Starting phenix.real_space_refine on Thu Mar 5 10:03:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t74_25733/03_2026/7t74_25733.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t74_25733/03_2026/7t74_25733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t74_25733/03_2026/7t74_25733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t74_25733/03_2026/7t74_25733.map" model { file = "/net/cci-nas-00/data/ceres_data/7t74_25733/03_2026/7t74_25733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t74_25733/03_2026/7t74_25733.cif" } resolution = 3.35 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= 0.033 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 129 5.16 5 C 13254 2.51 5 N 3523 2.21 5 O 4293 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21199 Number of models: 1 Model: "" Number of chains: 41 Chain: "A" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3305 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 20, 'TRANS': 398} Chain breaks: 3 Chain: "B" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "G" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "H" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1018 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3305 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 20, 'TRANS': 398} Chain breaks: 3 Chain: "D" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "N" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "E" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3305 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 20, 'TRANS': 398} Chain breaks: 3 Chain: "F" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 962 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "I" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "J" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "O" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} 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 Chain: "P" 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: "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: 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: "Y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: "i" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 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: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "D" 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: "E" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "F" 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 Time building chain proxies: 4.69, per 1000 atoms: 0.22 Number of scatterers: 21199 At special positions: 0 Unit cell: (128.75, 121.54, 190.55, 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 129 16.00 O 4293 8.00 N 3523 7.00 C 13254 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.05 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.02 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.05 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.06 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA O 3 " - " MAN O 7 " " MAN O 4 " - " MAN O 5 " " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 4 " " BMA Y 3 " - " MAN Y 4 " " BMA f 3 " - " MAN f 4 " ALPHA1-6 " BMA O 3 " - " MAN O 4 " " MAN O 4 " - " MAN O 6 " BETA1-4 " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " BETA1-6 " NAG T 1 " - " FUC T 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG U 1 " - " FUC U 2 " " NAG a 1 " - " FUC a 2 " " NAG b 1 " - " FUC b 2 " " NAG h 1 " - " FUC h 2 " " NAG i 1 " - " FUC i 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 137 " " NAG A 604 " - " ASN A 355 " " NAG A 605 " - " ASN A 276 " " NAG A 606 " - " ASN A 392 " " NAG A 607 " - " ASN A 339 " " NAG A 608 " - " ASN A 295 " " NAG A 609 " - " ASN A 448 " " NAG A 610 " - " ASN A 301 " " NAG A 611 " - " ASN A 197 " " NAG A 612 " - " ASN A 133 " " NAG B 701 " - " ASN B 625 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 137 " " NAG C 604 " - " ASN C 355 " " NAG C 605 " - " ASN C 276 " " NAG C 606 " - " ASN C 392 " " NAG C 607 " - " ASN C 339 " " NAG C 608 " - " ASN C 295 " " NAG C 609 " - " ASN C 448 " " NAG C 610 " - " ASN C 301 " " NAG C 611 " - " ASN C 197 " " NAG C 612 " - " ASN C 133 " " NAG D 701 " - " ASN D 625 " " NAG D 702 " - " ASN D 637 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 234 " " NAG E 603 " - " ASN E 137 " " NAG E 604 " - " ASN E 355 " " NAG E 605 " - " ASN E 276 " " NAG E 606 " - " ASN E 392 " " NAG E 607 " - " ASN E 339 " " NAG E 608 " - " ASN E 295 " " NAG E 609 " - " ASN E 448 " " NAG E 610 " - " ASN E 301 " " NAG E 611 " - " ASN E 197 " " NAG E 612 " - " ASN E 133 " " NAG F 701 " - " ASN F 625 " " NAG F 702 " - " ASN F 637 " " NAG O 1 " - " ASN A 160 " " NAG P 1 " - " ASN A 386 " " NAG Q 1 " - " ASN A 332 " " NAG R 1 " - " ASN A 262 " " NAG S 1 " - " ASN A 156 " " NAG T 1 " - " ASN B 618 " " NAG U 1 " - " ASN B 611 " " NAG V 1 " - " ASN C 160 " " NAG W 1 " - " ASN C 386 " " NAG X 1 " - " ASN C 332 " " NAG Y 1 " - " ASN C 262 " " NAG Z 1 " - " ASN C 156 " " NAG a 1 " - " ASN D 618 " " NAG b 1 " - " ASN D 611 " " NAG c 1 " - " ASN E 160 " " NAG d 1 " - " ASN E 386 " " NAG e 1 " - " ASN E 332 " " NAG f 1 " - " ASN E 262 " " NAG g 1 " - " ASN E 156 " " NAG h 1 " - " ASN F 618 " " NAG i 1 " - " ASN F 611 " Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 996.9 milliseconds 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4662 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 37 sheets defined 20.7% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.695A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.684A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 194 through 199 removed outlier: 4.503A pdb=" N THR A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.951A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 526 removed outlier: 4.426A pdb=" N GLY B 525 " --> pdb=" O GLY B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 532 Processing helix chain 'B' and resid 534 through 540 Processing helix chain 'B' and resid 572 through 596 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 52A through 54 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'C' and resid 99 through 116 removed outlier: 3.722A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 143 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.559A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.531A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 526 removed outlier: 4.326A pdb=" N GLY D 525 " --> pdb=" O GLY D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 532 Processing helix chain 'D' and resid 534 through 540 Processing helix chain 'D' and resid 572 through 596 Processing helix chain 'D' and resid 618 through 626 removed outlier: 3.673A pdb=" N ASP D 624 " --> pdb=" O SER D 620 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET D 626 " --> pdb=" O ILE D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 661 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.265A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 139 through 143 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.520A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 527 through 532 Processing helix chain 'F' and resid 534 through 540 Processing helix chain 'F' and resid 572 through 596 Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 661 removed outlier: 