - 1.58: 11293 1.58 - 1.72: 0 1.72 - 1.85: 186 Bond restraints: 20587 Sorted by residual: bond pdb=" C3 NAG a 1 " pdb=" C4 NAG a 1 " ideal model delta sigma weight residual 1.524 1.449 0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C3 BMA d 3 " pdb=" O3 BMA d 3 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C4 NAG a 1 " pdb=" C5 NAG a 1 " ideal model delta sigma weight residual 1.532 1.463 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C3 NAG a 2 " pdb=" C4 NAG a 2 " ideal model delta sigma weight residual 1.524 1.455 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C7 NAG a 1 " pdb=" C8 NAG a 1 " ideal model delta sigma weight residual 1.509 1.443 0.066 2.00e-02 2.50e+03 1.07e+01 ... (remaining 20582 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 27272 3.58 - 7.16: 552 7.16 - 10.75: 92 10.75 - 14.33: 9 14.33 - 17.91: 9 Bond angle restraints: 27934 Sorted by residual: angle pdb=" N LEU J 45 " pdb=" CA LEU J 45 " pdb=" C LEU J 45 " ideal model delta sigma weight residual 110.80 125.23 -14.43 2.13e+00 2.20e-01 4.59e+01 angle pdb=" N LEU H 45 " pdb=" CA LEU H 45 " pdb=" C LEU H 45 " ideal model delta sigma weight residual 110.80 125.22 -14.42 2.13e+00 2.20e-01 4.58e+01 angle pdb=" N LEU D 45 " pdb=" CA LEU D 45 " pdb=" C LEU D 45 " ideal model delta sigma weight residual 110.80 125.19 -14.39 2.13e+00 2.20e-01 4.57e+01 angle pdb=" C3 NAG a 1 " pdb=" C2 NAG a 1 " pdb=" N2 NAG a 1 " ideal model delta sigma weight residual 110.74 92.83 17.91 3.00e+00 1.11e-01 3.56e+01 angle pdb=" N VAL B 371 " pdb=" CA VAL B 371 " pdb=" C VAL B 371 " ideal model delta sigma weight residual 113.42 106.98 6.44 1.17e+00 7.31e-01 3.03e+01 ... (remaining 27929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.12: 12478 22.12 - 44.23: 703 44.23 - 66.35: 116 66.35 - 88.47: 74 88.47 - 110.59: 31 Dihedral angle restraints: 13402 sinusoidal: 6382 harmonic: 7020 Sorted by residual: dihedral pdb=" CA LYS J 13 " pdb=" C LYS J 13 " pdb=" N PRO J 14 " pdb=" CA PRO J 14 " ideal model delta harmonic sigma weight residual 180.00 -123.10 -56.90 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" CA LYS H 13 " pdb=" C LYS H 13 " pdb=" N PRO H 14 " pdb=" CA PRO H 14 " ideal model delta harmonic sigma weight residual 180.00 -123.14 -56.86 0 5.00e+00 4.00e-02 1.29e+02 dihedral pdb=" CA LYS D 13 " pdb=" C LYS D 13 " pdb=" N PRO D 14 " pdb=" CA PRO D 14 " ideal model delta harmonic sigma weight residual -180.00 -123.15 -56.85 0 5.00e+00 4.00e-02 1.29e+02 ... (remaining 13399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.166: 3213 0.166 - 0.333: 109 0.333 - 0.499: 11 0.499 - 0.666: 0 0.666 - 0.832: 4 Chirality restraints: 3337 Sorted by residual: chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-02 2.50e+03 1.65e+02 chirality pdb=" C5 NAG a 1 " pdb=" C4 NAG a 1 " pdb=" C6 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.41 -1.58 -0.83 2.00e-01 2.50e+01 1.73e+01 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 618 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -1.61 -0.79 2.00e-01 2.50e+01 1.54e+01 ... (remaining 3334 not shown) Planarity restraints: 3514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 2 " -0.404 2.00e-02 2.50e+03 3.32e-01 1.38e+03 pdb=" C7 NAG a 2 " 0.166 2.00e-02 2.50e+03 pdb=" C8 NAG a 2 " -0.243 2.00e-02 2.50e+03 pdb=" N2 NAG a 2 " 0.545 2.00e-02 2.50e+03 pdb=" O7 NAG a 2 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 1 " 0.366 2.00e-02 2.50e+03 3.15e-01 1.24e+03 pdb=" C7 NAG a 1 " -0.127 2.00e-02 2.50e+03 pdb=" C8 NAG a 1 " 0.181 2.00e-02 2.50e+03 pdb=" N2 NAG a 1 " -0.545 2.00e-02 2.50e+03 pdb=" O7 NAG a 1 " 0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 13 " 0.064 5.00e-02 4.00e+02 9.67e-02 1.50e+01 pdb=" N PRO D 14 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO D 14 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO D 14 " 0.053 5.00e-02 4.00e+02 ... (remaining 3511 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 297 2.61 - 3.18: 17193 3.18 - 3.76: 30218 3.76 - 4.33: 37608 4.33 - 4.90: 59246 Nonbonded interactions: 144562 Sorted by model distance: nonbonded pdb=" O4 NAG a 2 " pdb=" O6 NAG a 2 " model vdw 2.039 3.040 nonbonded pdb=" O4 NAG a 1 " pdb=" O6 NAG a 1 " model vdw 2.136 3.040 nonbonded pdb=" OG1 THR J 68 " pdb=" O GLN J 81 " model vdw 2.241 3.040 nonbonded pdb=" OG1 THR H 68 " pdb=" O GLN H 81 " model vdw 2.242 3.040 nonbonded pdb=" OG1 THR D 68 " pdb=" O GLN D 81 " model vdw 2.243 3.040 ... (remaining 144557 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' selection = chain 'C' selection = chain 'F' } ncs_group { reference = (chain 'B' and resid 31 through 619) selection = chain 'G' selection = (chain 'I' and resid 31 through 619) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'h' } ncs_group { reference = chain 'O' selection = chain 'd' } ncs_group { reference = chain 'P' selection = chain 'U' selection = chain 'X' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.860 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 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 : 0.008 0.075 20698 Z= 0.382 Angle : 1.390 25.597 28237 Z= 0.685 Chirality : 0.077 0.832 3337 Planarity : 0.011 0.332 3463 Dihedral : 15.528 110.585 8809 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.34 % Allowed : 16.29 % Favored : 83.38 % Rotamer: Outliers : 1.04 % Allowed : 7.81 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.61 % 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: -4.97 (0.13), residues: 2388 helix: -4.26 (0.15), residues: 288 sheet: -2.27 (0.23), residues: 459 loop : -3.69 (0.12), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 61 TYR 0.037 0.004 TYR I 134 PHE 0.023 0.003 PHE L 98 TRP 0.026 0.003 TRP I 35 HIS 0.013 0.003 HIS E 76 Details of bonding type rmsd covalent geometry : bond 0.00807 (20587) covalent geometry : angle 1.30914 (27934) SS BOND : bond 0.01467 ( 27) SS BOND : angle 2.13191 ( 54) hydrogen bonds : bond 0.32322 ( 414) hydrogen bonds : angle 9.35896 ( 1026) Misc. bond : bond 0.01549 ( 1) link_ALPHA1-3 : bond 0.01074 ( 2) link_ALPHA1-3 : angle 4.50965 ( 6) link_ALPHA1-6 : bond 0.00052 ( 2) link_ALPHA1-6 : angle 1.90239 ( 6) link_BETA1-4 : bond 0.00910 ( 28) link_BETA1-4 : angle 4.53708 ( 84) link_NAG-ASN : bond 0.00943 ( 51) link_NAG-ASN : angle 5.45183 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 618 time to evaluate : 0.752 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: A 540 GLN cc_start: 0.8982 (mp-120) cc_final: 0.8722 (mp10) REVERT: A 574 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8332 (mttm) REVERT: A 584 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8315 (tm-30) REVERT: A 588 ARG cc_start: 0.9131 (ttt180) cc_final: 0.8894 (ttt90) REVERT: A 621 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8494 (tm-30) REVERT: A 647 GLU cc_start: 0.9051 (pp20) cc_final: 0.8848 (pp20) REVERT: A 648 GLU cc_start: 0.9036 (pp20) cc_final: 0.8704 (pp20) REVERT: A 654 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8770 (tp30) REVERT: B 80 ASN cc_start: 0.8902 (t0) cc_final: 0.8439 (p0) REVERT: B 104 MET cc_start: 0.8942 (ttm) cc_final: 0.8595 (ttm) REVERT: B 114 GLN cc_start: 0.9278 (tm-30) cc_final: 0.9048 (tm-30) REVERT: B 161 MET cc_start: 0.9228 (tpp) cc_final: 0.8841 (tpp) REVERT: B 256 SER cc_start: 0.9266 (m) cc_final: 0.9009 (m) REVERT: B 340 GLU cc_start: 0.9317 (tp30) cc_final: 0.9107 (tp30) REVERT: C 535 MET cc_start: 0.8927 (mtt) cc_final: 0.8592 (mmm) REVERT: C 542 ARG cc_start: 0.9260 (mtp-110) cc_final: 0.9003 (ttp80) REVERT: C 543 ASN cc_start: 0.8918 (t0) cc_final: 0.8643 (t0) REVERT: C 574 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8783 (ttmm) REVERT: C 584 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8343 (tm-30) REVERT: C 621 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8298 (tm-30) REVERT: C 648 GLU cc_start: 0.9151 (pp20) cc_final: 0.8713 (pm20) REVERT: D 34 MET cc_start: 0.9026 (mpt) cc_final: 0.8781 (mmm) REVERT: D 36 TRP cc_start: 0.8331 (m100) cc_final: 0.8024 (m-10) REVERT: D 75 LYS cc_start: 0.9087 (mtmt) cc_final: 0.8847 (mtpt) REVERT: D 82 LEU cc_start: 0.9165 (mt) cc_final: 0.8755 (mt) REVERT: D 85 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8659 (pp20) REVERT: E 37 GLN cc_start: 0.7675 (pp30) cc_final: 0.7096 (pp30) REVERT: E 38 GLN cc_start: 0.8843 (pt0) cc_final: 0.8462 (pt0) REVERT: E 72 THR cc_start: 0.7080 (t) cc_final: 0.6748 (t) REVERT: F 574 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8669 (ttmm) REVERT: F 584 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8485 (tm-30) REVERT: F 621 GLU cc_start: 0.8845 (tm-30) cc_final: 0.7487 (tm-30) REVERT: F 622 ILE cc_start: 0.9196 (pp) cc_final: 0.7976 (pp) REVERT: F 624 ASP cc_start: 0.8804 (m-30) cc_final: 0.8532 (m-30) REVERT: F 648 GLU cc_start: 0.9104 (pp20) cc_final: 0.8833 (pp20) REVERT: F 654 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8725 (tp30) REVERT: F 655 LYS cc_start: 0.8833 (pptt) cc_final: 0.8614 (pptt) REVERT: G 114 GLN cc_start: 0.9394 (tm-30) cc_final: 0.9115 (tm-30) REVERT: G 150 MET cc_start: 0.8892 (tmt) cc_final: 0.8542 (tmm) REVERT: G 161 MET cc_start: 0.9127 (tpp) cc_final: 0.8758 (tpp) REVERT: G 252 LYS cc_start: 0.9251 (mtmm) cc_final: 0.8993 (mtpp) REVERT: G 302 ASN cc_start: 0.8304 (t0) cc_final: 0.7879 (t0) REVERT: G 321 ASP cc_start: 0.8678 (t70) cc_final: 0.8301 (t70) REVERT: H 1 