Starting phenix.real_space_refine on Sun Feb 18 07:22:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t74_25733/02_2024/7t74_25733_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t74_25733/02_2024/7t74_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t74_25733/02_2024/7t74_25733.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t74_25733/02_2024/7t74_25733.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t74_25733/02_2024/7t74_25733_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t74_25733/02_2024/7t74_25733_updated.pdb" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Residue "B GLU 621": "OE1" <-> "OE2" Residue "K GLU 1": "OE1" <-> "OE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 97": "OE1" <-> "OE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 269": "OE1" <-> "OE2" Residue "M GLU 1": "OE1" <-> "OE2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: 11.10, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 8.96 Conformation dependent library (CDL) restraints added in 3.7 seconds 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... running ksdssp... Secondary structure from input PDB file: 58 helices and 52 sheets defined 18.5% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.96 Creating SS restraints... Processing helix chain 'A' and resid 100 through 116 removed outlier: 3.695A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 194 through 198 removed outlier: 3.817A pdb=" N ASN A 197 " --> pdb=" O ILE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.986A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 475 through 485 removed outlier: 5.052A pdb=" N TYR A 484 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS A 485 " --> pdb=" O GLU A 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 525 removed outlier: 4.426A pdb=" N GLY B 525 " --> pdb=" O GLY B 522 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 522 through 525' Processing helix chain 'B' and resid 528 through 541 removed outlier: 5.176A pdb=" N MET B 533 " --> pdb=" O GLY B 529 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU B 535 " --> pdb=" O ALA B 531 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N THR B 536 " --> pdb=" O SER B 532 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL B 537 " --> pdb=" O MET B 533 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN B 541 " --> pdb=" O VAL B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 595 Processing helix chain 'B' and resid 619 through 623 Processing helix chain 'B' and resid 628 through 634 Processing helix chain 'B' and resid 636 through 661 removed outlier: 5.087A pdb=" N GLN B 640 " --> pdb=" O ASN B 637 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 31 No H-bonds generated for 'chain 'K' and resid 29 through 31' Processing helix chain 'K' and resid 61 through 63 No H-bonds generated for 'chain 'K' and resid 61 through 63' Processing helix chain 'K' and resid 84 through 86 No H-bonds generated for 'chain 'K' and resid 84 through 86' Processing helix chain 'G' and resid 80 through 82 No H-bonds generated for 'chain 'G' and resid 80 through 82' Processing helix chain 'L' and resid 31 through 33 No H-bonds generated for 'chain 'L' and resid 31 through 33' Processing helix chain 'L' and resid 81 through 83 No H-bonds generated for 'chain 'L' and resid 81 through 83' Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 52B through 53 No H-bonds generated for 'chain 'H' and resid 52B through 53' 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 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' 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 140 through 142 No H-bonds generated for 'chain 'C' and resid 140 through 142' Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 335 through 351 removed outlier: 3.819A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 475 through 485 removed outlier: 5.097A pdb=" N TYR C 484 " --> pdb=" O SER C 481 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS C 485 " --> pdb=" O GLU C 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 525 removed outlier: 4.326A pdb=" N GLY D 525 " --> pdb=" O GLY D 522 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 522 through 525' Processing helix chain 'D' and resid 528 through 541 removed outlier: 5.182A pdb=" N MET D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU D 535 " --> pdb=" O ALA D 531 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR D 536 " --> pdb=" O SER D 532 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL D 537 " --> pdb=" O MET D 533 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN D 541 " --> pdb=" O VAL D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 595 Processing helix chain 'D' and resid 619 through 625 removed outlier: 3.673A pdb=" N ASP D 624 " --> pdb=" O SER D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 634 Processing helix chain 'D' and resid 636 through 660 removed outlier: 3.822A pdb=" N THR D 639 " --> pdb=" O SER D 636 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N GLN D 640 " --> pdb=" O ASN D 637 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR D 643 " --> pdb=" O GLN D 640 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 31 No H-bonds generated for 'chain 'M' and resid 29 through 31' Processing helix chain 'M' and resid 61 through 63 No H-bonds generated for 'chain 'M' and resid 61 through 63' Processing helix chain 'M' and resid 84 through 86 No H-bonds generated for 'chain 'M' and resid 84 through 86' Processing helix chain 'N' and resid 80 through 82 No H-bonds generated for 'chain 'N' and resid 80 through 82' Processing helix chain 'E' and resid 99 through 116 removed outlier: 3.730A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 125 No H-bonds generated for 'chain 'E' and resid 123 through 125' Processing helix chain 'E' and resid 140 through 142 No H-bonds generated for 'chain 'E' and resid 140 through 142' Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 194 through 196 No H-bonds generated for 'chain 'E' and resid 194 through 196' Processing helix chain 'E' and resid 335 through 351 removed outlier: 4.038A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 372 No H-bonds generated for 'chain 'E' and resid 369 through 372' Processing helix chain 'E' and resid 475 through 485 removed outlier: 5.063A pdb=" N TYR E 484 " --> pdb=" O SER E 481 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS E 485 " --> pdb=" O GLU E 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 528 through 541 removed outlier: 5.000A pdb=" N MET F 533 " --> pdb=" O GLY F 529 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N THR F 534 " --> pdb=" O ALA F 530 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU F 535 " --> pdb=" O ALA F 531 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR F 536 " --> pdb=" O SER F 532 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL F 537 " --> pdb=" O MET F 533 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN F 541 " --> pdb=" O VAL F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 595 Processing helix chain 'F' and resid 619 through 623 Processing helix chain 'F' and resid 628 through 634 Processing helix chain 'F' and resid 636 through 661 removed outlier: 4.541A pdb=" N GLN F 640 " --> pdb=" O ASN F 637 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE F 641 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR F 643 " --> pdb=" O GLN F 640 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 31 No H-bonds generated for 'chain 'I' and resid 29 through 31' Processing helix chain 'I' and resid 61 through 63 No H-bonds generated for 'chain 'I' and resid 61 through 63' Processing helix chain 'I' and resid 84 through 86 No H-bonds generated for 'chain 'I' and resid 84 through 86' Processing helix chain 'J' and resid 80 through 82 No H-bonds generated for 'chain 'J' and resid 80 through 82' Processing sheet with id= A, first strand: chain 'A' and resid 35 through 40 Processing sheet with id= B, 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= C, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= D, first strand: chain 'A' and resid 91 through 94 Processing sheet with id= E, first strand: chain 'A' and resid 130 through 133 Processing sheet with id= F, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= G, first strand: chain 'A' and resid 271 through 274 Processing sheet with id= H, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.066A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 301 through 308 removed outlier: 3.966A pdb=" N ASN A 301 " --> pdb=" O ILE A 323A" (cutoff:3.500A) removed outlier: 5.920A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'K' and resid 3 through 6 Processing sheet with id= K, first strand: chain 'K' and resid 107 through 109 removed outlier: 5.925A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'K' and resid 93 through 95 Processing sheet with id= M, first strand: chain 'G' and resid 19 through 24 Processing sheet with id= N, first strand: chain 'G' and resid 102 through 104 removed outlier: 3.562A pdb=" N