3.512A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.405A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.776A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.570A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 6.830A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323A current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 466 through 470 Processing sheet with id=AA8, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AA9, first strand: chain 'K' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 11 through 12 current: chain 'K' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 57 through 59 current: chain 'K' and resid 100H through 103 Processing sheet with id=AB1, first strand: chain 'G' and resid 12 through 13 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 12 through 13 current: chain 'G' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 45 through 48 current: chain 'G' and resid 96 through 98 No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'G' and resid 19 through 24 Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 7 removed outlier: 5.554A pdb=" N THR L 70 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 9.533A pdb=" N GLN L 27 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 9.785A pdb=" N SER L 68 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.552A pdb=" N VAL L 29 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 11.761A pdb=" N SER L 66 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.822A pdb=" N PHE L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N TYR L 50 " --> pdb=" O PHE L 34 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB6, first strand: chain 'H' and resid 34 through 39 removed outlier: 6.954A pdb=" N MET H 34 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N HIS H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100H through 103 Processing sheet with id=AB7, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.413A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.672A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AC1, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AC3, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.539A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 312 removed outlier: 7.005A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 323A current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 466 through 470 Processing sheet with id=AC5, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AC6, first strand: chain 'M' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 11 through 12 current: chain 'M' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 57 through 59 current: chain 'M' and resid 100H through 103 Processing sheet with id=AC7, first strand: chain 'N' and resid 11 through 13 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 11 through 13 current: chain 'N' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 45 through 48 current: chain 'N' and resid 96 through 98 No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AC9, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.392A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.795A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AD3, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AD4, first strand: chain 'E' and resid 169 through 177 removed outlier: 5.190A pdb=" N THR E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) removed outlier: 11.389A pdb=" N ASN E 133 " --> pdb=" O ASN E 187 " (cutoff:3.500A) removed outlier: 16.671A pdb=" N ASN E 187 " --> pdb=" O ASN E 133 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ASN E 190 " --> pdb=" O MET E 184 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.593A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 6.773A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323A current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 466 through 470 Processing sheet with id=AD7, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AD8, first strand: chain 'I' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 11 through 12 current: chain 'I' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 57 through 59 current: chain 'I' and resid 100H through 103 Processing sheet with id=AD9, first strand: chain 'J' and resid 12 through 13 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 12 through 13 current: chain 'J' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 45 through 48 current: chain 'J' and resid 96 through 98 No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'J' and resid 19 through 24 590 hydrogen bonds defined for protein. 1521 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: 3.30 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 4488 1.32 - 1.46: 7000 1.46 - 1.59: 9893 1.59 - 1.73: 60 1.73 - 1.87: 175 Bond restraints: 21616 Sorted by residual: bond pdb=" CB HIS B 570 " pdb=" CG HIS B 570 " ideal model delta sigma weight residual 1.497 1.582 -0.085 1.40e-02 5.10e+03 3.71e+01 bond pdb=" CB ASP J 27B" pdb=" CG ASP J 27B" ideal model delta sigma weight residual 1.516 1.364 0.152 2.50e-02 1.60e+03 3.70e+01 bond pdb=" CB LEU N 107 " pdb=" CG LEU N 107 " ideal model delta sigma weight residual 1.530 1.648 -0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" CB ASP N 27B" pdb=" CG ASP N 27B" ideal model delta sigma weight residual 1.516 1.369 0.147 2.50e-02 1.60e+03 3.44e+01 bond pdb=" CB LEU J 107 " pdb=" CG LEU J 107 " ideal model delta sigma weight residual 1.530 1.645 -0.115 2.00e-02 2.50e+03 3.30e+01 ... (remaining 21611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.67: 29284 7.67 - 15.33: 34 15.33 - 23.00: 0 23.00 - 30.66: 0 30.66 - 38.33: 5 Bond angle restraints: 29323 Sorted by residual: angle pdb=" C2 NAG e 1 " pdb=" N2 NAG e 1 " pdb=" C7 NAG e 1 " ideal model delta sigma weight residual 124.56 162.89 -38.33 3.00e+00 1.11e-01 1.63e+02 angle pdb=" C2 NAG b 1 " pdb=" N2 NAG b 1 " pdb=" C7 NAG b 1 " ideal model delta sigma weight residual 124.56 162.59 -38.03 3.00e+00 1.11e-01 1.61e+02 angle pdb=" C2 NAG Q 1 " pdb=" N2 NAG Q 1 " pdb=" C7 NAG Q 1 " ideal model delta sigma weight residual 124.56 161.34 -36.78 3.00e+00 1.11e-01 1.50e+02 angle pdb=" C2 NAG B 701 " pdb=" N2 NAG B 701 " pdb=" C7 NAG B 701 " ideal model delta sigma weight residual 124.56 160.92 -36.36 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C2 NAG D 701 " pdb=" N2 NAG D 701 " pdb=" C7 NAG D 701 " ideal model delta sigma weight residual 124.56 160.82 -36.26 3.00e+00 1.11e-01 1.46e+02 ... (remaining 29318 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.89: 13660 23.89 - 47.79: 296 47.79 - 71.68: 84 71.68 - 95.57: 43 95.57 - 119.47: 28 Dihedral angle restraints: 14111 sinusoidal: 6824 harmonic: 7287 Sorted by residual: dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -125.73 39.73 1 1.00e+01 1.00e-02 2.22e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -123.97 37.97 1 1.00e+01 1.00e-02 2.03e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -123.91 37.91 1 1.00e+01 1.00e-02 2.03e+01 ... (remaining 14108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.038: 3548 1.038 - 2.076: 0 2.076 - 3.114: 0 3.114 - 4.151: 0 4.151 - 5.189: 1 Chirality restraints: 3549 Sorted by residual: chirality pdb=" C4 FUC i 2 " pdb=" C3 FUC i 2 " pdb=" C5 FUC i 2 " pdb=" O4 FUC i 2 " both_signs ideal model delta sigma weight residual False -2.49 2.70 -5.19 2.00e-01 2.50e+01 6.73e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-02 2.50e+03 1.94e+02 chirality pdb=" C1 NAG d 2 " pdb=" O4 NAG d 1 " pdb=" C2 NAG d 2 " pdb=" O5 NAG d 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.35e+02 ... (remaining 3546 not shown) Planarity restraints: 3673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 702 " 0.256 2.00e-02 2.50e+03 2.19e-01 5.97e+02 pdb=" C7 NAG F 702 " -0.058 2.00e-02 2.50e+03 pdb=" C8 NAG F 702 " -0.029 2.00e-02 2.50e+03 pdb=" N2 NAG F 702 " -0.363 2.00e-02 2.50e+03 pdb=" O7 NAG F 702 " 0.194 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG c 2 " -0.240 2.00e-02 2.50e+03 2.02e-01 5.11e+02 pdb=" C7 NAG c 2 " 0.062 2.00e-02 2.50e+03 pdb=" C8 NAG c 2 " -0.163 2.00e-02 2.50e+03 pdb=" N2 NAG c 2 " 0.342 2.00e-02 2.50e+03 pdb=" O7 NAG c 2 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG c 1 " -0.179 2.00e-02 2.50e+03 1.49e-01 2.76e+02 pdb=" C7 NAG c 1 " 0.048 2.00e-02 2.50e+03 pdb=" C8 NAG c 1 " -0.131 2.00e-02 2.50e+03 pdb=" N2 NAG c 1 " 0.242 2.00e-02 2.50e+03 pdb=" O7 NAG c 1 " 0.020 2.00e-02 2.50e+03 ... (remaining 3670 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 6602 2.85 - 3.36: 18676 3.36 - 3.87: 35487 3.87 - 4.39: 42075 4.39 - 4.90: 67263 Nonbonded interactions: 170103 Sorted by model distance: nonbonded pdb=" C THR H 100L" pdb=" OG1 THR H 100L" model vdw 2.337 2.616 nonbonded pdb=" N ASP K 84 " pdb=" OD1 ASP K 84 " model vdw 2.362 3.120 nonbonded pdb=" N ASP I 84 " pdb=" OD1 ASP I 84 " model vdw 2.363 3.120 nonbonded pdb=" N ASP M 84 " pdb=" OD1 ASP M 84 " model vdw 2.364 3.120 nonbonded pdb=" NZ LYS C 46 " pdb=" OD2 ASP D 632 " model vdw 2.390 3.120 ... (remaining 170098 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 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = (chain 'F' and (resid 518 through 661 or (resid 662 and (name N or name CA or na \ me C or name O or name CB )) or resid 701 through 702)) } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'M' } ncs_group { reference = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'W' and resid 1) selection = (chain 'X' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'a' and resid 1) selection = (chain 'b' and resid 1) selection = (chain 'c' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'e' and resid 1) selection = (chain 'g' and resid 1) selection = (chain 'h' and resid 1) selection = (chain 'i' and resid 1) } ncs_group { reference = chain 'R' selection = chain 'S' selection = chain 'Y' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.160 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.290 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 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 : 0.023 0.152 21751 Z= 1.205 Angle : 1.798 38.326 29691 Z= 1.126 Chirality : 0.160 5.189 3549 Planarity : 0.010 0.219 3610 Dihedral : 12.706 119.466 9338 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 0.77 Ramachandran Plot: Outliers : 0.56 % Allowed : 2.48 % Favored : 96.96 % Rotamer: Outliers : 0.64 % Allowed : 0.91 % Favored : 98.45 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.16), residues: 2497 helix: 0.10 (0.24), residues: 390 sheet: 0.81 (0.18), residues: 817 loop : 0.53 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 71 TYR 0.049 0.007 TYR J 96 PHE 0.034 0.006 PHE E 353 TRP 0.061 0.009 TRP C 96 HIS 0.012 0.003 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.02239 (21616) covalent geometry : angle 1.77186 (29323) SS BOND : bond 0.00884 ( 37) SS BOND : angle 2.55441 ( 74) hydrogen bonds : bond 0.16605 ( 590) hydrogen bonds : angle 6.64191 ( 1521) link_ALPHA1-3 : bond 0.06562 ( 6) link_ALPHA1-3 : angle 4.16153 ( 18) link_ALPHA1-6 : bond 0.00814 ( 2) link_ALPHA1-6 : angle 1.64499 ( 6) link_BETA1-4 : bond 0.06176 ( 21) link_BETA1-4 : angle 4.53813 ( 63) link_BETA1-6 : bond 0.07806 ( 6) link_BETA1-6 : angle 4.25299 ( 18) link_NAG-ASN : bond 0.07559 ( 63) link_NAG-ASN : angle 2.83916 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 408 time to evaluate : 0.791 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: G 5 THR cc_start: 0.8628 (m) cc_final: 0.8338 (p) REVERT: G 24 THR cc_start: 0.8937 (m) cc_final: 0.8523 (p) REVERT: L 34 PHE cc_start: 0.7476 (t80) cc_final: 0.7149 (t80) REVERT: L 40 ARG cc_start: 0.8939 (tmt170) cc_final: 0.8712 (tpp-160) REVERT: L 47 LEU cc_start: 0.5709 (tp) cc_final: 0.5147 (tp) REVERT: L 96 PHE cc_start: 0.4907 (m-80) cc_final: 0.4670 (m-80) REVERT: H 34 MET cc_start: 0.5555 (mmm) cc_final: 0.4653 (mmm) REVERT: H 78 LEU cc_start: 0.7303 (tp) cc_final: 0.6928 (tp) REVERT: H 93 MET cc_start: 0.6065 (OUTLIER) cc_final: 0.5426 (ppp) REVERT: C 207 LYS cc_start: 0.8564 (pttt) cc_final: 0.8315 (tmtt) REVERT: M 28 THR cc_start: 0.9154 (m) cc_final: 0.8829 (p) REVERT: M 68 THR cc_start: 0.9255 (m) cc_final: 0.9051 (p) REVERT: N 94 ARG cc_start: 0.5968 (mpt180) cc_final: 0.4893 (mmt180) REVERT: E 187 ASN cc_start: 0.6751 (t0) cc_final: 0.6474 (m-40) REVERT: F 632 ASP cc_start: 0.8550 (t70) cc_final: 0.8304 (t0) REVERT: J 94 ARG cc_start: 0.5959 (mpt180) cc_final: 0.4971 (mtp85) REVERT: J 97 ILE cc_start: 0.9134 (pt) cc_final: 0.8920 (pt) outliers start: 14 outliers final: 4 residues processed: 417 average time/residue: 0.1759 time to fit residues: 105.8997 Evaluate side-chains 226 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 221 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ASN Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 201 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 247 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 570 HIS G 6 GLN C 187 ASN N 6 GLN N 79 GLN F 575 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.093174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.069590 restraints weight = 50491.954| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.31 r_work: 0.2942 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21751 Z= 0.156 Angle : 0.734 19.675 29691 Z= 0.359 Chirality : 0.049 0.654 3549 Planarity : 0.004 0.054 3610 Dihedral : 9.329 80.642 4761 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.88 % Favored : 96.96 % Rotamer: Outliers : 1.91 % Allowed : 5.45 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.16), residues: 2497 helix: 1.97 (0.27), residues: 378 sheet: 0.77 (0.18), residues: 820 loop : -0.06 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 588 TYR 0.018 0.001 TYR C 173 PHE 0.024 0.002 PHE L 84 TRP 0.027 0.001 TRP E 479 HIS 0.009 0.001 HIS B 570 Details of bonding type rmsd covalent geometry : bond 0.00341 (21616) covalent geometry : angle 0.68301 (29323) SS BOND : bond 0.00304 ( 37) SS BOND : angle 0.87881 ( 74) hydrogen bonds : bond 0.05195 ( 590) hydrogen bonds : angle 4.97251 ( 1521) link_ALPHA1-3 : bond 0.01000 ( 6) link_ALPHA1-3 : angle 2.78319 ( 18) link_ALPHA1-6 : bond 0.00299 ( 2) link_ALPHA1-6 : angle 1.70557 ( 6) link_BETA1-4 : bond 0.00689 ( 21) link_BETA1-4 : angle 2.86478 ( 63) link_BETA1-6 : bond 0.00527 ( 6) link_BETA1-6 : angle 1.26782 ( 18) link_NAG-ASN : bond 0.00521 ( 63) link_NAG-ASN : angle 2.85784 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 292 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8087 (ttm110) cc_final: 0.7869 (mtm180) REVERT: K 34 MET cc_start: 0.8748 (mtt) cc_final: 0.8530 (mtm) REVERT: K 72 ASP cc_start: 0.8038 (t0) cc_final: 0.7565 (t70) REVERT: G 5 THR cc_start: 0.8705 (m) cc_final: 0.8331 (p) REVERT: G 24 THR cc_start: 0.9201 (m) cc_final: 0.8609 (p) REVERT: L 33 TYR cc_start: 0.7657 (m-80) cc_final: 0.7343 (m-80) REVERT: L 34 PHE cc_start: 0.7251 (t80) cc_final: 0.6871 (t80) REVERT: L 36 TRP cc_start: 0.7642 (m100) cc_final: 0.7432 (m100) REVERT: L 54 ARG cc_start: 0.7738 (mtp85) cc_final: 0.7462 (mtp85) REVERT: L 63 PHE cc_start: 0.7894 (m-80) cc_final: 0.7231 (m-80) REVERT: L 90 ARG cc_start: 0.8209 (ttm-80) cc_final: 0.7319 (ttm-80) REVERT: L 96 PHE cc_start: 0.7321 (m-80) cc_final: 0.6944 (m-80) REVERT: H 46 GLU cc_start: 0.8105 (tt0) cc_final: 0.7539 (tt0) REVERT: H 66 ARG cc_start: 0.7497 (ptp-170) cc_final: 0.6984 (ptm160) REVERT: H 79 TYR cc_start: 0.7549 (m-10) cc_final: 0.7332 (m-10) REVERT: H 93 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.6856 (ppp) REVERT: C 207 LYS cc_start: 0.8804 (pttt) cc_final: 0.8352 (tmtt) REVERT: C 475 MET cc_start: 0.8930 (mmm) cc_final: 0.8708 (tpt) REVERT: D 588 ARG cc_start: 0.8551 (ttm-80) cc_final: 0.8199 (mtt-85) REVERT: D 624 ASP cc_start: 0.9093 (m-30) cc_final: 0.8541 (m-30) REVERT: M 28 THR cc_start: 0.8741 (m) cc_final: 0.8308 (p) REVERT: M 72 ASP cc_start: 0.7696 (t0) cc_final: 0.7493 (t0) REVERT: M 83 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6688 (mpp80) REVERT: M 110 THR cc_start: 0.8900 (m) cc_final: 0.8669 (t) REVERT: N 60 ASP cc_start: 0.8181 (p0) cc_final: 0.6828 (t0) REVERT: N 83 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7534 (mm-30) REVERT: N 91 TYR cc_start: 0.9144 (t80) cc_final: 0.8896 (t80) REVERT: N 94 ARG cc_start: 0.5599 (mpt180) cc_final: 0.4296 (mmt180) REVERT: J 31 ASN cc_start: 0.8660 (m-40) cc_final: 0.8335 (m110) REVERT: J 94 ARG cc_start: 0.5645 (mpt180) cc_final: 0.4576 (mtp85) outliers start: 42 outliers final: 16 residues processed: 316 average time/residue: 0.1679 time to fit residues: 77.8738 Evaluate side-chains 239 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 221 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain M residue 83 ARG Chi-restraints excluded: chain N residue 17 GLN Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain F residue 588 ARG Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 27 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 45 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 167 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 86 optimal weight: 20.0000 chunk 80 optimal weight: 7.9990 chunk 197 optimal weight: 5.9990 chunk 243 optimal weight: 0.0060 chunk 72 optimal weight: 9.9990 overall best weight: 3.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 6 GLN I 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.087877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.063766 restraints weight = 52710.076| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.38 r_work: 0.2844 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 21751 Z= 0.283 Angle : 0.758 20.237 29691 Z= 0.372 Chirality : 0.051 0.718 3549 Planarity : 0.005 0.040 3610 Dihedral : 7.937 70.449 4756 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.96 % Favored : 95.96 % Rotamer: Outliers : 2.50 % Allowed : 6.41 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.17), residues: 2497 helix: 1.88 (0.28), residues: 384 sheet: 0.66 (0.18), residues: 786 loop : -0.41 (0.16), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 503 TYR 0.014 0.002 TYR C 173 PHE 0.026 0.002 PHE B 520 TRP 0.031 0.002 TRP H 47 HIS 0.007 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00666 (21616) covalent geometry : angle 0.71322 (29323) SS BOND : bond 0.00446 ( 37) SS BOND : angle 1.03310 ( 74) hydrogen bonds : bond 0.05281 ( 590) hydrogen bonds : angle 4.81912 ( 1521) link_ALPHA1-3 : bond 0.00972 ( 6) link_ALPHA1-3 : angle 2.33389 ( 18) link_ALPHA1-6 : bond 0.00419 ( 2) link_ALPHA1-6 : angle 1.89091 ( 6) link_BETA1-4 : bond 0.00556 ( 21) link_BETA1-4 : angle 2.43497 ( 63) link_BETA1-6 : bond 0.00376 ( 6) link_BETA1-6 : angle 1.41828 ( 18) link_NAG-ASN : bond 0.01088 ( 63) link_NAG-ASN : angle 2.85472 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 230 time to evaluate : 0.769 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: A 143 ARG cc_start: 0.8073 (ttm110) cc_final: 0.7805 (mtm180) REVERT: A 184 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7785 (ttp) REVERT: K 4 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8255 (mm) REVERT: G 5 THR cc_start: 0.8892 (m) cc_final: 0.8458 (p) REVERT: G 24 THR cc_start: 0.9156 (m) cc_final: 0.8649 (p) REVERT: G 103 ARG cc_start: 0.8449 (tpp-160) cc_final: 0.8050 (mtp85) REVERT: L 13 LEU cc_start: 0.7324 (mt) cc_final: 0.7098 (mp) REVERT: L 33 TYR cc_start: 0.7916 (m-80) cc_final: 0.7470 (m-10) REVERT: L 54 ARG cc_start: 0.7858 (mtp85) cc_final: 0.7297 (mtp85) REVERT: L 63 PHE cc_start: 0.7487 (m-80) cc_final: 0.7072 (m-80) REVERT: H 71 ARG cc_start: 0.6842 (ttm110) cc_final: 0.6271 (ttm170) REVERT: C 207 LYS cc_start: 0.8592 (pttt) cc_final: 0.8214 (tmtt) REVERT: D 588 ARG cc_start: 0.8703 (ttm-80) cc_final: 0.8146 (mtt-85) REVERT: D 624 ASP cc_start: 0.8959 (m-30) cc_final: 0.8249 (m-30) REVERT: D 654 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8107 (mt-10) REVERT: M 19 LYS cc_start: 0.8851 (tttt) cc_final: 0.8401 (tttp) REVERT: M 28 THR cc_start: 0.8999 (m) cc_final: 0.8650 (p) REVERT: M 72 ASP cc_start: 0.7889 (t0) cc_final: 0.7610 (t0) REVERT: N 60 ASP cc_start: 0.8191 (p0) cc_final: 0.7141 (t0) REVERT: N 83 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7807 (mm-30) REVERT: N 94 ARG cc_start: 0.5980 (mpt180) cc_final: 0.4865 (tpt170) REVERT: E 187 ASN cc_start: 0.7088 (t0) cc_final: 0.6825 (m-40) REVERT: I 82 MET cc_start: 0.8020 (mtm) cc_final: 0.7781 (mtm) REVERT: J 31 ASN cc_start: 0.8860 (m-40) cc_final: 0.8630 (m-40) REVERT: J 79 GLN cc_start: 0.7230 (mp10) cc_final: 0.6914 (mp10) REVERT: J 94 ARG cc_start: 0.6240 (mpt180) cc_final: 0.4613 (mtp85) outliers start: 55 outliers final: 30 residues processed: 265 average time/residue: 0.1672 time to fit residues: 65.4971 Evaluate side-chains 238 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 205 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain M residue 83 ARG Chi-restraints excluded: chain N residue 17 GLN Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain F residue 571 TRP Chi-restraints excluded: chain F residue 588 ARG Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 97 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 62 optimal weight: 2.9990 chunk 209 optimal weight: 0.8980 chunk 214 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 228 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 220 optimal weight: 0.8980 chunk 135 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.089719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.065557 restraints weight = 52287.300| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.41 r_work: 0.2866 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21751 Z= 0.145 Angle : 0.642 21.707 29691 Z= 0.310 Chirality : 0.048 0.770 3549 Planarity : 0.004 0.034 3610 Dihedral : 6.999 64.494 4753 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.64 % Favored : 96.28 % Rotamer: Outliers : 1.73 % Allowed : 7.73 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.17), residues: 2497 helix: 2.08 (0.28), residues: 384 sheet: 0.79 (0.19), residues: 768 loop : -0.47 (0.16), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 71 TYR 0.030 0.001 TYR N 91 PHE 0.020 0.002 PHE C 53 TRP 0.037 0.001 TRP H 47 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00330 (21616) covalent geometry : angle 0.58769 (29323) SS BOND : bond 0.00376 ( 37) SS BOND : angle 0.80361 ( 74) hydrogen bonds : bond 0.04139 ( 590) hydrogen bonds : angle 4.40777 ( 1521) link_ALPHA1-3 : bond 0.00995 ( 6) link_ALPHA1-3 : angle 2.42565 ( 18) link_ALPHA1-6 : bond 0.00214 ( 2) link_ALPHA1-6 : angle 1.71737 ( 6) link_BETA1-4 : bond 0.00501 ( 21) link_BETA1-4 : angle 2.00315 ( 63) link_BETA1-6 : bond 0.00377 ( 6) link_BETA1-6 : angle 1.27811 ( 18) link_NAG-ASN : bond 0.00644 ( 63) link_NAG-ASN : angle 2.96582 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 235 time to evaluate : 0.704 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: A 173 TYR cc_start: 0.8509 (p90) cc_final: 0.8125 (p90) REVERT: A 184 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7777 (ttp) REVERT: K 72 ASP cc_start: 0.8217 (t0) cc_final: 0.7665 (t70) REVERT: G 103 ARG cc_start: 0.8317 (tpp-160) cc_final: 0.7990 (mtp85) REVERT: L 13 LEU cc_start: 0.7319 (mt) cc_final: 0.7108 (mp) REVERT: L 33 TYR cc_start: 0.7934 (m-80) cc_final: 0.7496 (m-10) REVERT: L 54 ARG cc_start: 0.7973 (mtp85) cc_final: 0.7475 (mtp85) REVERT: L 63 PHE cc_start: 0.7552 (m-80) cc_final: 0.7272 (m-80) REVERT: L 90 ARG cc_start: 0.8313 (ttm-80) cc_final: 0.7861 (ttm-80) REVERT: H 46 GLU cc_start: 0.8125 (tt0) cc_final: 0.7836 (tt0) REVERT: C 207 LYS cc_start: 0.8604 (pttt) cc_final: 0.8199 (tmtt) REVERT: D 624 ASP cc_start: 0.8955 (m-30) cc_final: 0.8377 (m-30) REVERT: D 654 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8022 (mt-10) REVERT: M 19 LYS cc_start: 0.8902 (tttt) cc_final: 0.8647 (tttp) REVERT: M 28 THR cc_start: 0.8947 (m) cc_final: 0.8625 (p) REVERT: M 72 ASP cc_start: 0.7788 (t0) cc_final: 0.7454 (t0) REVERT: M 83 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6656 (mtm-85) REVERT: N 60 ASP cc_start: 0.8114 (p0) cc_final: 0.7021 (t0) REVERT: N 83 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7573 (mm-30) REVERT: N 94 ARG cc_start: 0.5780 (mpt180) cc_final: 0.4789 (tpt170) REVERT: E 475 MET cc_start: 0.8607 (mmt) cc_final: 0.8184 (mmt) REVERT: I 13 GLN cc_start: 0.9033 (pm20) cc_final: 0.8828 (pm20) REVERT: I 82 MET cc_start: 0.8044 (mtm) cc_final: 0.7792 (mtm) REVERT: J 31 ASN cc_start: 0.8856 (m-40) cc_final: 0.8479 (m110) REVERT: J 94 ARG cc_start: 0.6187 (mpt180) cc_final: 0.4751 (mtp85) outliers start: 38 outliers final: 22 residues processed: 260 average time/residue: 0.1620 time to fit residues: 62.4994 Evaluate side-chains 235 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 210 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain M residue 64 LYS Chi-restraints excluded: chain M residue 83 ARG Chi-restraints excluded: chain N residue 17 GLN Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain F residue 662 GLU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 27 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 53 optimal weight: 6.9990 chunk 197 optimal weight: 0.0010 chunk 1 optimal weight: 5.9990 chunk 236 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 133 optimal weight: 0.0970 chunk 96 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 231 optimal weight: 1.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 6 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.089644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.065655 restraints weight = 51708.561| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.38 r_work: 0.2875 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21751 Z= 0.134 Angle : 0.593 13.924 29691 Z= 0.289 Chirality : 0.045 0.427 3549 Planarity : 0.004 0.032 3610 Dihedral : 6.410 60.040 4753 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.76 % Favored : 96.16 % Rotamer: Outliers : 1.91 % Allowed : 8.32 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.17), residues: 2497 helix: 2.18 (0.28), residues: 384 sheet: 0.91 (0.19), residues: 764 loop : -0.47 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 40 TYR 0.022 0.001 TYR N 91 PHE 0.024 0.001 PHE C 53 TRP 0.016 0.001 TRP L 36 HIS 0.005 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00307 (21616) covalent geometry : angle 0.55705 (29323) SS BOND : bond 0.00309 ( 37) SS BOND : angle 0.79067 ( 74) hydrogen bonds : bond 0.03918 ( 590) hydrogen bonds : angle 4.24310 ( 1521) link_ALPHA1-3 : bond 0.00930 ( 6) link_ALPHA1-3 : angle 2.25326 ( 18) link_ALPHA1-6 : bond 0.00247 ( 2) link_ALPHA1-6 : angle 1.59502 ( 6) link_BETA1-4 : bond 0.00498 ( 21) link_BETA1-4 : angle 1.85892 ( 63) link_BETA1-6 : bond 0.00375 ( 6) link_BETA1-6 : angle 1.28694 ( 18) link_NAG-ASN : bond 0.00292 ( 63) link_NAG-ASN : angle 2.22622 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 233 time to evaluate : 0.730 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: A 143 ARG cc_start: 0.8166 (ttm110) cc_final: 0.7517 (mmt90) REVERT: A 173 TYR cc_start: 0.8523 (p90) cc_final: 0.8178 (p90) REVERT: A 184 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.8015 (ttp) REVERT: K 3 GLN cc_start: 0.8564 (mt0) cc_final: 0.8350 (mm-40) REVERT: K 72 ASP cc_start: 0.8232 (t0) cc_final: 0.7647 (t70) REVERT: G 6 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7543 (pt0) REVERT: G 103 ARG cc_start: 0.8304 (tpp-160) cc_final: 0.7974 (mtp85) REVERT: L 13 LEU cc_start: 0.7368 (mt) cc_final: 0.7152 (mp) REVERT: L 33 TYR cc_start: 0.7925 (m-80) cc_final: 0.7470 (m-10) REVERT: L 49 ILE cc_start: 0.8732 (mp) cc_final: 0.8154 (tt) REVERT: L 54 ARG cc_start: 0.7717 (mtp85) cc_final: 0.7323 (mtp85) REVERT: H 3 GLN cc_start: 0.7364 (pm20) cc_final: 0.7073 (pm20) REVERT: H 46 GLU cc_start: 0.8078 (tt0) cc_final: 0.7812 (tt0) REVERT: H 79 TYR cc_start: 0.7825 (m-10) cc_final: 0.7494 (m-80) REVERT: C 207 LYS cc_start: 0.8764 (pttt) cc_final: 0.8342 (tmtt) REVERT: D 624 ASP cc_start: 0.8947 (m-30) cc_final: 0.8265 (m-30) REVERT: D 654 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7985 (mt-10) REVERT: M 19 LYS cc_start: 0.8933 (tttt) cc_final: 0.8716 (tttp) REVERT: M 28 THR cc_start: 0.8967 (m) cc_final: 0.8643 (p) REVERT: M 72 ASP cc_start: 0.7601 (t0) cc_final: 0.7243 (t0) REVERT: M 83 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.6441 (mtm-85) REVERT: N 60 ASP cc_start: 0.8078 (p0) cc_final: 0.7027 (t0) REVERT: N 83 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7689 (mm-30) REVERT: N 94 ARG cc_start: 0.5757 (mpt180) cc_final: 0.4819 (tpt170) REVERT: E 430 ILE cc_start: 0.8982 (mp) cc_final: 0.8709 (mp) REVERT: F 533 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8632 (mtp) REVERT: I 3 GLN cc_start: 0.8565 (mt0) cc_final: 0.8168 (mm-40) REVERT: J 31 ASN cc_start: 0.8893 (m-40) cc_final: 0.8688 (m-40) REVERT: J 94 ARG cc_start: 0.6189 (mpt180) cc_final: 0.4701 (mtp85) outliers start: 42 outliers final: 24 residues processed: 262 average time/residue: 0.1628 time to fit residues: 63.1892 Evaluate side-chains 241 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain M residue 43 LYS Chi-restraints excluded: chain M residue 83 ARG Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain F residue 588 ARG Chi-restraints excluded: chain F residue 662 GLU Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 27 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 