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8389 (pm20) REVERT: H 29 PHE cc_start: 0.8894 (t80) cc_final: 0.8579 (t80) REVERT: H 51 ILE cc_start: 0.8556 (pt) cc_final: 0.8303 (pt) REVERT: H 67 PHE cc_start: 0.8728 (p90) cc_final: 0.8353 (p90) REVERT: I 80 ASN cc_start: 0.9034 (t0) cc_final: 0.8607 (p0) REVERT: I 114 GLN cc_start: 0.9351 (tm-30) cc_final: 0.9088 (tm-30) REVERT: I 125 LEU cc_start: 0.8971 (tt) cc_final: 0.8686 (tt) REVERT: I 194 ILE cc_start: 0.9296 (tp) cc_final: 0.8974 (tp) REVERT: I 211 GLU cc_start: 0.9021 (tm-30) cc_final: 0.8747 (tm-30) REVERT: I 217 TYR cc_start: 0.8111 (m-10) cc_final: 0.7031 (m-10) REVERT: I 230 ASP cc_start: 0.8785 (t0) cc_final: 0.8569 (t0) REVERT: I 252 LYS cc_start: 0.9348 (mtmm) cc_final: 0.8942 (mtpp) REVERT: I 340 GLU cc_start: 0.9287 (tp30) cc_final: 0.9014 (tm-30) REVERT: I 425 ASN cc_start: 0.9354 (p0) cc_final: 0.9099 (p0) REVERT: I 452 LEU cc_start: 0.9181 (mm) cc_final: 0.8444 (tt) REVERT: I 477 ASP cc_start: 0.9278 (p0) cc_final: 0.9075 (p0) REVERT: I 479 TRP cc_start: 0.8841 (m-10) cc_final: 0.8464 (m-10) REVERT: I 482 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8630 (mm-30) REVERT: J 1 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8244 (pm20) REVERT: J 27 PHE cc_start: 0.8394 (m-10) cc_final: 0.8029 (m-10) REVERT: J 29 PHE cc_start: 0.8710 (t80) cc_final: 0.8480 (t80) REVERT: J 34 MET cc_start: 0.9346 (mpt) cc_final: 0.9103 (mmm) REVERT: J 36 TRP cc_start: 0.8285 (m100) cc_final: 0.7885 (m100) REVERT: J 71 ARG cc_start: 0.8473 (tmt90) cc_final: 0.8150 (ttt-90) REVERT: J 82 LEU cc_start: 0.8863 (mt) cc_final: 0.8015 (mt) REVERT: J 83 LYS cc_start: 0.7458 (tppt) cc_final: 0.7237 (tppp) REVERT: J 85 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8408 (pp20) REVERT: J 91 TYR cc_start: 0.8743 (m-80) cc_final: 0.8534 (m-80) REVERT: K 37 GLN cc_start: 0.8014 (pp30) cc_final: 0.7190 (pp30) REVERT: K 38 GLN cc_start: 0.8597 (pt0) cc_final: 0.8307 (pp30) REVERT: K 45 LYS cc_start: 0.8632 (tptm) cc_final: 0.8256 (ttpt) REVERT: K 81 GLU cc_start: 0.9277 (pp20) cc_final: 0.8966 (pp20) REVERT: L 37 GLN cc_start: 0.8466 (pp30) cc_final: 0.7783 (pp30) REVERT: L 38 GLN cc_start: 0.8651 (pt0) cc_final: 0.8304 (pp30) REVERT: L 45 LYS cc_start: 0.8997 (tptm) cc_final: 0.8639 (ttpt) outliers start: 22 outliers final: 10 residues processed: 629 average time/residue: 0.1480 time to fit residues: 140.9765 Evaluate side-chains 435 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 422 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 0.0060 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 4.9990 overall best weight: 1.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 HIS A 590 GLN A 651 ASN B 66 HIS B 203 GLN B 258 GLN ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 HIS C 590 GLN C 616 ASN C 651 ASN D 81 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 HIS F 590 GLN F 616 ASN F 651 ASN G 66 HIS G 293 GLN G 300 ASN G 440 GLN H 81 GLN I 258 GLN J 81 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.088342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.070943 restraints weight = 64427.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.073312 restraints weight = 34033.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.074919 restraints weight = 21944.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.076014 restraints weight = 16056.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.076775 restraints weight = 12811.229| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20698 Z= 0.167 Angle : 0.957 19.148 28237 Z= 0.446 Chirality : 0.054 0.481 3337 Planarity : 0.006 0.091 3463 Dihedral : 12.923 97.114 4330 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.21 % Allowed : 13.53 % Favored : 86.26 % Rotamer: Outliers : 0.47 % Allowed : 4.83 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.35 % 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: -4.35 (0.14), residues: 2388 helix: -2.40 (0.22), residues: 336 sheet: -1.52 (0.26), residues: 408 loop : -3.65 (0.12), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 178 TYR 0.023 0.002 TYR G 134 PHE 0.020 0.002 PHE B 376 TRP 0.018 0.002 TRP I 35 HIS 0.010 0.001 HIS K 76 Details of bonding type rmsd covalent geometry : bond 0.00357 (20587) covalent geometry : angle 0.89744 (27934) SS BOND : bond 0.00563 ( 27) SS BOND : angle 1.95690 ( 54) hydrogen bonds : bond 0.05739 ( 414) hydrogen bonds : angle 6.31644 ( 1026) Misc. bond : bond 0.00052 ( 1) link_ALPHA1-3 : bond 0.00502 ( 2) link_ALPHA1-3 : angle 2.94782 ( 6) link_ALPHA1-6 : bond 0.00802 ( 2) link_ALPHA1-6 : angle 1.28638 ( 6) link_BETA1-4 : bond 0.00718 ( 28) link_BETA1-4 : angle 2.92672 ( 84) link_NAG-ASN : bond 0.00711 ( 51) link_NAG-ASN : angle 3.94075 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 577 time to evaluate : 0.649 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: A 535 MET cc_start: 0.8736 (mmt) cc_final: 0.8533 (mmm) REVERT: A 584 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8494 (tm-30) REVERT: A 617 ARG cc_start: 0.8636 (mtt180) cc_final: 0.7998 (mtm-85) REVERT: A 626 MET cc_start: 0.8290 (mtm) cc_final: 0.7625 (mtt) REVERT: A 648 GLU cc_start: 0.9020 (pp20) cc_final: 0.8767 (pp20) REVERT: B 80 ASN cc_start: 0.8860 (t0) cc_final: 0.8335 (p0) REVERT: B 98 ASN cc_start: 0.8448 (t0) cc_final: 0.6783 (t0) REVERT: B 99 ASN cc_start: 0.9225 (m-40) cc_final: 0.8571 (m-40) REVERT: B 102 GLU cc_start: 0.9275 (mp0) cc_final: 0.8790 (mp0) REVERT: B 114 GLN cc_start: 0.9313 (tm-30) cc_final: 0.9056 (tm-30) REVERT: B 161 MET cc_start: 0.9174 (tpp) cc_final: 0.8971 (tpp) REVERT: B 321 ASP cc_start: 0.8923 (t70) cc_final: 0.8464 (t0) REVERT: B 452 LEU cc_start: 0.9441 (pt) cc_final: 0.8884 (pp) REVERT: B 475 MET cc_start: 0.7582 (tmm) cc_final: 0.7215 (tmm) REVERT: C 584 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8485 (tm-30) REVERT: C 617 ARG cc_start: 0.8619 (mtt180) cc_final: 0.7912 (mtm180) REVERT: C 621 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8086 (tm-30) REVERT: C 622 ILE cc_start: 0.9106 (pt) cc_final: 0.8831 (mp) REVERT: C 626 MET cc_start: 0.8356 (mtm) cc_final: 0.7769 (mtm) REVERT: C 648 GLU cc_start: 0.9057 (pp20) cc_final: 0.8659 (pm20) REVERT: C 654 GLU cc_start: 0.8813 (tp30) cc_final: 0.8417 (tp30) REVERT: D 1 GLU cc_start: 0.6728 (pm20) cc_final: 0.6236 (pm20) REVERT: D 82 MET cc_start: 0.8420 (mmm) cc_final: 0.8178 (mmm) REVERT: D 82 LEU cc_start: 0.8685 (mt) cc_final: 0.8415 (tp) REVERT: D 102 TYR cc_start: 0.9417 (m-80) cc_final: 0.8926 (m-80) REVERT: E 35 TRP cc_start: 0.8246 (m-90) cc_final: 0.8036 (m-90) REVERT: E 37 GLN cc_start: 0.7914 (pp30) cc_final: 0.7344 (pp30) REVERT: E 45 LYS cc_start: 0.8846 (tptp) cc_final: 0.8422 (ttpp) REVERT: E 72 THR cc_start: 0.7009 (t) cc_final: 0.6556 (t) REVERT: E 97 THR cc_start: 0.8992 (m) cc_final: 0.8700 (p) REVERT: F 573 ILE cc_start: 0.9259 (pt) cc_final: 0.9048 (pt) REVERT: F 577 GLN cc_start: 0.9147 (mt0) cc_final: 0.8836 (mt0) REVERT: F 584 GLU cc_start: 0.8961 (tm-30) cc_final: 0.8690 (tm-30) REVERT: F 624 ASP cc_start: 0.8915 (m-30) cc_final: 0.8650 (m-30) REVERT: F 648 GLU cc_start: 0.9061 (pp20) cc_final: 0.8553 (pm20) REVERT: G 98 ASN cc_start: 0.8705 (t0) cc_final: 0.7887 (t0) REVERT: G 102 GLU cc_start: 0.9323 (mp0) cc_final: 0.9100 (mp0) REVERT: G 114 GLN cc_start: 0.9406 (tm-30) cc_final: 0.9117 (tm-30) REVERT: G 302 ASN cc_start: 0.8344 (t0) cc_final: 0.7818 (t0) REVERT: G 321 ASP cc_start: 0.8660 (t70) cc_final: 0.8214 (t70) REVERT: G 325 ASP cc_start: 0.8875 (p0) cc_final: 0.8321 (p0) REVERT: G 426 MET cc_start: 0.8765 (ptm) cc_final: 0.8262 (ptm) REVERT: G 434 MET cc_start: 0.8089 (tmm) cc_final: 0.7660 (tmm) REVERT: H 1 GLU cc_start: 0.8775 (tm-30) cc_final: 0.7974 (pm20) REVERT: H 27 PHE cc_start: 0.8205 (m-10) cc_final: 0.7813 (m-80) REVERT: H 58 TYR cc_start: 0.5872 (p90) cc_final: 0.5147 (p90) REVERT: H 67 PHE cc_start: 0.8778 (p90) cc_final: 0.8175 (p90) REVERT: I 59 LYS cc_start: 0.8222 (tptp) cc_final: 0.8017 (tptp) REVERT: I 98 ASN cc_start: 0.8456 (t0) cc_final: 0.7494 (t0) REVERT: I 102 GLU cc_start: 0.9261 (mp0) cc_final: 0.8826 (mp0) REVERT: I 114 GLN cc_start: 0.9401 (tm-30) cc_final: 0.9074 (tm-30) REVERT: I 217 TYR cc_start: 0.7085 (m-10) cc_final: 0.6341 (m-10) REVERT: I 230 ASP cc_start: 0.8533 (t0) cc_final: 0.8326 (t0) REVERT: I 252 LYS cc_start: 0.9352 (mtmm) cc_final: 0.8929 (mtpp) REVERT: I 340 GLU cc_start: 0.9177 (tp30) cc_final: 0.8976 (tp30) REVERT: I 425 ASN cc_start: 0.9358 (p0) cc_final: 0.9068 (p0) REVERT: I 475 MET cc_start: 0.6198 (tmm) cc_final: 0.5928 (tmm) REVERT: I 482 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8568 (mm-30) REVERT: J 1 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8091 (pm20) REVERT: J 27 PHE cc_start: 0.8225 (m-10) cc_final: 0.7886 (m-10) REVERT: J 29 PHE cc_start: 0.8696 (t80) cc_final: 0.8442 (t80) REVERT: J 36 TRP cc_start: 0.8324 (m100) cc_final: 0.7828 (m100) REVERT: J 44 ARG cc_start: 0.5770 (mmt-90) cc_final: 0.5298 (mmt-90) REVERT: J 82 LEU cc_start: 0.8461 (mt) cc_final: 0.7978 (tp) REVERT: J 85 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8090 (tm-30) REVERT: J 91 TYR cc_start: 0.8634 (m-80) cc_final: 0.8161 (m-80) REVERT: J 102 TYR cc_start: 0.9292 (m-80) cc_final: 0.8547 (m-80) REVERT: K 23 CYS cc_start: 0.8874 (t) cc_final: 0.8204 (t) REVERT: K 37 GLN cc_start: 0.8044 (pp30) cc_final: 0.7137 (pp30) REVERT: K 38 GLN cc_start: 0.8671 (pt0) cc_final: 0.7564 (tt0) REVERT: K 45 LYS cc_start: 0.9028 (tptm) cc_final: 0.8810 (ttpt) REVERT: L 37 GLN cc_start: 0.8069 (pp30) cc_final: 0.7289 (pp30) REVERT: L 38 GLN cc_start: 0.8675 (pt0) cc_final: 0.7553 (tt0) REVERT: L 97 THR cc_start: 0.9049 (m) cc_final: 0.8813 (p) outliers start: 10 outliers final: 7 residues processed: 584 average time/residue: 0.1328 time to fit residues: 120.6784 Evaluate side-chains 448 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 441 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 153 optimal weight: 9.9990 chunk 226 optimal weight: 3.9990 chunk 28 optimal weight: 0.0870 chunk 23 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 122 optimal weight: 0.0370 chunk 155 optimal weight: 8.9990 overall best weight: 0.9438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 258 GLN C 650 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN F 650 GLN G 66 HIS G 440 GLN I 66 HIS K 6 GLN ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 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 = 0.3312 r_free = 0.3312 target = 0.089648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.072078 restraints weight = 64053.