ALA G 84 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLN G 37 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LEU G 46 " --> pdb=" O GLN G 37 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 89 through 91 Processing sheet with id= P, first strand: chain 'L' and resid 4 through 7 Processing sheet with id= Q, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.611A pdb=" N LYS L 103 " --> pdb=" O LEU L 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'L' and resid 86 through 91 removed outlier: 6.043A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= T, first strand: chain 'H' and resid 107 through 109 removed outlier: 5.894A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'H' and resid 93 through 100C removed outlier: 3.651A pdb=" N ASN H 100K" --> pdb=" O ASP H 100 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= W, 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= X, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= Y, first strand: chain 'C' and resid 91 through 94 Processing sheet with id= Z, first strand: chain 'C' and resid 130 through 133 Processing sheet with id= AA, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= AB, first strand: chain 'C' and resid 271 through 274 Processing sheet with id= AC, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.412A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 301 through 308 removed outlier: 4.072A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) removed outlier: 5.975A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'M' and resid 3 through 6 Processing sheet with id= AF, first strand: chain 'M' and resid 107 through 109 removed outlier: 6.014A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'M' and resid 93 through 95 Processing sheet with id= AH, first strand: chain 'N' and resid 11 through 13 removed outlier: 3.551A pdb=" N ALA N 84 " --> pdb=" O LEU N 104 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLN N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LEU N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'N' and resid 19 through 24 Processing sheet with id= AJ, first strand: chain 'N' and resid 89 through 91 Processing sheet with id= AK, first strand: chain 'E' and resid 35 through 40 Processing sheet with id= AL, 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= AM, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= AN, first strand: chain 'E' and resid 91 through 94 Processing sheet with id= AO, first strand: chain 'E' and resid 130 through 133 Processing sheet with id= AP, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.625A pdb=" N ALA E 433 " --> pdb=" O THR E 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= AP Processing sheet with id= AQ, first strand: chain 'E' and resid 271 through 273 Processing sheet with id= AR, first strand: chain 'E' and resid 374 through 378 removed outlier: 4.051A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'E' and resid 181 through 184 removed outlier: 5.603A pdb=" N ASN E 190 " --> pdb=" O MET E 184 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'E' and resid 301 through 308 removed outlier: 3.917A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 6.016A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'I' and resid 3 through 6 Processing sheet with id= AV, first strand: chain 'I' and resid 107 through 109 removed outlier: 5.977A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'I' and resid 93 through 95 Processing sheet with id= AX, first strand: chain 'J' and resid 19 through 24 Processing sheet with id= AY, first strand: chain 'J' and resid 102 through 104 removed outlier: 3.587A pdb=" N ALA J 84 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'J' and resid 89 through 91 734 hydrogen bonds defined for protein. 1752 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: 7.13 Time building geometry restraints manager: 9.59 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: 96.36 - 109.66: 5050 109.66 - 122.97: 21950 122.97 - 136.27: 2318 136.27 - 149.58: 0 149.58 - 162.89: 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: 6593 2.85 - 3.36: 18549 3.36 - 3.87: 35233 3.87 - 4.39: 41902 4.39 - 4.90: 67250 Nonbonded interactions: 169527 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 2.520 nonbonded pdb=" N ASP I 84 " pdb=" OD1 ASP I 84 " model vdw 2.363 2.520 nonbonded pdb=" N ASP M 84 " pdb=" OD1 ASP M 84 " model vdw 2.364 2.520 nonbonded pdb=" NZ LYS C 46 " pdb=" OD2 ASP D 632 " model vdw 2.390 2.520 ... (remaining 169522 