136 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 204 optimal weight: 1.9990 chunk 245 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 205 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 chunk 187 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 6 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.087971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.063790 restraints weight = 52394.610| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 3.39 r_work: 0.2831 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 21751 Z= 0.223 Angle : 0.649 13.335 29691 Z= 0.316 Chirality : 0.046 0.367 3549 Planarity : 0.004 0.033 3610 Dihedral : 6.384 57.417 4753 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.16 % Favored : 95.75 % Rotamer: Outliers : 2.23 % Allowed : 8.55 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.17), residues: 2497 helix: 2.02 (0.28), residues: 384 sheet: 0.77 (0.19), residues: 771 loop : -0.58 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 40 TYR 0.019 0.001 TYR N 91 PHE 0.024 0.002 PHE C 53 TRP 0.022 0.001 TRP L 36 HIS 0.006 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00529 (21616) covalent geometry : angle 0.60894 (29323) SS BOND : bond 0.00387 ( 37) SS BOND : angle 0.87429 ( 74) hydrogen bonds : bond 0.04451 ( 590) hydrogen bonds : angle 4.41372 ( 1521) link_ALPHA1-3 : bond 0.00855 ( 6) link_ALPHA1-3 : angle 2.36752 ( 18) link_ALPHA1-6 : bond 0.00168 ( 2) link_ALPHA1-6 : angle 1.67275 ( 6) link_BETA1-4 : bond 0.00466 ( 21) link_BETA1-4 : angle 1.96792 ( 63) link_BETA1-6 : bond 0.00328 ( 6) link_BETA1-6 : angle 1.43060 ( 18) link_NAG-ASN : bond 0.00406 ( 63) link_NAG-ASN : angle 2.49303 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 220 time to evaluate : 0.701 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: A 184 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7635 (ptm) REVERT: K 72 ASP cc_start: 0.8303 (t0) cc_final: 0.7703 (t70) REVERT: G 103 ARG cc_start: 0.8292 (tpp-160) cc_final: 0.8001 (mtp85) REVERT: L 33 TYR cc_start: 0.7959 (m-80) cc_final: 0.7530 (m-10) REVERT: L 49 ILE cc_start: 0.8763 (mp) cc_final: 0.8135 (tt) REVERT: L 54 ARG cc_start: 0.7637 (mtp85) cc_final: 0.7260 (mtp85) REVERT: H 79 TYR cc_start: 0.7932 (m-10) cc_final: 0.7526 (m-80) REVERT: C 207 LYS cc_start: 0.8685 (pttt) cc_final: 0.8277 (tmtt) REVERT: D 654 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7989 (mt-10) REVERT: M 19 LYS cc_start: 0.9047 (tttt) cc_final: 0.8810 (tttp) REVERT: M 72 ASP cc_start: 0.7643 (t0) cc_final: 0.7290 (t0) REVERT: M 83 ARG cc_start: 0.7145 (OUTLIER) cc_final: 0.6652 (mtm-85) REVERT: N 60 ASP cc_start: 0.8234 (p0) cc_final: 0.7154 (t0) REVERT: N 83 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7673 (mm-30) REVERT: N 94 ARG cc_start: 0.6012 (mpt180) cc_final: 0.4652 (tpt170) REVERT: E 208 VAL cc_start: 0.9111 (t) cc_final: 0.8901 (m) REVERT: E 430 ILE cc_start: 0.9018 (mp) cc_final: 0.8728 (mm) REVERT: F 533 MET cc_start: 0.9092 (OUTLIER) cc_final: 0.8775 (mtp) REVERT: I 3 GLN cc_start: 0.8602 (mt0) cc_final: 0.8301 (mm-40) REVERT: I 82 MET cc_start: 0.7958 (mtm) cc_final: 0.7753 (mtm) REVERT: J 31 ASN cc_start: 0.8892 (m-40) cc_final: 0.8505 (m110) outliers start: 49 outliers final: 32 residues processed: 249 average time/residue: 0.1625 time to fit residues: 60.1804 Evaluate side-chains 248 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 212 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain M residue 83 ARG Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain F residue 588 ARG Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 97 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 238 optimal weight: 9.9990 chunk 221 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 198 optimal weight: 0.9990 chunk 147 optimal weight: 0.7980 chunk 126 optimal weight: 0.3980 chunk 226 optimal weight: 9.9990 chunk 235 optimal weight: 1.9990 chunk 59 optimal weight: 0.0670 chunk 58 optimal weight: 3.9990 chunk 236 optimal weight: 0.4980 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 6 GLN M 105 GLN E 99 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.090063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.066056 restraints weight = 51964.887| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.40 r_work: 0.2877 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 21751 Z= 0.105 Angle : 0.575 14.079 29691 Z= 0.282 Chirality : 0.044 0.471 3549 Planarity : 0.003 0.034 3610 Dihedral : 5.922 56.496 4753 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.64 % Favored : 96.20 % Rotamer: Outliers : 1.86 % Allowed : 9.27 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.17), residues: 2497 helix: 2.25 (0.28), residues: 384 sheet: 0.85 (0.19), residues: 773 loop : -0.55 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 617 TYR 0.013 0.001 TYR K 100G PHE 0.022 0.001 PHE C 53 TRP 0.021 0.001 TRP L 36 HIS 0.003 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00229 (21616) covalent geometry : angle 0.53631 (29323) SS BOND : bond 0.00286 ( 37) SS BOND : angle 0.71472 ( 74) hydrogen bonds : bond 0.03618 ( 590) hydrogen bonds : angle 4.11964 ( 1521) link_ALPHA1-3 : bond 0.00924 ( 6) link_ALPHA1-3 : angle 2.16484 ( 18) link_ALPHA1-6 : bond 0.00379 ( 2) link_ALPHA1-6 : angle 1.49462 ( 6) link_BETA1-4 : bond 0.00482 ( 21) link_BETA1-4 : angle 1.70173 ( 63) link_BETA1-6 : bond 0.00411 ( 6) link_BETA1-6 : angle 1.24132 ( 18) link_NAG-ASN : bond 0.00322 ( 63) link_NAG-ASN : angle 2.35934 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 232 time to evaluate : 0.758 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: A 143 ARG cc_start: 0.8275 (ttm110) cc_final: 0.7666 (mmt90) REVERT: A 184 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.7720 (ptm) REVERT: K 72 ASP cc_start: 0.8252 (t0) cc_final: 0.7677 (t70) REVERT: G 103 ARG cc_start: 0.8261 (tpp-160) cc_final: 0.8023 (mtp85) REVERT: L 33 TYR cc_start: 0.7873 (m-80) cc_final: 0.7462 (m-10) REVERT: L 36 TRP cc_start: 0.7829 (m100) cc_final: 0.7578 (m100) REVERT: L 49 ILE cc_start: 0.8825 (mp) cc_final: 0.8372 (tt) REVERT: L 54 ARG cc_start: 0.7630 (mtp85) cc_final: 0.7360 (mtp85) REVERT: H 3 GLN cc_start: 0.7339 (pm20) cc_final: 0.7041 (pm20) REVERT: H 46 GLU cc_start: 0.7979 (tt0) cc_final: 0.7710 (tt0) REVERT: H 79 TYR cc_start: 0.7945 (m-10) cc_final: 0.7654 (m-80) REVERT: C 201 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8501 (mt) REVERT: C 207 LYS cc_start: 0.8766 (pttt) cc_final: 0.8352 (tmtt) REVERT: M 19 LYS cc_start: 0.8972 (tttt) cc_final: 0.8766 (tttp) REVERT: M 28 THR cc_start: 0.8939 (m) cc_final: 0.8733 (p) REVERT: M 72 ASP cc_start: 0.7657 (t0) cc_final: 0.7306 (t0) REVERT: M 83 ARG cc_start: 0.6939 (OUTLIER) cc_final: 0.6398 (mtm-85) REVERT: N 60 ASP cc_start: 0.8178 (p0) cc_final: 0.7127 (t0) REVERT: N 83 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7811 (mm-30) REVERT: N 94 ARG cc_start: 0.5924 (mpt180) cc_final: 0.4790 (tpt170) REVERT: E 430 ILE cc_start: 0.9031 (mp) cc_final: 0.8810 (mm) REVERT: E 475 MET cc_start: 0.8603 (mmt) cc_final: 0.8360 (tpp) REVERT: I 3 GLN cc_start: 0.8654 (mt0) cc_final: 0.8398 (mm-40) REVERT: I 82 MET cc_start: 0.7908 (mtm) cc_final: 0.7672 (mtm) REVERT: I 105 GLN cc_start: 0.8787 (pm20) cc_final: 0.8334 (mm-40) REVERT: J 31 ASN cc_start: 0.8873 (m-40) cc_final: 0.8491 (m110) REVERT: J 