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.074459 restraints weight = 33955.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.076090 restraints weight = 21997.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.077209 restraints weight = 16090.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.077944 restraints weight = 12825.673| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20698 Z= 0.141 Angle : 0.882 18.161 28237 Z= 0.414 Chirality : 0.052 0.322 3337 Planarity : 0.005 0.084 3463 Dihedral : 11.213 94.440 4330 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.21 % Allowed : 14.41 % Favored : 85.39 % Rotamer: Outliers : 0.14 % Allowed : 5.68 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 4.90 % Twisted General : 0.30 % 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: -4.01 (0.15), residues: 2388 helix: -1.67 (0.25), residues: 339 sheet: -1.15 (0.27), residues: 387 loop : -3.55 (0.12), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 71 TYR 0.031 0.002 TYR I 217 PHE 0.025 0.001 PHE D 27 TRP 0.030 0.001 TRP B 479 HIS 0.010 0.002 HIS E 76 Details of bonding type rmsd covalent geometry : bond 0.00295 (20587) covalent geometry : angle 0.83425 (27934) SS BOND : bond 0.01691 ( 27) SS BOND : angle 1.80907 ( 54) hydrogen bonds : bond 0.04720 ( 414) hydrogen bonds : angle 5.81492 ( 1026) Misc. bond : bond 0.00044 ( 1) link_ALPHA1-3 : bond 0.00539 ( 2) link_ALPHA1-3 : angle 3.16694 ( 6) link_ALPHA1-6 : bond 0.00849 ( 2) link_ALPHA1-6 : angle 1.33690 ( 6) link_BETA1-4 : bond 0.00688 ( 28) link_BETA1-4 : angle 2.55304 ( 84) link_NAG-ASN : bond 0.00614 ( 51) link_NAG-ASN : angle 3.36679 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 591 time to evaluate : 0.850 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: A 535 MET cc_start: 0.8851 (mmt) cc_final: 0.8593 (mmm) REVERT: A 536 THR cc_start: 0.9141 (m) cc_final: 0.8858 (p) REVERT: A 584 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8389 (tm-30) REVERT: A 621 GLU cc_start: 0.8396 (tm-30) cc_final: 0.7759 (tm-30) REVERT: A 626 MET cc_start: 0.8228 (mtm) cc_final: 0.8016 (mtp) REVERT: A 635 ILE cc_start: 0.9412 (mp) cc_final: 0.8803 (mp) REVERT: A 648 GLU cc_start: 0.9039 (pp20) cc_final: 0.8699 (pp20) REVERT: B 98 ASN cc_start: 0.8485 (t0) cc_final: 0.7260 (t0) REVERT: B 161 MET cc_start: 0.9232 (tpp) cc_final: 0.8980 (tpp) REVERT: B 203 GLN cc_start: 0.9137 (pp30) cc_final: 0.8925 (pp30) REVERT: B 321 ASP cc_start: 0.8922 (t70) cc_final: 0.8470 (t0) REVERT: B 452 LEU cc_start: 0.9418 (pt) cc_final: 0.8842 (pp) REVERT: C 576 LEU cc_start: 0.9149 (tt) cc_final: 0.8874 (tt) REVERT: C 584 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8390 (tm-30) REVERT: C 617 ARG cc_start: 0.8461 (mtt180) cc_final: 0.8002 (mtm180) REVERT: C 621 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7845 (tm-30) REVERT: C 622 ILE cc_start: 0.9192 (pt) cc_final: 0.8981 (pt) REVERT: C 626 MET cc_start: 0.7914 (mtm) cc_final: 0.7321 (mtm) REVERT: C 648 GLU cc_start: 0.9099 (pp20) cc_final: 0.8685 (pm20) REVERT: D 39 GLN cc_start: 0.8723 (mm-40) cc_final: 0.7835 (mm-40) REVERT: D 44 ARG cc_start: 0.6774 (mmt180) cc_final: 0.6570 (mmt-90) REVERT: D 91 TYR cc_start: 0.7681 (m-80) cc_final: 0.6944 (m-10) REVERT: E 37 GLN cc_start: 0.7963 (pp30) cc_final: 0.7383 (pp30) REVERT: E 45 LYS cc_start: 0.8842 (tptp) cc_final: 0.8383 (ttpp) REVERT: E 72 THR cc_start: 0.6950 (t) cc_final: 0.6355 (t) REVERT: E 78 VAL cc_start: 0.8369 (m) cc_final: 0.8106 (p) REVERT: E 82 ASP cc_start: 0.8948 (m-30) cc_final: 0.8565 (m-30) REVERT: F 536 THR cc_start: 0.9171 (m) cc_final: 0.8770 (p) REVERT: F 584 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8608 (tm-30) REVERT: F 621 GLU cc_start: 0.8584 (tm-30) cc_final: 0.7272 (tm-30) REVERT: F 626 MET cc_start: 0.7588 (mtt) cc_final: 0.7154 (mpp) REVERT: F 648 GLU cc_start: 0.8969 (pp20) cc_final: 0.8542 (pm20) REVERT: G 92 GLU cc_start: 0.5303 (pt0) cc_final: 0.5075 (pt0) REVERT: G 98 ASN cc_start: 0.8372 (t0) cc_final: 0.7425 (t0) REVERT: G 102 GLU cc_start: 0.9289 (mp0) cc_final: 0.8826 (mp0) REVERT: G 114 GLN cc_start: 0.9445 (tm-30) cc_final: 0.9149 (tm-30) REVERT: G 211 GLU cc_start: 0.9142 (tm-30) cc_final: 0.8901 (tm-30) REVERT: G 252 LYS cc_start: 0.9360 (mmtp) cc_final: 0.9033 (mmmm) REVERT: G 302 ASN cc_start: 0.8178 (t0) cc_final: 0.7683 (t0) REVERT: G 321 ASP cc_start: 0.8637 (t70) cc_final: 0.8310 (t70) REVERT: G 325 ASP cc_start: 0.8909 (p0) cc_final: 0.8352 (p0) REVERT: G 434 MET cc_start: 0.8184 (tmm) cc_final: 0.7699 (tmm) REVERT: H 1 GLU cc_start: 0.8795 (tm-30) cc_final: 0.7914 (pm20) REVERT: H 18 LEU cc_start: 0.7664 (mm) cc_final: 0.7429 (mm) REVERT: H 27 PHE cc_start: 0.8215 (m-10) cc_final: 0.7733 (m-80) REVERT: H 67 PHE cc_start: 0.8696 (p90) cc_final: 0.8118 (p90) REVERT: I 98 ASN cc_start: 0.8047 (t0) cc_final: 0.7518 (t0) REVERT: I 102 GLU cc_start: 0.9288 (mp0) cc_final: 0.8738 (mp0) REVERT: I 104 MET cc_start: 0.9266 (mmt) cc_final: 0.8956 (mmt) REVERT: I 114 GLN cc_start: 0.9384 (tm-30) cc_final: 0.9076 (tm-30) REVERT: I 252 LYS cc_start: 0.9319 (mtmm) cc_final: 0.8942 (mtpp) REVERT: I 425 ASN cc_start: 0.9337 (p0) cc_final: 0.9067 (p0) REVERT: I 482 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8644 (mm-30) REVERT: J 1 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8268 (pm20) REVERT: J 57 THR cc_start: 0.7401 (m) cc_final: 0.6861 (m) REVERT: J 67 PHE cc_start: 0.8198 (p90) cc_final: 0.7636 (p90) REVERT: J 82 LEU cc_start: 0.8787 (mt) cc_final: 0.8254 (tp) REVERT: J 91 TYR cc_start: 0.8635 (m-80) cc_final: 0.8341 (m-80) REVERT: K 37 GLN cc_start: 0.8081 (pp30) cc_final: 0.7304 (pp30) REVERT: K 38 GLN cc_start: 0.8609 (pt0) cc_final: 0.7421 (tt0) REVERT: K 45 LYS cc_start: 0.9155 (tptm) cc_final: 0.8698 (ttpt) REVERT: K 81 GLU cc_start: 0.9044 (pp20) cc_final: 0.8570 (pp20) REVERT: L 37 GLN cc_start: 0.8157 (pp30) cc_final: 0.7357 (pp30) REVERT: L 38 GLN cc_start: 0.8617 (pt0) cc_final: 0.7842 (tt0) REVERT: L 78 VAL cc_start: 0.8313 (m) cc_final: 0.7902 (m) REVERT: L 82 ASP cc_start: 0.8845 (m-30) cc_final: 0.7657 (m-30) outliers start: 3 outliers final: 1 residues processed: 593 average time/residue: 0.1368 time to fit residues: 125.9117 Evaluate side-chains 429 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 428 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 43 optimal weight: 8.9990 chunk 234 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 123 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 205 optimal weight: 9.9990 chunk 12 optimal weight: 0.3980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 258 GLN ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN G 66 HIS G 440 GLN ** I 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 440 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.088197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.070433 restraints weight = 69250.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.072656 restraints weight = 37561.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.074194 restraints weight = 24926.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.075256 restraints weight = 18669.