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.100 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 57.600 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.210 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.190 ------------------------------------------------------------------------------- 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 : 0.022 0.152 21616 Z= 1.426 Angle : 1.772 38.326 29323 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.061 0.009 TRP C 96 HIS 0.012 0.003 HIS H 50 PHE 0.034 0.006 PHE E 353 TYR 0.049 0.007 TYR J 96 ARG 0.010 0.001 ARG K 71 *********************** 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 fitting. rotamer outliers: 14 poor density : 408 time to evaluate : 2.761 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: 0.4171 time to fit residues: 250.9052 Evaluate side-chains 226 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 221 time to evaluate : 2.565 ------------------------------------------------------------------------------- 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 209 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 118 optimal weight: 0.8980 chunk 144 optimal weight: 0.9990 chunk 225 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 79 GLN F 575 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21616 Z= 0.216 Angle : 0.682 16.322 29323 Z= 0.352 Chirality : 0.049 0.654 3549 Planarity : 0.005 0.056 3610 Dihedral : 9.229 80.612 4761 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.80 % Favored : 97.00 % Rotamer: Outliers : 1.95 % Allowed : 5.68 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.16), residues: 2497 helix: 0.93 (0.26), residues: 360 sheet: 0.85 (0.18), residues: 779 loop : -0.00 (0.16), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 479 HIS 0.009 0.001 HIS B 570 PHE 0.023 0.002 PHE A 53 TYR 0.021 0.002 TYR C 173 ARG 0.006 0.001 ARG D 588 *********************** 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 333 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 290 time to evaluate : 2.153 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: A 142 MET cc_start: 0.8151 (mmm) cc_final: 0.7759 (mmt) REVERT: G 95 THR cc_start: 0.8299 (p) cc_final: 0.8098 (p) REVERT: L 34 PHE cc_start: 0.5987 (t80) cc_final: 0.4551 (t80) REVERT: L 36 TRP cc_start: 0.5377 (m100) cc_final: 0.4930 (m100) REVERT: L 72 PHE cc_start: 0.4164 (m-80) cc_final: 0.2568 (m-10) REVERT: H 66 ARG cc_start: 0.6539 (ptp-170) cc_final: 0.6062 (ptm160) REVERT: H 93 MET cc_start: 0.5761 (OUTLIER) cc_final: 0.5015 (ppp) REVERT: C 207 LYS cc_start: 0.8515 (pttt) cc_final: 0.8282 (tmtt) REVERT: D 624 ASP cc_start: 0.8485 (m-30) cc_final: 0.8258 (m-30) REVERT: M 28 THR cc_start: 0.9196 (m) cc_final: 0.8903 (p) REVERT: N 94 ARG cc_start: 0.5926 (mpt180) cc_final: 0.4836 (mmt180) REVERT: J 31 ASN cc_start: 0.8339 (m-40) cc_final: 0.8034 (m110) REVERT: J 60 ASP cc_start: 0.8462 (p0) cc_final: 0.8233 (p0) REVERT: J 94 ARG cc_start: 0.5867 (mpt180) cc_final: 0.5002 (mtp85) outliers start: 43 outliers final: 21 residues processed: 315 average time/residue: 0.4075 time to fit residues: 188.5494 Evaluate side-chains 235 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 213 time to evaluate : 2.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 81 ASP 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 C residue 368 ASP Chi-restraints excluded: chain M residue 6 GLU Chi-restraints excluded: chain N residue 60 ASP 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 201 ILE 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 Chi-restraints excluded: chain J residue 70 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 153 optimal weight: 0.7980 chunk 62 optimal weight: 8.9990 chunk 225 optimal weight: 2.9990 chunk 243 optimal weight: 8.9990 chunk 200 optimal weight: 6.9990 chunk 223 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 180 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 21616 Z= 0.436 Angle : 0.713 14.749 29323 Z= 0.366 Chirality : 0.051 0.804 3549 Planarity : 0.005 0.080 3610 Dihedral : 7.991 72.844 4758 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.84 % Favored : 96.04 % Rotamer: Outliers : 2.68 % Allowed : 6.45 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.16), residues: 2497 helix: 0.62 (0.27), residues: 363 sheet: 0.68 (0.18), residues: 785 loop : -0.38 (0.16), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 47 HIS 0.007 0.001 HIS E 105 PHE 0.029 0.003 PHE L 96 TYR 0.018 0.002 TYR E 484 ARG 0.009 0.001 ARG M 83 *********************** 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 283 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 224 time to evaluate : 2.