79 GLN cc_start: 0.6831 (mp10) cc_final: 0.6454 (mp10) outliers start: 41 outliers final: 24 residues processed: 255 average time/residue: 0.1548 time to fit residues: 59.1619 Evaluate side-chains 243 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 216 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain M residue 83 ARG Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain F residue 662 GLU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain J residue 27 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 74 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 201 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 220 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 217 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 6 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.087818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.063743 restraints weight = 51933.402| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.36 r_work: 0.2829 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.121 21751 Z= 0.231 Angle : 0.726 30.113 29691 Z= 0.350 Chirality : 0.049 0.779 3549 Planarity : 0.004 0.092 3610 Dihedral : 6.087 55.297 4751 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.53 % Favored : 95.27 % Rotamer: Outliers : 2.27 % Allowed : 8.95 % Favored : 88.77 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.17), residues: 2497 helix: 2.10 (0.28), residues: 384 sheet: 0.72 (0.19), residues: 773 loop : -0.64 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 90 TYR 0.015 0.001 TYR M 27 PHE 0.026 0.002 PHE C 53 TRP 0.014 0.001 TRP A 479 HIS 0.006 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00547 (21616) covalent geometry : angle 0.65898 (29323) SS BOND : bond 0.00484 ( 37) SS BOND : angle 1.03767 ( 74) hydrogen bonds : bond 0.04402 ( 590) hydrogen bonds : angle 4.39003 ( 1521) link_ALPHA1-3 : bond 0.00778 ( 6) link_ALPHA1-3 : angle 2.30229 ( 18) link_ALPHA1-6 : bond 0.00087 ( 2) link_ALPHA1-6 : angle 1.64912 ( 6) link_BETA1-4 : bond 0.00448 ( 21) link_BETA1-4 : angle 1.90677 ( 63) link_BETA1-6 : bond 0.00367 ( 6) link_BETA1-6 : angle 1.48152 ( 18) link_NAG-ASN : bond 0.00502 ( 63) link_NAG-ASN : angle 3.61427 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 218 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.7851 (ptm) REVERT: K 72 ASP cc_start: 0.8415 (t0) cc_final: 0.7795 (t70) REVERT: G 24 THR cc_start: 0.9153 (m) cc_final: 0.8669 (p) REVERT: G 102 THR cc_start: 0.8521 (m) cc_final: 0.8272 (p) REVERT: G 103 ARG cc_start: 0.8311 (tpp-160) cc_final: 0.8072 (mtp85) REVERT: L 33 TYR cc_start: 0.7929 (m-80) cc_final: 0.7508 (m-10) REVERT: L 49 ILE cc_start: 0.8811 (mp) cc_final: 0.8320 (tt) REVERT: L 54 ARG cc_start: 0.7657 (mtp85) cc_final: 0.7409 (mtp85) REVERT: L 62 ARG cc_start: 0.4765 (OUTLIER) cc_final: 0.4106 (tmm160) REVERT: L 84 PHE cc_start: 0.6964 (m-80) cc_final: 0.6645 (m-80) REVERT: L 90 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8106 (ttm-80) REVERT: H 3 GLN cc_start: 0.7436 (pm20) cc_final: 0.7106 (pm20) REVERT: H 46 GLU cc_start: 0.8019 (tt0) cc_final: 0.7763 (tt0) REVERT: H 79 TYR cc_start: 0.7999 (m-10) cc_final: 0.7676 (m-10) REVERT: C 201 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8555 (mt) REVERT: C 207 LYS cc_start: 0.8772 (pttt) cc_final: 0.8337 (tmtt) REVERT: M 19 LYS cc_start: 0.9066 (tttt) cc_final: 0.8845 (tttp) REVERT: M 72 ASP cc_start: 0.7706 (t0) cc_final: 0.7338 (t0) REVERT: M 83 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.6601 (mtm-85) REVERT: N 60 ASP cc_start: 0.8226 (p0) cc_final: 0.7273 (t0) REVERT: N 83 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7674 (mm-30) REVERT: N 94 ARG cc_start: 0.6121 (mpt180) cc_final: 0.4668 (tpt170) REVERT: E 475 MET cc_start: 0.8687 (mmt) cc_final: 0.8465 (tpp) REVERT: F 533 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8833 (mtp) REVERT: I 3 GLN cc_start: 0.8657 (mt0) cc_final: 0.8381 (mm-40) REVERT: I 82 MET cc_start: 0.7985 (mtm) cc_final: 0.7665 (mtm) REVERT: I 105 GLN cc_start: 0.8874 (pm20) cc_final: 0.8531 (mm-40) REVERT: J 31 ASN cc_start: 0.8875 (m-40) cc_final: 0.8486 (m110) outliers start: 50 outliers final: 30 residues processed: 250 average time/residue: 0.1524 time to fit residues: 57.3324 Evaluate side-chains 243 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 207 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 90 ARG Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain M residue 64 LYS Chi-restraints excluded: chain M residue 83 ARG Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 27 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 166 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 173 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 178 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 6 GLN E 85 HIS ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.089299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.065320 restraints weight = 51614.949| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.37 r_work: 0.2868 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 21751 Z= 0.130 Angle : 0.619 23.133 29691 Z= 0.302 Chirality : 0.046 0.680 3549 Planarity : 0.004 0.055 3610 Dihedral : 5.973 59.817 4751 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.56 % Favored : 96.24 % Rotamer: Outliers : 1.64 % Allowed : 10.09 % Favored : 88.27 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.17), residues: 2497 helix: 2.20 (0.28), residues: 384 sheet: 0.80 (0.19), residues: 773 loop : -0.63 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 90 TYR 0.022 0.001 TYR N 91 PHE 0.025 0.001 PHE C 53 TRP 0.039 0.001 TRP H 47 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00297 (21616) covalent geometry : angle 0.57199 (29323) SS BOND : bond 0.00388 ( 37) SS BOND : angle 0.89791 ( 74) hydrogen bonds : bond 0.03779 ( 590) hydrogen bonds : angle 4.21445 ( 1521) link_ALPHA1-3 : bond 0.00866 ( 6) link_ALPHA1-3 : angle 2.18401 ( 18) link_ALPHA1-6 : bond 0.00312 ( 2) link_ALPHA1-6 : angle 1.49901 ( 6) link_BETA1-4 : bond 0.00473 ( 21) link_BETA1-4 : angle 1.70111 ( 63) link_BETA1-6 : bond 0.00369 ( 6) link_BETA1-6 : angle 1.39543 ( 18) link_NAG-ASN : bond 0.00416 ( 63) link_NAG-ASN : angle 2.71202 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 218 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8199 (ttm110) cc_final: 0.7563 (mmt90) REVERT: A 184 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7834 (ptm) REVERT: K 72 ASP cc_start: 0.8311 (t0) cc_final: 0.7710 (t70) REVERT: G 24 THR cc_start: 0.9132 (m) cc_final: 0.8642 (p) REVERT: G 47 MET cc_start: 0.8418 (mmm) cc_final: 0.8063 (mmt) REVERT: G 102 THR cc_start: 0.8490 (m) cc_final: 0.8247 (p) REVERT: G 103 ARG cc_start: 0.8250 (tpp-160) cc_final: 0.8025 (mtp85) REVERT: L 33 TYR cc_start: 0.7872 (m-80) cc_final: 0.7464 (m-10) REVERT: L 49 ILE cc_start: 0.8845 (mp) cc_final: 0.8423 (tt) REVERT: L 62 ARG cc_start: 0.4723 (OUTLIER) cc_final: 0.4061 (tmm160) REVERT: L 72 PHE cc_start: 0.7166 (m-10) cc_final: 0.6698 (m-10) REVERT: L 84 PHE cc_start: 0.6989 (m-80) cc_final: 0.6669 (m-80) REVERT: H 3 GLN cc_start: 0.7395 (pm20) cc_final: 0.7076 (pm20) REVERT: H 46 GLU cc_start: 0.7915 (tt0) cc_final: 0.7669 (tt0) REVERT: H 79 TYR cc_start: 0.8037 (m-10) cc_final: 0.7776 (m-80) REVERT: C 201 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8468 (mt) REVERT: C 207 LYS cc_start: 0.8739 (pttt) cc_final: 0.8326 (tmtt) REVERT: M 19 LYS cc_start: 0.8973 (tttt) cc_final: 0.8756 (tttp) REVERT: M 28 THR cc_start: 0.9055 (m) cc_final: 0.8843 (m) REVERT: M 72 ASP cc_start: 0.7628 (t0) cc_final: 0.7261 (t0) REVERT: M 83 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6471 (mtm-85) REVERT: N 60 ASP cc_start: 0.8231 (p0) cc_final: 0.7230 (t0) REVERT: N 83 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7739 (mm-30) REVERT: N 94 ARG cc_start: 0.6011 (mpt180) cc_final: 0.4714 (tpt170) REVERT: F 533 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8766 (mtp) REVERT: I 3 GLN cc_start: 0.8641 (mt0) cc_final: 0.8353 (mm-40) REVERT: I 82 MET cc_start: 0.8027 (mtm) cc_final: 0.7748 (mtm) REVERT: I 105 GLN cc_start: 0.8767 (pm20) cc_final: 0.8442 (mm-40) REVERT: J 31 ASN cc_start: 0.8849 (m-40) cc_final: 0.8457 (m110) REVERT: J 79 GLN cc_start: 0.6828 (mp10) cc_final: 0.6352 (mp-120) outliers start: 36 outliers final: 26 residues processed: 240 average time/residue: 0.1610 time to fit residues: 57.9735 Evaluate side-chains 243 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 212 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain M residue 83 ARG Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain F residue 662 GLU Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain J residue 27 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 70 optimal weight: 0.5980 chunk 195 optimal weight: 0.9990 chunk 93 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 204 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.088528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.064494 restraints weight = 52373.094| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.38 r_work: 0.2847 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21751 Z= 0.178 Angle : 0.635 19.676 29691 Z= 0.309 Chirality : 0.049 0.922 3549 Planarity : 0.004 0.043 3610 Dihedral : 6.118 59.444 4751 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.25 % Favored : 95.55 % Rotamer: Outliers : 1.55 % Allowed : 10.27 % Favored : 88.18 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.17), residues: 2497 helix: 2.16 (0.28), residues: 384 sheet: 0.77 (0.19), residues: 773 loop : -0.66 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 54 TYR 0.015 0.001 TYR M 27 PHE 0.026 0.002 PHE C 53 TRP 0.056 0.002 TRP H 47 HIS 0.005 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00419 (21616) covalent geometry : angle 0.59313 (29323) SS BOND : bond 0.00413 ( 37) SS BOND : angle 0.92450 ( 74) hydrogen bonds : bond 0.04055 ( 590) hydrogen bonds : angle 4.26269 ( 1521) link_ALPHA1-3 : bond 0.00933 ( 6) link_ALPHA1-3 : angle 2.11408 ( 18) link_ALPHA1-6 : bond 0.00335 ( 2) link_ALPHA1-6 : angle 1.39096 ( 6) link_BETA1-4 : bond 0.00460 ( 21) link_BETA1-4 : angle 1.75625 ( 63) link_BETA1-6 : bond 0.00366 ( 6) link_BETA1-6 : angle 1.40460 ( 18) link_NAG-ASN : bond 0.00448 ( 63) link_NAG-ASN : angle 2.58201 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 217 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8237 (ttm110) cc_final: 0.7586 (mmt90) REVERT: A 184 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.7936 (ptm) REVERT: K 43 LYS cc_start: 0.8134 (mmtt) cc_final: 0.7902 (pttp) REVERT: K 72 ASP cc_start: 0.8348 (t0) cc_final: 0.7738 (t70) REVERT: G 24 THR cc_start: 0.9131 (m) cc_final: 0.8651 (p) REVERT: G 47 MET cc_start: 0.8428 (mmm) cc_final: 0.8059 (mmt) REVERT: G 103 ARG cc_start: 0.8257 (tpp-160) cc_final: 0.8044 (mtp85) REVERT: L 33 TYR cc_start: 0.7890 (m-80) cc_final: 0.7463 (m-10) REVERT: L 49 ILE cc_start: 0.8819 (mp) cc_final: 0.8363 (tt) REVERT: L 62 ARG cc_start: 0.4733 (OUTLIER) cc_final: 0.4096 (tmm160) REVERT: L 72 PHE cc_start: 0.7195 (m-10) cc_final: 0.6900 (m-10) REVERT: L 84 PHE cc_start: 0.7010 (m-80) cc_final: 0.6681 (m-80) REVERT: H 3 GLN cc_start: 0.7418 (pm20) cc_final: 0.7095 (pm20) REVERT: H 46 GLU cc_start: 0.7827 (tt0) cc_final: 0.7557 (tt0) REVERT: H 79 TYR cc_start: 0.8053 (m-10) cc_final: 0.7788 (m-10) REVERT: C 201 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8479 (mt) REVERT: C 207 LYS cc_start: 0.8740 (pttt) cc_final: 0.8328 (tmtt) REVERT: C 426 MET cc_start: 0.8226 (mmm) cc_final: 0.7890 (mtp) REVERT: D 624 ASP cc_start: 0.8658 (m-30) cc_final: 0.8346 (m-30) REVERT: M 19 LYS cc_start: 0.9036 (tttt) cc_final: 0.8826 (tttp) REVERT: M 28 THR cc_start: 0.9053 (m) cc_final: 0.8847 (m) REVERT: M 72 ASP cc_start: 0.7653 (t0) cc_final: 0.7282 (t0) REVERT: M 83 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.6550 (mtm-85) REVERT: N 60 ASP cc_start: 0.8285 (p0) cc_final: 0.7290 (t0) REVERT: N 83 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7828 (mm-30) REVERT: N 94 ARG cc_start: 0.6057 (mpt180) cc_final: 0.4519 (tpt170) REVERT: F 533 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8816 (mtp) REVERT: I 3 GLN cc_start: 0.8664 (mt0) cc_final: 0.8389 (mm-40) REVERT: I 82 MET cc_start: 0.8060 (mtm) cc_final: 0.7731 (mtm) REVERT: I 105 GLN cc_start: 0.8765 (pm20) cc_final: 0.8476 (mm-40) REVERT: J 31 ASN cc_start: 0.8859 (m-40) cc_final: 0.8641 (m110) REVERT: J 79 GLN cc_start: 0.6863 (mp10) cc_final: 0.6378 (mp-120) outliers start: 34 outliers final: 25 residues processed: 239 average time/residue: 0.1582 time to fit residues: 56.5839 Evaluate side-chains 241 residues out of total 2202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 211 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain M residue 83 ARG Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain J residue 27 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 233 optimal weight: 5.9990 chunk 214 optimal weight: 6.9990 chunk 200 optimal weight: 6.9990 chunk 211 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 177 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 6 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.087123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.062968 restraints weight = 52487.584| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.39 r_work: 0.2812 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 21751 Z= 0.264 Angle : 0.698 19.313 29691 Z= 0.339 Chirality : 0.048 0.366 3549 Planarity : 0.004 0.036 3610 Dihedral : 6.191 51.727 4751 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.93 % Favored : 94.87 % Rotamer: Outliers : 1.77 % Allowed : 10.27 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.17), residues: 2497 helix: 1.97 (0.28), residues: 384 sheet: 0.83 (0.20), residues: 728 loop : -0.88 (0.16), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 54 TYR 0.024 0.002 TYR N 91 PHE 0.025 0.002 PHE C 53 TRP 0.053 0.002 TRP H 47 HIS 0.006 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00628 (21616) covalent geometry : angle 0.65388 (29323) SS BOND : bond 0.00495 ( 37) SS BOND : angle 1.06998 ( 74) hydrogen bonds : bond 0.04616 ( 590) hydrogen bonds : angle 4.44768 ( 1521) link_ALPHA1-3 : bond 0.00801 ( 6) link_ALPHA1-3 : angle 2.19103 ( 18) link_ALPHA1-6 : bond 0.00078 ( 2) link_ALPHA1-6 : angle 1.68443 ( 6) link_BETA1-4 : bond 0.00456 ( 21) link_BETA1-4 : angle 1.90894 ( 63) link_BETA1-6 : bond 0.00344 ( 6) link_BETA1-6 : angle 1.53395 ( 18) link_NAG-ASN : bond 0.00467 ( 63) link_NAG-ASN : angle 2.77315 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4228.83 seconds wall clock time: 73 minutes 35.02 seconds (4415.02 seconds total)