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.075849 restraints weight = 15200.716| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 20698 Z= 0.171 Angle : 0.887 16.802 28237 Z= 0.420 Chirality : 0.052 0.329 3337 Planarity : 0.005 0.084 3463 Dihedral : 10.508 93.441 4330 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 15.16 % Favored : 84.67 % Rotamer: Outliers : 0.05 % Allowed : 3.74 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 4.90 % Twisted General : 0.30 % 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: -3.84 (0.15), residues: 2388 helix: -1.48 (0.26), residues: 357 sheet: -1.13 (0.28), residues: 381 loop : -3.43 (0.13), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 44 TYR 0.048 0.002 TYR J 91 PHE 0.020 0.002 PHE D 27 TRP 0.029 0.002 TRP L 35 HIS 0.011 0.002 HIS E 76 Details of bonding type rmsd covalent geometry : bond 0.00381 (20587) covalent geometry : angle 0.84329 (27934) SS BOND : bond 0.00678 ( 27) SS BOND : angle 1.77159 ( 54) hydrogen bonds : bond 0.04274 ( 414) hydrogen bonds : angle 5.59217 ( 1026) Misc. bond : bond 0.00006 ( 1) link_ALPHA1-3 : bond 0.00487 ( 2) link_ALPHA1-3 : angle 3.31938 ( 6) link_ALPHA1-6 : bond 0.01051 ( 2) link_ALPHA1-6 : angle 1.19550 ( 6) link_BETA1-4 : bond 0.00604 ( 28) link_BETA1-4 : angle 2.41048 ( 84) link_NAG-ASN : bond 0.00591 ( 51) link_NAG-ASN : angle 3.25211 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 523 time to evaluate : 0.721 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: A 535 MET cc_start: 0.8909 (mmt) cc_final: 0.8665 (mmm) REVERT: A 536 THR cc_start: 0.9173 (m) cc_final: 0.8911 (p) REVERT: A 584 GLU cc_start: 0.8842 (tm-30) cc_final: 0.8535 (tm-30) REVERT: A 621 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7897 (tm-30) REVERT: A 626 MET cc_start: 0.7963 (mtm) cc_final: 0.7588 (mtp) REVERT: A 648 GLU cc_start: 0.9130 (pp20) cc_final: 0.8847 (pp20) REVERT: B 98 ASN cc_start: 0.8295 (t0) cc_final: 0.7631 (t0) REVERT: B 114 GLN cc_start: 0.9343 (tm-30) cc_final: 0.9105 (tm-30) REVERT: B 161 MET cc_start: 0.9160 (tpp) cc_final: 0.8910 (tpp) REVERT: B 427 TRP cc_start: 0.8658 (m100) cc_final: 0.8352 (m100) REVERT: B 452 LEU cc_start: 0.9452 (pt) cc_final: 0.9135 (pp) REVERT: C 530 MET cc_start: 0.8737 (mmp) cc_final: 0.8284 (mmp) REVERT: C 584 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8473 (tm-30) REVERT: C 617 ARG cc_start: 0.8553 (mtt180) cc_final: 0.8117 (mtm180) REVERT: C 621 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8158 (tm-30) REVERT: C 626 MET cc_start: 0.8012 (mtm) cc_final: 0.7777 (mtm) REVERT: C 648 GLU cc_start: 0.9108 (pp20) cc_final: 0.8708 (pm20) REVERT: D 39 GLN cc_start: 0.8797 (mm-40) cc_final: 0.8110 (mm110) REVERT: D 44 ARG cc_start: 0.6691 (mmt180) cc_final: 0.6274 (mmt-90) REVERT: D 67 PHE cc_start: 0.8680 (p90) cc_final: 0.7956 (p90) REVERT: D 91 TYR cc_start: 0.7684 (m-80) cc_final: 0.6839 (m-10) REVERT: D 102 TYR cc_start: 0.9366 (m-80) cc_final: 0.8934 (m-80) REVERT: E 33 MET cc_start: 0.7564 (ptt) cc_final: 0.5926 (mtm) REVERT: E 37 GLN cc_start: 0.7627 (pp30) cc_final: 0.7317 (pp30) REVERT: E 45 LYS cc_start: 0.8811 (tptp) cc_final: 0.8410 (ttpp) REVERT: E 78 VAL cc_start: 0.8317 (m) cc_final: 0.8027 (p) REVERT: E 82 ASP cc_start: 0.8918 (m-30) cc_final: 0.8425 (m-30) REVERT: F 536 THR cc_start: 0.9142 (m) cc_final: 0.8793 (p) REVERT: F 584 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8591 (tm-30) REVERT: F 621 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8559 (tm-30) REVERT: F 624 ASP cc_start: 0.9079 (m-30) cc_final: 0.8878 (m-30) REVERT: F 647 GLU cc_start: 0.9047 (pp20) cc_final: 0.8567 (pp20) REVERT: F 648 GLU cc_start: 0.9105 (pp20) cc_final: 0.8541 (pm20) REVERT: G 98 ASN cc_start: 0.8269 (t0) cc_final: 0.7409 (t0) REVERT: G 102 GLU cc_start: 0.9341 (mp0) cc_final: 0.8842 (mp0) REVERT: G 104 MET cc_start: 0.9271 (ttp) cc_final: 0.9010 (ttp) REVERT: G 114 GLN cc_start: 0.9435 (tm-30) cc_final: 0.9170 (tm-30) REVERT: G 252 LYS cc_start: 0.9440 (mmtp) cc_final: 0.9026 (mmmm) REVERT: G 302 ASN cc_start: 0.8201 (t0) cc_final: 0.7920 (t0) REVERT: G 434 MET cc_start: 0.8356 (tmm) cc_final: 0.7843 (tmm) REVERT: H 1 GLU cc_start: 0.8981 (tm-30) cc_final: 0.8297 (pm20) REVERT: H 18 LEU cc_start: 0.7939 (mm) cc_final: 0.7666 (mm) REVERT: H 39 GLN cc_start: 0.8538 (mm-40) cc_final: 0.8107 (mm-40) REVERT: H 57 THR cc_start: 0.7888 (m) cc_final: 0.7342 (t) REVERT: H 67 PHE cc_start: 0.8445 (p90) cc_final: 0.7758 (p90) REVERT: I 59 LYS cc_start: 0.7982 (tptp) cc_final: 0.7763 (tptp) REVERT: I 98 ASN cc_start: 0.8055 (t0) cc_final: 0.7594 (t0) REVERT: I 102 GLU cc_start: 0.9296 (mp0) cc_final: 0.8586 (mp0) REVERT: I 104 MET cc_start: 0.9573 (mmt) cc_final: 0.9169 (tpp) REVERT: I 114 GLN cc_start: 0.9437 (tm-30) cc_final: 0.9123 (tm-30) REVERT: I 205 CYS cc_start: 0.7220 (t) cc_final: 0.6992 (t) REVERT: I 230 ASP cc_start: 0.8704 (t0) cc_final: 0.8420 (t0) REVERT: I 252 LYS cc_start: 0.9349 (mtmm) cc_final: 0.8952 (mtpp) REVERT: I 425 ASN cc_start: 0.9366 (p0) cc_final: 0.9083 (p0) REVERT: I 434 MET cc_start: 0.9141 (tpt) cc_final: 0.8914 (tpp) REVERT: J 1 GLU cc_start: 0.8998 (tm-30) cc_final: 0.8329 (pm20) REVERT: J 57 THR cc_start: 0.7487 (m) cc_final: 0.6943 (m) REVERT: J 67 PHE cc_start: 0.8593 (p90) cc_final: 0.7951 (p90) REVERT: K 27 TYR cc_start: 0.7557 (p90) cc_final: 0.7233 (p90) REVERT: K 33 MET cc_start: 0.7269 (ptt) cc_final: 0.6920 (mtm) REVERT: K 37 GLN cc_start: 0.8145 (pp30) cc_final: 0.7589 (pp30) REVERT: K 45 LYS cc_start: 0.9146 (tptm) cc_final: 0.8752 (ttpt) REVERT: L 38 GLN cc_start: 0.8888 (pt0) cc_final: 0.7963 (tt0) REVERT: L 81 GLU cc_start: 0.9065 (pp20) cc_final: 0.8864 (pp20) outliers start: 1 outliers final: 0 residues processed: 523 average time/residue: 0.1302 time to fit residues: 107.2497 Evaluate side-chains 412 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 48 optimal weight: 8.9990 chunk 163 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 231 optimal weight: 0.0870 chunk 157 optimal weight: 8.9990 chunk 113 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 overall best weight: 2.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN G 66 HIS G 258 GLN ** G 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 440 GLN I 66 HIS ** I 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.087550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.069639 restraints weight = 68942.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.071847 restraints weight = 37559.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.073347 restraints weight = 25044.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.074381 restraints weight = 18849.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.075111 restraints weight = 15395.807| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20698 Z= 0.171 Angle : 0.866 16.014 28237 Z= 0.411 Chirality : 0.052 0.356 3337 Planarity : 0.005 0.080 3463 Dihedral : 10.118 92.508 4330 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.91 % Favored : 85.01 % Rotamer: Outliers : 0.19 % Allowed : 3.50 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 3.92 % Twisted General : 0.30 % 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: -3.77 (0.15), residues: 2388 helix: -1.28 (0.26), residues: 354 sheet: -1.16 (0.27), residues: 387 loop : -3.40 (0.13), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 44 TYR 0.026 0.002 TYR J 58 PHE 0.023 0.002 PHE J 29 TRP 0.047 0.002 TRP L 35 HIS 0.016 0.002 HIS E 76 Details of bonding type rmsd covalent geometry : bond 0.00383 (20587) covalent geometry : angle 0.82672 (27934) SS BOND : bond 0.00518 ( 27) SS BOND : angle 1.68488 ( 54) hydrogen bonds : bond 0.04117 ( 414) hydrogen bonds : angle 5.58011 ( 1026) Misc. bond : bond 0.00000 ( 1) link_ALPHA1-3 : bond 0.00429 ( 2) link_ALPHA1-3 : angle 3.33884 ( 6) link_ALPHA1-6 : bond 0.01094 ( 2) link_ALPHA1-6 : angle 1.42588 ( 6) link_BETA1-4 : bond 0.00599 ( 28) link_BETA1-4 : angle 2.25099 ( 84) link_NAG-ASN : bond 0.00526 ( 51) link_NAG-ASN : angle 3.04495 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 515 time to evaluate : 0.631 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: A 536 THR cc_start: 0.9169 (m) cc_final: 0.8966 (p) REVERT: A 584 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8512 (tm-30) REVERT: A 621 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7960 (tm-30) REVERT: A 626 MET cc_start: 0.7869 (mtm) cc_final: 0.7619 (mtm) REVERT: A 648 GLU cc_start: 0.9173 (pp20) cc_final: 0.8598 (pm20) REVERT: A 654 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8670 (tp30) REVERT: B 98 ASN cc_start: 0.8147 (t0) cc_final: 0.7534 (t0) REVERT: B 104 MET cc_start: 0.9396 (ttp) cc_final: 0.9062 (ttp) REVERT: B 114 GLN cc_start: 0.9363 (tm-30) cc_final: 0.9122 (tm-30) REVERT: B 161 MET cc_start: 0.9138 (tpp) cc_final: 0.8891 (tpp) REVERT: B 211 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8718 (tm-30) REVERT: C 584 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8475 (tm-30) REVERT: C 588 ARG cc_start: 0.9250 (ttt180) cc_final: 0.8891 (ttm-80) REVERT: C 617 ARG cc_start: 0.8599 (mtt180) cc_final: 0.8262 (mtm180) REVERT: C 621 GLU cc_start: 0.8514 (tm-30) cc_final: 0.7978 (tm-30) REVERT: C 622 ILE cc_start: 0.9210 (pt) cc_final: 0.8861 (pt) REVERT: C 626 MET cc_start: 0.7982 (mtm) cc_final: 0.7315 (mtm) REVERT: C 645 LEU cc_start: 0.9418 (tp) cc_final: 0.8830 (tp) REVERT: C 648 GLU cc_start: 0.9138 (pp20) cc_final: 0.8741 (pm20) REVERT: D 39 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8414 (mm110) REVERT: D 91 TYR cc_start: 0.7690 (m-80) cc_final: 0.7018 (m-10) REVERT: E 33 MET cc_start: 0.7611 (ptt) cc_final: 0.6686 (mtm) REVERT: E 37 GLN cc_start: 0.7502 (pp30) cc_final: 0.7208 (pp30) REVERT: E 45 LYS cc_start: 0.8902 (tptp) cc_final: 0.8514 (ttpp) REVERT: E 78 VAL cc_start: 0.8272 (m) cc_final: 0.8006 (p) REVERT: E 82 ASP cc_start: 0.8975 (m-30) cc_final: 0.8524 (m-30) REVERT: F 536 THR cc_start: 0.9118 (m) cc_final: 0.8769 (p) REVERT: F 584 GLU cc_start: 0.8996 (tm-30) cc_final: 0.8698 (tm-30) REVERT: F 621 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8522 (tm-30) REVERT: F 648 GLU cc_start: 0.9082 (pp20) cc_final: 0.8686 (pm20) REVERT: G 98 ASN cc_start: 0.8427 (t0) cc_final: 0.7608 (t0) REVERT: G 102 GLU cc_start: 0.9343 (mp0) cc_final: 0.8819 (mp0) REVERT: G 104 MET cc_start: 0.9219 (ttp) cc_final: 