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.8271 (mmm) cc_final: 0.7915 (mmt) REVERT: A 184 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7518 (ttp) REVERT: G 95 THR cc_start: 0.8443 (p) cc_final: 0.8242 (p) REVERT: L 36 TRP cc_start: 0.5007 (m100) cc_final: 0.4732 (m100) REVERT: L 72 PHE cc_start: 0.2907 (m-80) cc_final: 0.2475 (m-10) REVERT: H 93 MET cc_start: 0.5227 (ppp) cc_final: 0.4997 (ppp) REVERT: C 207 LYS cc_start: 0.8429 (pttt) cc_final: 0.8195 (tmtt) REVERT: D 624 ASP cc_start: 0.8605 (m-30) cc_final: 0.8194 (m-30) REVERT: M 19 LYS cc_start: 0.8823 (tttt) cc_final: 0.8597 (tttp) REVERT: M 28 THR cc_start: 0.9312 (m) cc_final: 0.9087 (p) REVERT: N 94 ARG cc_start: 0.6062 (mpt180) cc_final: 0.5333 (tpt170) REVERT: F 571 TRP cc_start: 0.7140 (t-100) cc_final: 0.6896 (t60) REVERT: J 83 GLU cc_start: 0.7068 (pp20) cc_final: 0.6644 (pt0) REVERT: J 94 ARG cc_start: 0.6522 (mpt180) cc_final: 0.5067 (mtp85) outliers start: 59 outliers final: 38 residues processed: 262 average time/residue: 0.3979 time to fit residues: 157.1973 Evaluate side-chains 234 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 195 time to evaluate : 2.549 ------------------------------------------------------------------------------- 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 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 434 MET Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain H residue 2 VAL 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 195 ASN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain M residue 6 GLU Chi-restraints excluded: chain M residue 105 GLN Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 201 ILE 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 588 ARG Chi-restraints excluded: chain I residue 61 ASP 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 0.9990 chunk 169 optimal weight: 9.9990 chunk 117 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 226 optimal weight: 9.9990 chunk 239 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 214 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 6 GLN M 3 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 17 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 21616 Z= 0.305 Angle : 0.629 13.365 29323 Z= 0.320 Chirality : 0.049 0.884 3549 Planarity : 0.004 0.035 3610 Dihedral : 7.194 68.179 4755 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.84 % Favored : 96.08 % Rotamer: Outliers : 2.36 % Allowed : 7.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.16), residues: 2497 helix: 0.58 (0.27), residues: 363 sheet: 0.72 (0.19), residues: 734 loop : -0.63 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP H 47 HIS 0.004 0.001 HIS C 105 PHE 0.018 0.002 PHE C 53 TYR 0.019 0.001 TYR L 50 ARG 0.010 0.001 ARG A 143 *********************** 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 277 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 225 time to evaluate : 2.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.8312 (mmm) cc_final: 0.7986 (mmt) REVERT: A 184 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7614 (ttp) REVERT: C 207 LYS cc_start: 0.8432 (pttt) cc_final: 0.8190 (tmtt) REVERT: D 624 ASP cc_start: 0.8521 (m-30) cc_final: 0.8145 (m-30) REVERT: M 19 LYS cc_start: 0.8880 (tttt) cc_final: 0.8676 (tttp) REVERT: M 28 THR cc_start: 0.9305 (m) cc_final: 0.9092 (p) REVERT: N 60 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.6733 (t0) REVERT: N 94 ARG cc_start: 0.6200 (mpt180) cc_final: 0.4876 (mmt180) REVERT: F 533 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8331 (mtp) REVERT: F 571 TRP cc_start: 0.7112 (t-100) cc_final: 0.6903 (t60) REVERT: J 31 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.8287 (m110) REVERT: J 79 GLN cc_start: 0.8291 (mp10) cc_final: 0.8006 (mp10) REVERT: J 83 GLU cc_start: 0.7345 (pp20) cc_final: 0.6780 (pt0) REVERT: J 94 ARG cc_start: 0.6591 (mpt180) cc_final: 0.5220 (mtp85) outliers start: 52 outliers final: 29 residues processed: 251 average time/residue: 0.3621 time to fit residues: 137.1123 Evaluate side-chains 238 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 205 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 434 MET Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 100 ASP 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 172 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain M residue 6 