0.8923 (mtp) REVERT: G 114 GLN cc_start: 0.9457 (tm-30) cc_final: 0.9181 (tm-30) REVERT: G 252 LYS cc_start: 0.9451 (mmtp) cc_final: 0.9051 (mmmm) REVERT: G 302 ASN cc_start: 0.8177 (t0) cc_final: 0.7943 (t0) REVERT: G 434 MET cc_start: 0.8361 (tmm) cc_final: 0.7894 (tmm) REVERT: G 475 MET cc_start: 0.7577 (tmm) cc_final: 0.6734 (tmm) REVERT: H 1 GLU cc_start: 0.9018 (tm-30) cc_final: 0.8595 (tm-30) REVERT: H 18 LEU cc_start: 0.7847 (mm) cc_final: 0.7639 (mm) REVERT: H 39 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8387 (mm-40) REVERT: H 67 PHE cc_start: 0.8757 (p90) cc_final: 0.8141 (p90) REVERT: H 72 ASP cc_start: 0.8801 (t70) cc_final: 0.8479 (t0) REVERT: I 59 LYS cc_start: 0.7969 (tptp) cc_final: 0.7759 (tptp) REVERT: I 98 ASN cc_start: 0.8064 (t0) cc_final: 0.7656 (t0) REVERT: I 102 GLU cc_start: 0.9280 (mp0) cc_final: 0.8530 (mp0) REVERT: I 104 MET cc_start: 0.9618 (mmt) cc_final: 0.9284 (mmm) REVERT: I 114 GLN cc_start: 0.9432 (tm-30) cc_final: 0.9136 (tm-30) REVERT: I 230 ASP cc_start: 0.8560 (t0) cc_final: 0.8315 (t0) REVERT: I 252 LYS cc_start: 0.9363 (mtmm) cc_final: 0.8985 (mtpp) REVERT: I 425 ASN cc_start: 0.9352 (p0) cc_final: 0.9104 (p0) REVERT: I 434 MET cc_start: 0.9190 (tpt) cc_final: 0.8795 (tpp) REVERT: J 1 GLU cc_start: 0.9072 (tm-30) cc_final: 0.8762 (tm-30) REVERT: J 57 THR cc_start: 0.7604 (m) cc_final: 0.6741 (m) REVERT: J 67 PHE cc_start: 0.8718 (p90) cc_final: 0.7890 (p90) REVERT: J 85 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8277 (mp0) REVERT: K 27 TYR cc_start: 0.7733 (p90) cc_final: 0.7393 (p90) REVERT: K 33 MET cc_start: 0.7437 (ptt) cc_final: 0.6670 (mtm) REVERT: K 37 GLN cc_start: 0.7761 (pp30) cc_final: 0.6933 (pp30) REVERT: K 45 LYS cc_start: 0.9181 (tptm) cc_final: 0.8576 (ttpp) REVERT: L 37 GLN cc_start: 0.7792 (pp30) cc_final: 0.7469 (pp30) outliers start: 4 outliers final: 0 residues processed: 517 average time/residue: 0.1332 time to fit residues: 108.1763 Evaluate side-chains 407 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 29 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 223 optimal weight: 8.9990 chunk 156 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 120 optimal weight: 0.0870 chunk 69 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 overall best weight: 1.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 HIS ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN C 585 HIS ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN E 76 HIS F 585 HIS F 616 ASN G 66 HIS G 258 GLN G 422 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.089483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.071346 restraints weight = 68219.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.073606 restraints weight = 37128.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.075149 restraints weight = 24700.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.076208 restraints weight = 18538.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.076947 restraints weight = 15106.825| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20698 Z= 0.138 Angle : 0.871 15.178 28237 Z= 0.407 Chirality : 0.052 0.343 3337 Planarity : 0.005 0.074 3463 Dihedral : 9.773 91.268 4330 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 14.53 % Favored : 85.43 % Rotamer: Outliers : 0.24 % Allowed : 2.60 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 3.92 % Twisted General : 0.30 % 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: -3.63 (0.15), residues: 2388 helix: -1.27 (0.26), residues: 357 sheet: -1.24 (0.26), residues: 420 loop : -3.26 (0.13), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 38 TYR 0.030 0.002 TYR J 90 PHE 0.027 0.001 PHE J 29 TRP 0.038 0.002 TRP L 35 HIS 0.009 0.001 HIS L 76 Details of bonding type rmsd covalent geometry : bond 0.00300 (20587) covalent geometry : angle 0.82508 (27934) SS BOND : bond 0.00755 ( 27) SS BOND : angle 1.57097 ( 54) hydrogen bonds : bond 0.03759 ( 414) hydrogen bonds : angle 5.38677 ( 1026) Misc. bond : bond 0.00166 ( 1) link_ALPHA1-3 : bond 0.00427 ( 2) link_ALPHA1-3 : angle 3.29207 ( 6) link_ALPHA1-6 : bond 0.01050 ( 2) link_ALPHA1-6 : angle 1.69335 ( 6) link_BETA1-4 : bond 0.00644 ( 28) link_BETA1-4 : angle 2.18258 ( 84) link_NAG-ASN : bond 0.00928 ( 51) link_NAG-ASN : angle 3.39951 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 521 time to evaluate : 0.729 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: A 536 THR cc_start: 0.9121 (m) cc_final: 0.8897 (p) REVERT: A 584 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8533 (tm-30) REVERT: A 621 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7974 (tm-30) REVERT: A 648 GLU cc_start: 0.9117 (pp20) cc_final: 0.8540 (pm20) REVERT: B 98 ASN cc_start: 0.7956 (t0) cc_final: 0.7628 (t0) REVERT: B 114 GLN cc_start: 0.9313 (tm-30) cc_final: 0.9049 (tm-30) REVERT: B 161 MET cc_start: 0.9082 (tpp) cc_final: 0.8831 (tpp) REVERT: B 211 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8717 (tm-30) REVERT: B 427 TRP cc_start: 0.8638 (m100) cc_final: 0.8208 (m100) REVERT: C 584 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8430 (tm-30) REVERT: C 588 ARG cc_start: 0.9205 (ttt180) cc_final: 0.8866 (ttm-80) REVERT: C 617 ARG cc_start: 0.8572 (mtt180) cc_final: 0.8302 (mtm180) REVERT: C 621 GLU cc_start: 0.8485 (tm-30) cc_final: 0.7924 (tm-30) REVERT: C 622 ILE cc_start: 0.9217 (pt) cc_final: 0.8785 (pt) REVERT: C 626 MET cc_start: 0.7967 (mtm) cc_final: 0.7296 (mtm) REVERT: C 645 LEU cc_start: 0.9382 (tp) cc_final: 0.8828 (tp) REVERT: C 648 GLU cc_start: 0.9120 (pp20) cc_final: 0.8711 (pm20) REVERT: D 36 TRP cc_start: 0.8574 (m100) cc_final: 0.8084 (m-10) REVERT: D 89 MET cc_start: 0.8237 (mmp) cc_final: 0.6498 (tpt) REVERT: D 102 TYR cc_start: 0.9341 (m-80) cc_final: 0.9034 (m-80) REVERT: E 33 MET cc_start: 0.7572 (ptt) cc_final: 0.7371 (ptp) REVERT: E 45 LYS cc_start: 0.8890 (tptp) cc_final: 0.8520 (ttpp) REVERT: E 82 ASP cc_start: 0.9047 (m-30) cc_final: 0.8781 (m-30) REVERT: F 536 THR cc_start: 0.9104 (m) cc_final: 0.8783 (p) REVERT: F 584 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8694 (tm-30) REVERT: F 621 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8458 (tm-30) REVERT: F 648 GLU cc_start: 0.9075 (pp20) cc_final: 0.8655 (pm20) REVERT: G 98 ASN cc_start: 0.8311 (t0) cc_final: 0.7633 (t0) REVERT: G 114 GLN cc_start: 0.9423 (tm-30) cc_final: 0.9168 (tm-30) REVERT: G 252 LYS cc_start: 0.9465 (mmtp) cc_final: 0.9040 (mmmm) REVERT: G 302 ASN cc_start: 0.7896 (t0) cc_final: 0.7622 (t0) REVERT: G 434 MET cc_start: 0.8336 (tmm) cc_final: 0.7833 (tmm) REVERT: G 475 MET cc_start: 0.7571 (tmm) cc_final: 0.7056 (tmm) REVERT: H 29 PHE cc_start: 0.8679 (t80) cc_final: 0.8381 (t80) REVERT: H 67 PHE cc_start: 0.8570 (p90) cc_final: 0.7879 (p90) REVERT: I 98 ASN cc_start: 0.8049 (t0) cc_final: 0.7807 (t0) REVERT: I 102 GLU cc_start: 0.9290 (mp0) cc_final: 0.8947 (mp0) REVERT: I 104 MET cc_start: 0.9605 (mmt) cc_final: 0.9150 (mmm) REVERT: I 114 GLN cc_start: 0.9435 (tm-30) cc_final: 0.9121 (tm-30) REVERT: I 205 CYS cc_start: 0.7203 (t) cc_final: 0.6964 (t) REVERT: I 230 ASP cc_start: 0.8542 (t0) cc_final: 0.8229 (t0) REVERT: I 425 ASN cc_start: 0.9316 (p0) cc_final: 0.9068 (p0) REVERT: I 434 MET cc_start: 0.9202 (tpt) cc_final: 0.8848 (tpp) REVERT: J 36 TRP cc_start: 0.8402 (m100) cc_final: 0.7772 (m100) REVERT: J 57 THR cc_start: 0.7581 (m) cc_final: 0.6758 (m) REVERT: J 67 PHE cc_start: 0.8499 (p90) cc_final: 0.7758 (p90) REVERT: J 85 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8134 (mp0) REVERT: K 27 TYR cc_start: 0.7931 (p90) cc_final: 0.7572 (p90) REVERT: K 33 MET cc_start: 0.7353 (ptt) cc_final: 0.6709 (mtm) REVERT: K 37 GLN cc_start: 0.7701 (pp30) cc_final: 0.7226 (pp30) REVERT: K 45 LYS cc_start: 0.9196 (tptm) cc_final: 0.8790 (ttpp) REVERT: K 72 THR cc_start: 0.8694 (p) cc_final: 0.8435 (p) REVERT: K 82 ASP cc_start: 0.9202 (m-30) cc_final: 0.8986 (m-30) REVERT: L 78 VAL cc_start: 0.8231 (m) cc_final: 0.7988 (p) REVERT: L 82 ASP cc_start: 0.8591 (m-30) cc_final: 0.8344 (m-30) outliers start: 5 outliers final: 0 residues processed: 523 average time/residue: 0.1358 time to fit residues: 112.8691 Evaluate side-chains 416 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 133 optimal weight: 0.9980 chunk 83 optimal weight: 40.0000 chunk 121 optimal weight: 20.0000 chunk 203 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 211 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 140 optimal weight: 4.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 GLN B 66 HIS B 203 GLN B 330 HIS B 352 HIS C 585 HIS C 650 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN ** E 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 650 GLN G 258 GLN ** G 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 330 HIS G 422 GLN G 440 GLN I 66 HIS ** I 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.085392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.067434 restraints weight = 69607.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.069550 restraints weight = 38308.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.071008 restraints weight = 25737.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.072007 restraints weight = 19515.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.072703 restraints weight = 16041.559| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20698 Z= 0.233 Angle : 0.925 14.744 28237 Z= 0.441 Chirality : 0.053 0.336 3337 Planarity : 0.005 0.067 3463 Dihedral : 10.044 91.856 4330 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 16.12 % Favored : 83.75 % Rotamer: Outliers : 0.24 % Allowed : 2.56 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 3.92 % Twisted General : 0.30 % 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: -3.75 (0.15), residues: 2388 helix: -1.15 (0.25), residues: 366 sheet: -1.18 (0.27), residues: 375 loop : -3.41 (0.13), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 44 TYR 0.024 0.002 TYR K 32 PHE 0.027 0.002 PHE J 29 TRP 0.047 0.003 TRP K 35 HIS 0.009 0.002 HIS I 66 Details of bonding type rmsd covalent geometry : bond 0.00519 (20587) covalent geometry : angle 0.88457 (27934) SS BOND : bond 0.00641 ( 27) SS BOND : angle 1.80088 ( 54) hydrogen bonds : bond 0.04270 ( 414) hydrogen bonds : angle 5.63282 ( 1026) Misc. bond : bond 0.00086 ( 1) link_ALPHA1-3 : bond 0.00390 ( 2) link_ALPHA1-3 : angle 3.23085 ( 6) link_ALPHA1-6 : bond 0.00938 ( 2) link_ALPHA1-6 : angle 1.89423 ( 6) link_BETA1-4 : bond 0.00602 ( 28) link_BETA1-4 : angle 2.25268 ( 84) link_NAG-ASN : bond 0.00679 ( 51) link_NAG-ASN : angle 3.25616 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 482 time to evaluate : 0.710 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: A 574 LYS cc_start: 0.8996 (mtpp) cc_final: 0.8781 (mtpp) REVERT: A 584 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8608 (tm-30) REVERT: A 626 MET cc_start: 0.8043 (mtm) cc_final: 0.7765 (mtt) REVERT: A 648 GLU cc_start: 0.9159 (pp20) cc_final: 0.8871 (pp20) REVERT: B 98 ASN cc_start: 0.8342 (t0) cc_final: 0.7697 (t0) REVERT: B 114 GLN cc_start: 0.9423 (tm-30) cc_final: 0.9142 (tm-30) REVERT: B 121 LYS cc_start: 0.9251 (ttmt) cc_final: 0.9023 (ttpp) REVERT: B 161 MET cc_start: 0.9157 (tpp) cc_final: 0.8915 (tpp) REVERT: B 203 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8725 (pp30) REVERT: B 427 TRP cc_start: 0.8813 (m100) cc_final: 0.8522 (m100) REVERT: B 434 MET cc_start: 0.8284 (tmm) cc_final: 0.8055 (tmm) REVERT: C 530 MET cc_start: 0.8983 (mmp) cc_final: 0.8357 (mmp) REVERT: C 584 GLU cc_start: 0.8998 (tm-30) cc_final: 0.8608 (tm-30) REVERT: C 621 GLU cc_start: 0.8513 (tm-30) cc_final: 0.7995 (tm-30) REVERT: C 622 ILE cc_start: 0.9279 (pt) cc_final: 0.8890 (pt) REVERT: C 626 MET cc_start: 0.8045 (mtm) cc_final: 0.7413 (mtm) REVERT: C 645 LEU cc_start: 0.9464 (tp) cc_final: 0.8937 (tp) REVERT: C 648 GLU cc_start: 0.9191 (pp20) cc_final: 0.8725 (pm20) REVERT: C 657 GLU cc_start: 0.9241 (mp0) cc_final: 0.8599 (mp0) REVERT: D 39 GLN cc_start: 0.8489 (mm110) cc_final: 0.8289 (mm110) REVERT: D 44 ARG cc_start: 0.6313 (mmt-90) cc_final: 0.5985 (mmt-90) REVERT: D 50 THR cc_start: 0.8809 (t) cc_final: 0.8603 (t) REVERT: D 98 THR cc_start: 0.9418 (p) cc_final: 0.9155 (t) REVERT: E 37 GLN cc_start: 0.7797 (pp30) cc_final: 0.7301 (pp30) REVERT: E 45 LYS cc_start: 0.9037 (tptp) cc_final: 0.8693 (ttpp) REVERT: E 82 ASP cc_start: 0.9067 (m-30) cc_final: 0.8724 (m-30) REVERT: E 97 THR cc_start: 0.8897 (p) cc_final: 0.8590 (t) REVERT: F 536 THR cc_start: 0.9231 (m) cc_final: 0.8945 (p) REVERT: F 584 GLU cc_start: 0.9020 (tm-30) cc_final: 0.8736 (tm-30) REVERT: F 621 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8475 (tm-30) REVERT: F 648 GLU cc_start: 0.9158 (pp20) cc_final: 0.8723 (pp20) REVERT: G 98 ASN cc_start: 0.8704 (t0) cc_final: 0.8125 (t0) REVERT: G 102 GLU cc_start: 0.9266 (mp0) cc_final: 0.8971 (mp0) REVERT: G 104 MET cc_start: 0.9235 (ttp) cc_final: 0.8805 (ttp) REVERT: G 114 GLN cc_start: 0.9471 (tm-30) cc_final: 0.9192 (tm-30) REVERT: G 434 MET cc_start: 0.8280 (tmm) cc_final: 0.7889 (tmm) REVERT: G 475 MET cc_start: 0.7774 (tmm) cc_final: 0.7314 (tmm) REVERT: H 39 GLN cc_start: 0.8881 (mm-40) cc_final: 0.8437 (mm110) REVERT: H 67 PHE cc_start: 0.8584 (p90) cc_final: 0.7927 (p90) REVERT: H 72 ASP cc_start: 0.9150 (t0) cc_final: 0.8863 (t0) REVERT: H 85 GLU cc_start: 0.8709 (pp20) cc_final: 0.8331 (pp20) REVERT: I 59 LYS cc_start: 0.7969 (tptp) cc_final: 0.7734 (tptp) REVERT: I 104 MET cc_start: 0.9537 (mmt) cc_final: 0.9090 (mmm) REVERT: I 114 GLN cc_start: 0.9485 (tm-30) cc_final: 0.9092 (tm-30) REVERT: I 205 CYS cc_start: 0.7103 (t) cc_final: 0.6866 (t) REVERT: I 252 LYS cc_start: 0.9350 (mtmm) cc_final: 0.9045 (mmmm) REVERT: I 425 ASN cc_start: 0.9366 (p0) cc_final: 0.9111 (p0) REVERT: J 44 ARG cc_start: 0.6134 (mmt180) cc_final: 0.5318 (mmt-90) REVERT: J 57 THR cc_start: 0.7604 (m) cc_final: 0.6853 (m) REVERT: J 67 PHE cc_start: 0.8497 (p90) cc_final: 0.7955 (p90) REVERT: J 102 TYR cc_start: 0.9185 (m-80) cc_final: 0.8695 (m-80) REVERT: K 27 TYR cc_start: 0.7581 (p90) cc_final: 0.7248 (p90) REVERT: K 37 GLN cc_start: 0.7731 (pp30) cc_final: 0.7338 (pp30) REVERT: K 45 LYS cc_start: 0.9129 (tptm) cc_final: 0.8746 (ttpp) REVERT: K 72 THR cc_start: 0.8494 (p) cc_final: 0.8191 (p) REVERT: K 82 ASP cc_start: 0.9255 (m-30) cc_final: 0.8985 (m-30) REVERT: L 82 ASP cc_start: 0.8902 (m-30) cc_final: 0.8640 (m-30) outliers start: 5 outliers final: 0 residues processed: 484 average time/residue: 0.1320 time to fit residues: 101.7404 Evaluate side-chains 393 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 392 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 177 optimal weight: 2.9990 chunk 150 optimal weight: 10.0000 chunk 200 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 171 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 186 optimal weight: 8.9990 chunk 178 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 HIS ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN E 76 HIS F 616 ASN G 66 HIS I 216 HIS J 76 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.088837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.070577 restraints weight = 68922.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.072806 restraints weight = 37882.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.074331 restraints weight = 25388.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.075387 restraints weight = 19188.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.076110 restraints weight = 15718.667| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20698 Z= 0.142 Angle : 0.882 19.369 28237 Z= 0.416 Chirality : 0.053 0.391 3337 Planarity : 0.005 0.063 3463 Dihedral : 9.687 88.839 4330 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.74 % Favored : 86.14 % Rotamer: Outliers : 0.19 % Allowed : 1.47 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 3.92 % Twisted General : 0.35 % 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: -3.60 (0.15), residues: 2388 helix: -1.03 (0.26), residues: 357 sheet: -1.19 (0.27), residues: 375 loop : -3.26 (0.13), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 61 TYR 0.035 0.002 TYR J 58 PHE 0.030 0.001 PHE J 29 TRP 0.033 0.002 TRP K 35 HIS 0.009 0.001 HIS L 76 Details of bonding type rmsd covalent geometry : bond 0.00310 (20587) covalent geometry : angle 0.83359 (27934) SS BOND : bond 0.00475 ( 27) SS BOND : angle 2.02427 ( 54) hydrogen bonds : bond 0.03767 ( 414) hydrogen bonds : angle 5.31527 ( 1026) Misc. bond : bond 0.00115 ( 1) link_ALPHA1-3 : bond 0.00579 ( 2) link_ALPHA1-3 : angle 2.93070 ( 6) link_ALPHA1-6 : bond 0.00949 ( 2) link_ALPHA1-6 : angle 1.57789 ( 6) link_BETA1-4 : bond 0.00710 ( 28) link_BETA1-4 : angle 2.08623 ( 84) link_NAG-ASN : bond 0.00771 ( 51) link_NAG-ASN : angle 3.50377 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 541 time to evaluate : 0.556 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: A 574 LYS cc_start: 0.8906 (mtpp) cc_final: 0.8322 (mtpp) REVERT: A 584 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8531 (tm-30) REVERT: A 648 GLU cc_start: 0.9096 (pp20) cc_final: 0.8841 (pp20) REVERT: A 657 GLU cc_start: 0.9023 (mp0) cc_final: 0.8289 (mp0) REVERT: A 658 GLN cc_start: 0.9241 (tt0) cc_final: 0.8708 (tm-30) REVERT: B 98 ASN cc_start: 0.7937 (t0) cc_final: 0.7523 (t0) REVERT: B 114 GLN cc_start: 0.9371 (tm-30) cc_final: 0.9086 (tm-30) REVERT: B 161 MET cc_start: 0.9102 (tpp) cc_final: 0.8851 (tpp) REVERT: B 195 ASN cc_start: 0.8377 (p0) cc_final: 0.8151 (m-40) REVERT: B 211 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8761 (tm-30) REVERT: B 252 LYS cc_start: 0.9381 (mtmm) cc_final: 0.9125 (mmmm) REVERT: C 540 GLN cc_start: 0.9017 (mp10) cc_final: 0.8796 (mp10) REVERT: C 573 ILE cc_start: 0.9136 (pt) cc_final: 0.8858 (pt) REVERT: C 577 GLN cc_start: 0.9115 (mt0) cc_final: 0.8828 (mt0) REVERT: C 584 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8467 (tm-30) REVERT: C 617 ARG cc_start: 0.8462 (mtt180) cc_final: 0.8158 (mtm-85) REVERT: C 621 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8070 (tm-30) REVERT: C 626 MET cc_start: 0.8015 (mtm) cc_final: 0.7672 (mtm) REVERT: C 645 LEU cc_start: 0.9395 (tp) cc_final: 0.8887 (tp) REVERT: C 648 GLU cc_start: 0.9130 (pp20) cc_final: 0.8672 (pm20) REVERT: C 657 GLU cc_start: 0.9204 (mp0) cc_final: 0.8514 (mp0) REVERT: C 658 GLN cc_start: 0.9175 (tp40) cc_final: 0.8792 (tm-30) REVERT: D 44 ARG cc_start: 0.6051 (mmt-90) cc_final: 0.5200 (mmt-90) REVERT: D 102 TYR cc_start: 0.9316 (m-80) cc_final: 0.9069 (m-80) REVERT: E 33 MET cc_start: 0.7060 (ptt) cc_final: 0.6826 (ptp) REVERT: E 45 LYS cc_start: 0.8995 (tptp) cc_final: 0.8567 (ttpp) REVERT: E 82 ASP cc_start: 0.9021 (m-30) cc_final: 0.8690 (m-30) REVERT: F 573 ILE cc_start: 0.9168 (pt) cc_final: 0.8836 (pt) REVERT: F 577 GLN cc_start: 0.9187 (mt0) cc_final: 0.8799 (mt0) REVERT: F 584 GLU cc_start: 0.9020 (tm-30) cc_final: 0.8719 (tm-30) REVERT: F 590 GLN cc_start: 0.9647 (tp40) cc_final: 0.9371 (tp40) REVERT: F 621 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8272 (tm-30) REVERT: F 647 GLU cc_start: 0.8989 (pp20) cc_final: 0.8390 (pp20) REVERT: F 648 GLU cc_start: 0.9083 (pp20) cc_final: 0.8535 (pm20) REVERT: F 658 GLN cc_start: 0.9245 (tp40) cc_final: 0.8753 (tm-30) REVERT: G 98 ASN cc_start: 0.8792 (t0) cc_final: 0.7691 (t0) REVERT: G 102 GLU cc_start: 0.9249 (mp0) cc_final: 0.8970 (mp0) REVERT: G 114 GLN cc_start: 0.9424 (tm-30) cc_final: 0.9164 (tm-30) REVERT: G 302 ASN cc_start: 0.8292 (t0) cc_final: 0.7936 (t0) REVERT: G 434 MET cc_start: 0.8209 (tmm) cc_final: 0.7715 (tmm) REVERT: G 475 MET cc_start: 0.7621 (tmm) cc_final: 0.7261 (tmm) REVERT: H 29 PHE cc_start: 0.8769 (t80) cc_final: 0.8468 (t80) REVERT: H 67 PHE cc_start: 0.8501 (p90) cc_final: 0.7752 (p90) REVERT: H 72 ASP cc_start: 0.9121 (t0) cc_final: 0.8822 (t0) REVERT: I 98 ASN cc_start: 0.8324 (t0) cc_final: 0.8032 (t0) REVERT: I 102 GLU cc_start: 0.9415 (mp0) cc_final: 0.9066 (mp0) REVERT: I 114 GLN cc_start: 0.9448 (tm-30) cc_final: 0.9100 (tm-30) REVERT: I 217 TYR cc_start: 0.7506 (m-80) cc_final: 0.7156 (m-80) REVERT: I 252 LYS cc_start: 0.9302 (mtmm) cc_final: 0.8999 (mmmm) REVERT: I 425 ASN cc_start: 0.9337 (p0) cc_final: 0.9116 (p0) REVERT: J 36 TRP cc_start: 0.8476 (m100) cc_final: 0.7951 (m100) REVERT: J 44 ARG cc_start: 0.6074 (mmt180) cc_final: 0.5484 (mmt-90) REVERT: J 57 THR cc_start: 0.7591 (m) cc_final: 0.6743 (m) REVERT: J 66 ARG cc_start: 0.9447 (mtm-85) cc_final: 0.8748 (mtt180) REVERT: J 67 PHE cc_start: 0.8581 (p90) cc_final: 0.7813 (p90) REVERT: K 27 TYR cc_start: 0.7621 (p90) cc_final: 0.7258 (p90) REVERT: K 33 MET cc_start: 0.7050 (ptt) cc_final: 0.6214 (ptt) REVERT: K 37 GLN cc_start: 0.7714 (pp30) cc_final: 0.7006 (pp30) REVERT: K 45 LYS cc_start: 0.9163 (tptm) cc_final: 0.8756 (ttpp) REVERT: K 72 THR cc_start: 0.8187 (p) cc_final: 0.7817 (p) REVERT: K 97 THR cc_start: 0.8775 (p) cc_final: 0.8515 (p) REVERT: K 103 LYS cc_start: 0.8581 (mmmm) cc_final: 0.8275 (mtmm) REVERT: L 72 THR cc_start: 0.8208 (p) cc_final: 0.7920 (p) outliers start: 4 outliers final: 0 residues processed: 541 average time/residue: 0.1297 time to fit residues: 110.4123 Evaluate side-chains 431 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 431 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 90 optimal weight: 9.9990 chunk 118 optimal weight: 0.0870 chunk 190 optimal weight: 3.9990 chunk 175 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 163 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 chunk 55 optimal weight: 0.4980 chunk 177 optimal weight: 2.9990 overall best weight: 1.2362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN E 76 HIS F 616 ASN I 66 HIS ** I 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.088937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.070769 restraints weight = 68169.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.073008 restraints weight = 37167.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.074540 restraints weight = 24785.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.075601 restraints weight = 18677.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.076336 restraints weight = 15258.025| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20698 Z= 0.148 Angle : 0.880 19.240 28237 Z= 0.418 Chirality : 0.054 0.758 3337 Planarity : 0.005 0.060 3463 Dihedral : 9.617 86.921 4330 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.78 % Favored : 85.09 % Rotamer: Outliers : 0.14 % Allowed : 0.52 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.35 % 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: -3.59 (0.15), residues: 2388 helix: -0.96 (0.26), residues: 366 sheet: -1.17 (0.27), residues: 390 loop : -3.30 (0.13), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 44 TYR 0.033 0.002 TYR J 58 PHE 0.028 0.001 PHE J 29 TRP 0.058 0.002 TRP K 35 HIS 0.009 0.001 HIS L 76 Details of bonding type rmsd covalent geometry : bond 0.00328 (20587) covalent geometry : angle 0.83314 (27934) SS BOND : bond 0.00536 ( 27) SS BOND : angle 2.00466 ( 54) hydrogen bonds : bond 0.03994 ( 414) hydrogen bonds : angle 5.27919 ( 1026) Misc. bond : bond 0.00079 ( 1) link_ALPHA1-3 : bond 0.00605 ( 2) link_ALPHA1-3 : angle 2.85364 ( 6) link_ALPHA1-6 : bond 0.00912 ( 2) link_ALPHA1-6 : angle 1.54136 ( 6) link_BETA1-4 : bond 0.00672 ( 28) link_BETA1-4 : angle 2.07606 ( 84) link_NAG-ASN : bond 0.00754 ( 51) link_NAG-ASN : angle 3.47471 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 538 time to evaluate : 0.721 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: A 574 LYS cc_start: 0.8941 (mtpp) cc_final: 0.8357 (mtpp) REVERT: A 577 GLN cc_start: 0.9104 (mt0) cc_final: 0.8732 (mt0) REVERT: A 584 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8569 (tm-30) REVERT: A 648 GLU cc_start: 0.9073 (pp20) cc_final: 0.8778 (pp20) REVERT: A 657 GLU cc_start: 0.9030 (mp0) cc_final: 0.8310 (mp0) REVERT: A 658 GLN cc_start: 0.9244 (tt0) cc_final: 0.8723 (tm-30) REVERT: B 98 ASN cc_start: 0.8373 (t0) cc_final: 0.7306 (t0) REVERT: B 114 GLN cc_start: 0.9359 (tm-30) cc_final: 0.9148 (tm-30) REVERT: B 211 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8727 (tm-30) REVERT: B 252 LYS cc_start: 0.9364 (mtmm) cc_final: 0.9106 (mmmm) REVERT: B 427 TRP cc_start: 0.8686 (m100) cc_final: 0.8318 (m100) REVERT: C 540 GLN cc_start: 0.9029 (mp10) cc_final: 0.8743 (mp10) REVERT: C 573 ILE cc_start: 0.9127 (pt) cc_final: 0.8818 (pt) REVERT: C 577 GLN cc_start: 0.9098 (mt0) cc_final: 0.8821 (mt0) REVERT: C 584 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8499 (tm-30) REVERT: C 617 ARG cc_start: 0.8383 (mtt180) cc_final: 0.8091 (mtt90) REVERT: C 621 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8113 (tm-30) REVERT: C 626 MET cc_start: 0.8076 (mtm) cc_final: 0.7604 (mtm) REVERT: C 658 GLN cc_start: 0.9124 (tp40) cc_final: 0.8841 (tm-30) REVERT: D 39 GLN cc_start: 0.8418 (mm-40) cc_final: 0.8164 (mm-40) REVERT: D 44 ARG cc_start: 0.6148 (mmt-90) cc_final: 0.5739 (mmt-90) REVERT: D 102 TYR cc_start: 0.9309 (m-80) cc_final: 0.9063 (m-80) REVERT: E 33 MET cc_start: 0.7089 (ptt) cc_final: 0.6783 (ptp) REVERT: E 45 LYS cc_start: 0.8983 (tptp) cc_final: 0.8575 (ttpp) REVERT: E 82 ASP cc_start: 0.8896 (m-30) cc_final: 0.8616 (m-30) REVERT: F 536 THR cc_start: 0.9268 (m) cc_final: 0.9004 (p) REVERT: F 573 ILE cc_start: 0.9189 (pt) cc_final: 0.8783 (pt) REVERT: F 577 GLN cc_start: 0.9160 (mt0) cc_final: 0.8900 (mt0) REVERT: F 584 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8729 (tm-30) REVERT: F 621 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8212 (tm-30) REVERT: F 624 ASP cc_start: 0.9024 (m-30) cc_final: 0.8816 (m-30) REVERT: F 652 GLN cc_start: 0.8894 (mp10) cc_final: 0.8602 (mp10) REVERT: F 658 GLN cc_start: 0.9245 (tp40) cc_final: 0.8756 (tm-30) REVERT: G 98 ASN cc_start: 0.8728 (t0) cc_final: 0.7777 (t0) REVERT: G 102 GLU cc_start: 0.9255 (mp0) cc_final: 0.9031 (mp0) REVERT: G 114 GLN cc_start: 0.9389 (tm-30) cc_final: 0.9113 (tm-30) REVERT: G 302 ASN cc_start: 0.8046 (t0) cc_final: 0.7668 (t0) REVERT: G 434 MET cc_start: 0.8200 (tmm) cc_final: 0.7688 (tmm) REVERT: H 13 LYS cc_start: 0.8962 (tppt) cc_final: 0.8649 (tppt) REVERT: H 29 PHE cc_start: 0.8794 (t80) cc_final: 0.8473 (t80) REVERT: H 67 PHE cc_start: 0.8482 (p90) cc_final: 0.7777 (p90) REVERT: H 72 ASP cc_start: 0.9123 (t0) cc_final: 0.8805 (t0) REVERT: I 102 GLU cc_start: 0.9349 (mp0) cc_final: 0.9116 (mp0) REVERT: I 114 GLN cc_start: 0.9470 (tm-30) cc_final: 0.9123 (tm-30) REVERT: I 217 TYR cc_start: 0.7320 (m-80) cc_final: 0.6932 (m-10) REVERT: I 252 LYS cc_start: 0.9294 (mtmm) cc_final: 0.8986 (mmmm) REVERT: I 425 ASN cc_start: 0.9336 (p0) cc_final: 0.9134 (p0) REVERT: I 475 MET cc_start: 0.6812 (tmm) cc_final: 0.4843 (tpp) REVERT: J 36 TRP cc_start: 0.8468 (m100) cc_final: 0.7992 (m100) REVERT: J 44 ARG cc_start: 0.5901 (mmt180) cc_final: 0.5260 (mmt-90) REVERT: J 57 THR cc_start: 0.7575 (m) cc_final: 0.6747 (m) REVERT: J 66 ARG cc_start: 0.9469 (mtm-85) cc_final: 0.8674 (mtt180) REVERT: J 67 PHE cc_start: 0.8480 (p90) cc_final: 0.7673 (p90) REVERT: K 21 ILE cc_start: 0.9108 (pt) cc_final: 0.8811 (pt) REVERT: K 27 TYR cc_start: 0.7382 (p90) cc_final: 0.7133 (p90) REVERT: K 33 MET cc_start: 0.6939 (ptt) cc_final: 0.6678 (ptt) REVERT: K 37 GLN cc_start: 0.7644 (pp30) cc_final: 0.6972 (pp30) REVERT: K 45 LYS cc_start: 0.9132 (tptm) cc_final: 0.8726 (ttpp) REVERT: K 72 THR cc_start: 0.8026 (p) cc_final: 0.7742 (p) REVERT: K 103 LYS cc_start: 0.8569 (mmmm) cc_final: 0.8264 (mtmm) REVERT: L 21 ILE cc_start: 0.9145 (pt) cc_final: 0.8831 (pt) REVERT: L 72 THR cc_start: 0.8080 (p) cc_final: 0.7536 (p) REVERT: L 82 ASP cc_start: 0.8759 (m-30) cc_final: 0.8540 (m-30) outliers start: 3 outliers final: 0 residues processed: 538 average time/residue: 0.1311 time to fit residues: 111.8153 Evaluate side-chains 424 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 424 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 166 optimal weight: 8.9990 chunk 100 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 151 optimal weight: 0.9980 chunk 220 optimal weight: 0.0670 chunk 94 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 203 optimal weight: 0.0370 chunk 82 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN E 76 HIS F 616 ASN G 66 HIS G 67 ASN J 76 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 34 ASN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.091218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.072901 restraints weight = 67855.