GLU Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 17 GLN Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 434 MET 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 61 ASP Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 31 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 0.0970 chunk 136 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21616 Z= 0.239 Angle : 0.578 12.306 29323 Z= 0.296 Chirality : 0.045 0.367 3549 Planarity : 0.004 0.033 3610 Dihedral : 6.696 64.968 4755 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.92 % Favored : 95.96 % Rotamer: Outliers : 1.91 % Allowed : 9.09 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.16), residues: 2497 helix: 0.80 (0.28), residues: 345 sheet: 0.70 (0.19), residues: 756 loop : -0.63 (0.16), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP H 47 HIS 0.004 0.001 HIS C 105 PHE 0.026 0.002 PHE C 53 TYR 0.021 0.001 TYR N 91 ARG 0.005 0.000 ARG L 54 *********************** 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 260 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 218 time to evaluate : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 207 LYS cc_start: 0.8521 (pttt) cc_final: 0.8285 (tmtt) REVERT: D 624 ASP cc_start: 0.8527 (m-30) cc_final: 0.8162 (m-30) REVERT: M 28 THR cc_start: 0.9313 (m) cc_final: 0.9061 (p) REVERT: N 60 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.6724 (t0) REVERT: N 94 ARG cc_start: 0.6236 (mpt180) cc_final: 0.5306 (tpt170) REVERT: F 571 TRP cc_start: 0.7097 (t-100) cc_final: 0.6890 (t60) REVERT: J 31 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.8276 (m110) REVERT: J 83 GLU cc_start: 0.7308 (pp20) cc_final: 0.6732 (pt0) REVERT: J 94 ARG cc_start: 0.6594 (mpt180) cc_final: 0.5145 (mtp85) outliers start: 42 outliers final: 33 residues processed: 238 average time/residue: 0.3654 time to fit residues: 131.5534 Evaluate side-chains 238 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 203 time to evaluate : 2.317 ------------------------------------------------------------------------------- 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 138 ILE Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain M residue 6 GLU Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain F residue 588 ARG Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 17 GLN Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 31 ASN Chi-restraints excluded: chain J residue 52 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 239 optimal weight: 2.9990 chunk 199 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 21616 Z= 0.393 Angle : 0.637 11.262 29323 Z= 0.325 Chirality : 0.047 0.413 3549 Planarity : 0.004 0.034 3610 Dihedral : 6.719 64.928 4755 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.61 % Favored : 95.23 % Rotamer: Outliers : 2.55 % Allowed : 9.05 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.16), residues: 2497 helix: 0.68 (0.28), residues: 345 sheet: 0.63 (0.19), residues: 755 loop : -0.77 (0.16), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 36 HIS 0.005 0.001 HIS C 105 PHE 0.024 0.002 PHE C 53 TYR 0.030 0.002 TYR L 50 ARG 0.007 0.001 ARG H 38 *********************** 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 265 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 209 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7728 (ttp) REVERT: H 78 LEU cc_start: 0.6743 (tp) cc_final: 0.6467 (tp) REVERT: C 207 LYS cc_start: 0.8433 (pttt) cc_final: 0.8203 (tmtt) REVERT: M 28 THR cc_start: 0.9345 (m) cc_final: 0.9101 (p) REVERT: N 60 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.6788 (t0) REVERT: N 94 ARG cc_start: 0.6396 (mpt180) cc_final: 0.5250 (tpt170) REVERT: E 430 ILE cc_start: 0.8816 (mp) cc_final: 0.8612 (mm) REVERT: F 533 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8411 (mtp) REVERT: F 571 TRP cc_start: 0.7076 (t-100) cc_final: 0.6819 (t60) REVERT: J 31 ASN cc_start: 0.8526 (OUTLIER) cc_final: 0.8293 (m110) REVERT: J 83 GLU cc_start: 0.7380 (pp20) cc_final: 0.6785 (pt0) REVERT: J 94 ARG cc_start: 0.6786 (mpt180) cc_final: 0.5749 (mmt180) outliers start: 56 outliers final: 42 residues processed: 236 average time/residue: 0.3689 time to fit residues: 130.2646 Evaluate side-chains 247 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 201 time to evaluate : 2.473 ------------------------------------------------------------------------------- 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 434 MET Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 100 ASP 