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.075190 restraints weight = 37119.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.076762 restraints weight = 24774.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.077836 restraints weight = 18637.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.078579 restraints weight = 15212.532| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20698 Z= 0.139 Angle : 0.887 18.363 28237 Z= 0.419 Chirality : 0.054 0.657 3337 Planarity : 0.005 0.057 3463 Dihedral : 9.430 84.276 4330 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.61 % Favored : 86.31 % Rotamer: Outliers : 0.14 % Allowed : 0.33 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.30 % 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: -3.49 (0.15), residues: 2388 helix: -0.74 (0.27), residues: 348 sheet: -1.05 (0.28), residues: 366 loop : -3.23 (0.13), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 61 TYR 0.036 0.002 TYR H 58 PHE 0.028 0.001 PHE J 29 TRP 0.096 0.002 TRP I 479 HIS 0.009 0.001 HIS L 76 Details of bonding type rmsd covalent geometry : bond 0.00296 (20587) covalent geometry : angle 0.84198 (27934) SS BOND : bond 0.00437 ( 27) SS BOND : angle 1.65184 ( 54) hydrogen bonds : bond 0.03721 ( 414) hydrogen bonds : angle 5.20931 ( 1026) Misc. bond : bond 0.00114 ( 1) link_ALPHA1-3 : bond 0.00703 ( 2) link_ALPHA1-3 : angle 2.75602 ( 6) link_ALPHA1-6 : bond 0.00920 ( 2) link_ALPHA1-6 : angle 1.49642 ( 6) link_BETA1-4 : bond 0.00707 ( 28) link_BETA1-4 : angle 2.02495 ( 84) link_NAG-ASN : bond 0.00752 ( 51) link_NAG-ASN : angle 3.46657 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 551 time to evaluate : 0.745 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: A 574 LYS cc_start: 0.8883 (mtpp) cc_final: 0.8328 (mtpp) REVERT: A 584 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8483 (tm-30) REVERT: A 647 GLU cc_start: 0.8789 (pp20) cc_final: 0.8562 (pp20) REVERT: A 648 GLU cc_start: 0.9034 (pp20) cc_final: 0.8749 (pp20) REVERT: A 657 GLU cc_start: 0.9023 (mp0) cc_final: 0.8270 (mp0) REVERT: A 658 GLN cc_start: 0.9232 (tt0) cc_final: 0.8710 (tm-30) REVERT: B 98 ASN cc_start: 0.8208 (t0) cc_final: 0.7420 (t0) REVERT: B 114 GLN cc_start: 0.9338 (tm-30) cc_final: 0.9126 (tm-30) REVERT: B 211 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8692 (tm-30) REVERT: B 252 LYS cc_start: 0.9369 (mtmm) cc_final: 0.9092 (mmmm) REVERT: B 427 TRP cc_start: 0.8675 (m100) cc_final: 0.8291 (m100) REVERT: B 434 MET cc_start: 0.7979 (tmm) cc_final: 0.7555 (tmm) REVERT: C 540 GLN cc_start: 0.9039 (mp10) cc_final: 0.8760 (mp10) REVERT: C 573 ILE cc_start: 0.9095 (pt) cc_final: 0.8774 (pt) REVERT: C 577 GLN cc_start: 0.9115 (mt0) cc_final: 0.8856 (mt0) REVERT: C 584 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8470 (tm-30) REVERT: C 622 ILE cc_start: 0.9113 (pt) cc_final: 0.8753 (pt) REVERT: C 658 GLN cc_start: 0.9092 (tp40) cc_final: 0.8883 (tm-30) REVERT: D 39 GLN cc_start: 0.8468 (mm-40) cc_final: 0.8208 (mm-40) REVERT: D 44 ARG cc_start: 0.6121 (mmt-90) cc_final: 0.5617 (mmt-90) REVERT: D 102 TYR cc_start: 0.9281 (m-80) cc_final: 0.9037 (m-80) REVERT: E 45 LYS cc_start: 0.8784 (tptp) cc_final: 0.8568 (ttpp) REVERT: E 82 ASP cc_start: 0.8953 (m-30) cc_final: 0.8676 (m-30) REVERT: F 536 THR cc_start: 0.9246 (m) cc_final: 0.8975 (p) REVERT: F 540 GLN cc_start: 0.8475 (mp10) cc_final: 0.8186 (mp10) REVERT: F 573 ILE cc_start: 0.9172 (pt) cc_final: 0.8651 (pt) REVERT: F 584 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8679 (tm-30) REVERT: F 599 SER cc_start: 0.8274 (p) cc_final: 0.7800 (m) REVERT: F 621 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8175 (tm-30) REVERT: F 624 ASP cc_start: 0.9025 (m-30) cc_final: 0.8813 (m-30) REVERT: F 630 GLN cc_start: 0.9376 (mm-40) cc_final: 0.9029 (mp10) REVERT: F 640 GLN cc_start: 0.9455 (mm110) cc_final: 0.9088 (mm-40) REVERT: F 645 LEU cc_start: 0.9322 (tp) cc_final: 0.8991 (tp) REVERT: F 648 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8287 (tm-30) REVERT: F 652 GLN cc_start: 0.8639 (mp10) cc_final: 0.8398 (mp10) REVERT: F 658 GLN cc_start: 0.9231 (tp40) cc_final: 0.8782 (tm-30) REVERT: G 98 ASN cc_start: 0.8692 (t0) cc_final: 0.7882 (t0) REVERT: G 102 GLU cc_start: 0.9249 (mp0) cc_final: 0.9024 (mp0) REVERT: G 104 MET cc_start: 0.8875 (ttp) cc_final: 0.8419 (ttp) REVERT: G 114 GLN cc_start: 0.9390 (tm-30) cc_final: 0.9110 (tm-30) REVERT: G 302 ASN cc_start: 0.7591 (t0) cc_final: 0.7277 (t0) REVERT: G 425 ASN cc_start: 0.8578 (p0) cc_final: 0.8338 (p0) REVERT: G 426 MET cc_start: 0.7950 (ppp) cc_final: 0.7697 (ppp) REVERT: G 434 MET cc_start: 0.8262 (tmm) cc_final: 0.7939 (tmm) REVERT: H 13 LYS cc_start: 0.8896 (tppt) cc_final: 0.8652 (tppt) REVERT: H 29 PHE cc_start: 0.8800 (t80) cc_final: 0.8401 (t80) REVERT: H 67 PHE cc_start: 0.8533 (p90) cc_final: 0.7589 (p90) REVERT: H 72 ASP cc_start: 0.9087 (t0) cc_final: 0.8765 (t0) REVERT: H 77 THR cc_start: 0.8877 (m) cc_final: 0.8499 (m) REVERT: I 59 LYS cc_start: 0.8015 (tptp) cc_final: 0.7789 (tptp) REVERT: I 98 ASN cc_start: 0.8231 (t0) cc_final: 0.7987 (t0) REVERT: I 102 GLU cc_start: 0.9333 (mp0) cc_final: 0.9086 (mp0) REVERT: I 114 GLN cc_start: 0.9441 (tm-30) cc_final: 0.9116 (tm-30) REVERT: I 180 ASP cc_start: 0.8782 (m-30) cc_final: 0.8552 (m-30) REVERT: I 252 LYS cc_start: 0.9261 (mtmm) cc_final: 0.8966 (mmmm) REVERT: I 425 ASN cc_start: 0.9285 (p0) cc_final: 0.9037 (p0) REVERT: J 36 TRP cc_start: 0.8471 (m100) cc_final: 0.7972 (m100) REVERT: J 44 ARG cc_start: 0.5802 (mmt180) cc_final: 0.5271 (mmt-90) REVERT: J 57 THR cc_start: 0.7412 (m) cc_final: 0.6501 (m) REVERT: J 66 ARG cc_start: 0.9501 (mtm-85) cc_final: 0.8807 (mtt180) REVERT: J 67 PHE cc_start: 0.8368 (p90) cc_final: 0.7669 (p90) REVERT: K 21 ILE cc_start: 0.8926 (pt) cc_final: 0.8595 (pt) REVERT: K 24 LYS cc_start: 0.8710 (pptt) cc_final: 0.8479 (pptt) REVERT: K 27 TYR cc_start: 0.7345 (p90) cc_final: 0.7138 (p90) REVERT: K 33 MET cc_start: 0.6783 (ptt) cc_final: 0.6498 (ptt) REVERT: K 37 GLN cc_start: 0.7452 (pp30) cc_final: 0.6902 (pp30) REVERT: K 45 LYS cc_start: 0.9109 (tptm) cc_final: 0.8791 (ttpp) REVERT: K 103 LYS cc_start: 0.8540 (mmmm) cc_final: 0.8157 (mtmm) REVERT: L 72 THR cc_start: 0.7356 (p) cc_final: 0.7140 (p) outliers start: 3 outliers final: 0 residues processed: 551 average time/residue: 0.1211 time to fit residues: 106.5813 Evaluate side-chains 447 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 447 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 71 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 81 optimal weight: 20.0000 chunk 221 optimal weight: 10.0000 chunk 217 optimal weight: 0.9980 chunk 224 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 199 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 230 optimal weight: 5.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 276 ASN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN ** E 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS ** I 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN L 89 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.086507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.068359 restraints weight = 70080.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.070528 restraints weight = 38666.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.072006 restraints weight = 26062.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.073022 restraints weight = 19801.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.073730 restraints weight = 16308.008| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20698 Z= 0.233 Angle : 0.932 18.443 28237 Z= 0.445 Chirality : 0.055 0.625 3337 Planarity : 0.005 0.053 3463 Dihedral : 9.831 86.711 4330 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.87 % Favored : 84.00 % Rotamer: Outliers : 0.14 % Allowed : 0.52 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.30 % 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: -3.59 (0.15), residues: 2388 helix: -0.84 (0.26), residues: 366 sheet: -1.22 (0.27), residues: 381 loop : -3.31 (0.13), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 71 TYR 0.043 0.003 TYR I 217 PHE 0.028 0.002 PHE J 29 TRP 0.050 0.003 TRP K 35 HIS 0.008 0.002 HIS L 76 Details of bonding type rmsd covalent geometry : bond 0.00520 (20587) covalent geometry : angle 0.88766 (27934) SS BOND : bond 0.00731 ( 27) SS BOND : angle 1.92626 ( 54) hydrogen bonds : bond 0.04242 ( 414) hydrogen bonds : angle 5.42348 ( 1026) Misc. bond : bond 0.00022 ( 1) link_ALPHA1-3 : bond 0.00570 ( 2) link_ALPHA1-3 : angle 2.92300 ( 6) link_ALPHA1-6 : bond 0.00844 ( 2) link_ALPHA1-6 : angle 1.55450 ( 6) link_BETA1-4 : bond 0.00594 ( 28) link_BETA1-4 : angle 2.10960 ( 84) link_NAG-ASN : bond 0.00677 ( 51) link_NAG-ASN : angle 3.52653 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3260.02 seconds wall clock time: 57 minutes 27.26 seconds (3447.26 seconds total)