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 265 LEU Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain M residue 6 GLU Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 17 GLN Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 434 MET 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 7 THR Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 31 ASN Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 70 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 175 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 239 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 HIS ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21616 Z= 0.235 Angle : 0.565 10.929 29323 Z= 0.290 Chirality : 0.045 0.398 3549 Planarity : 0.004 0.034 3610 Dihedral : 6.314 61.172 4755 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.92 % Favored : 95.92 % Rotamer: Outliers : 2.09 % Allowed : 9.82 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.17), residues: 2497 helix: 0.81 (0.28), residues: 345 sheet: 0.72 (0.20), residues: 736 loop : -0.81 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP L 36 HIS 0.004 0.001 HIS C 105 PHE 0.024 0.001 PHE C 53 TYR 0.025 0.001 TYR L 50 ARG 0.004 0.000 ARG H 64 *********************** 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 261 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 215 time to evaluate : 2.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7738 (ttp) REVERT: L 62 ARG cc_start: 0.5611 (mtm-85) cc_final: 0.5344 (mtp-110) REVERT: C 207 LYS cc_start: 0.8494 (pttt) cc_final: 0.8266 (tmtt) REVERT: N 60 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.6878 (t0) REVERT: N 83 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7954 (mm-30) REVERT: N 94 ARG cc_start: 0.6250 (mpt180) cc_final: 0.5182 (tpt170) REVERT: E 430 ILE cc_start: 0.8857 (mp) cc_final: 0.8649 (mm) REVERT: F 533 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8399 (mtp) REVERT: F 571 TRP cc_start: 0.7117 (t-100) cc_final: 0.6883 (t60) REVERT: J 31 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.8254 (m110) REVERT: J 79 GLN cc_start: 0.8373 (mp10) cc_final: 0.8162 (mp10) REVERT: J 83 GLU cc_start: 0.7433 (pp20) cc_final: 0.6919 (pt0) REVERT: J 94 ARG cc_start: 0.6736 (mpt180) cc_final: 0.5251 (mtp85) outliers start: 46 outliers final: 33 residues processed: 238 average time/residue: 0.3736 time to fit residues: 133.3093 Evaluate side-chains 244 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 207 time to evaluate : 2.481 ------------------------------------------------------------------------------- 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 7 THR Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 100 ASP 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 265 LEU Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain M residue 6 GLU Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 434 MET 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 61 ASP Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 31 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 142 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 217 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 3 GLN M 3 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.144 21616 Z= 0.340 Angle : 0.659 18.069 29323 Z= 0.343 Chirality : 0.048 0.603 3549 Planarity : 0.005 0.094 3610 Dihedral : 6.343 59.502 4755 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.81 % Favored : 95.03 % Rotamer: Outliers : 2.27 % Allowed : 9.64 % Favored : 88.09 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.17), residues: 2497 helix: 0.73 (0.28), residues: 345 sheet: 0.66 (0.19), residues: 743 loop : -0.90 (0.16), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP L 36 HIS 0.005 0.001 HIS C 105 PHE 0.022 0.002 PHE C 53 TYR 0.027 0.001 TYR L 50 ARG 0.005 0.000 ARG L 40 *********************** 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 261 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 211 time to evaluate : 2.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7729 (ttp) REVERT: L 62 ARG cc_start: 0.5684 (mtm-85) cc_final: 0.5409 (mtp-110) REVERT: C 201 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8787 (mt) REVERT: C 207 LYS cc_start: 0.8514 (pttt) cc_final: 0.8271 (tmtt) REVERT: M 83 ARG cc_start: 0.8319 (mpp80) cc_final: 0.8004 (mtp180) REVERT: N 94 ARG cc_start: 0.6265 (mpt180) cc_final: 0.5115 (tpt170) REVERT: F 533 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8441 (mtp) REVERT: F 571 TRP cc_start: 0.7058 (t-100) cc_final: 0.6808 (t60) REVERT: F 625 ASN cc_start: 0.7303 (OUTLIER) cc_final: 0.7061 (m110) REVERT: J 31 ASN cc_start: 0.8549 (OUTLIER) cc_final: 0.8322 (m110) REVERT: J 83 GLU cc_start: 0.7469 (pp20) cc_final: 0.6951 (pt0) REVERT: J 94 ARG cc_start: 0.6876 (mpt180) cc_final: 0.5042 (mtp85) outliers start: 50 outliers final: 39 residues processed: 236 average time/residue: 0.3763 time to fit residues: 131.7402 Evaluate side-chains 248 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 204 time to evaluate : 2.331 ------------------------------------------------------------------------------- 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 434 MET Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 34 MET 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 G residue 107 LEU Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 100 ASP 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 6 GLU Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 434 MET 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 625 ASN Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 31 ASN Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 70 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 0.7980 chunk 208 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 201 optimal weight: 6.9990 chunk 210 optimal weight: 4.9990 chunk 221 optimal weight: 0.9980 chunk 146 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21616 Z= 0.177 Angle : 0.566 11.475 29323 Z= 0.292 Chirality : 0.046 0.737 3549 Planarity : 0.004 0.048 3610 Dihedral : 5.960 53.388 4755 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.88 % Favored : 95.96 % Rotamer: Outliers : 1.95 % Allowed : 10.23 % Favored : 87.82 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.17), residues: 2497 helix: 0.90 (0.29), residues: 345 sheet: 0.74 (0.20), residues: 745 loop : -0.83 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP L 36 HIS 0.004 0.001 HIS C 105 PHE 0.024 0.001 PHE C 53 TYR 0.033 0.001 TYR L 50 ARG 0.006 0.000 ARG L 40 *********************** 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 266 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 223 time to evaluate : 2.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7726 (ttp) REVERT: K 43 LYS cc_start: 0.7566 (mmtm) cc_final: 0.7253 (pttm) REVERT: L 62 ARG cc_start: 0.5750 (mtm-85) cc_final: 0.5472 (mtp-110) REVERT: C 201 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8740 (mt) REVERT: C 207 LYS cc_start: 0.8479 (pttt) cc_final: 0.8258 (tmtt) REVERT: M 83 ARG cc_start: 0.8131 (mpp80) cc_final: 0.7778 (mtm-85) REVERT: N 60 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.6913 (t0) REVERT: N 83 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7921 (mm-30) REVERT: N 94 ARG cc_start: 0.6132 (mpt180) cc_final: 0.5095 (tpt170) REVERT: F 571 TRP cc_start: 0.7050 (t-100) cc_final: 0.6831 (t60) REVERT: J 31 ASN cc_start: 0.8493 (m-40) cc_final: 0.8283 (m110) REVERT: J 83 GLU cc_start: 0.7386 (pp20) cc_final: 0.6950 (pt0) REVERT: J 94 ARG cc_start: 0.6712 (mpt180) cc_final: 0.5251 (mtp85) outliers start: 43 outliers final: 33 residues processed: 248 average time/residue: 0.3688 time to fit residues: 136.7207 Evaluate side-chains 242 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 206 time to evaluate : 2.381 ------------------------------------------------------------------------------- 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 7 THR Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 100 ASP 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 636 SER Chi-restraints excluded: chain M residue 6 GLU Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 70 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 163 optimal weight: 0.5980 chunk 247 optimal weight: 5.9990 chunk 227 optimal weight: 0.0000 chunk 196 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 151 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 overall best weight: 2.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 21616 Z= 0.300 Angle : 0.608 12.719 29323 Z= 0.311 Chirality : 0.047 0.548 3549 Planarity : 0.004 0.042 3610 Dihedral : 6.129 54.762 4755 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.89 % Favored : 94.99 % Rotamer: Outliers : 2.00 % Allowed : 10.45 % Favored : 87.55 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.17), residues: 2497 helix: 0.85 (0.29), residues: 345 sheet: 0.71 (0.20), residues: 740 loop : -0.91 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP L 36 HIS 0.004 0.001 HIS C 105 PHE 0.022 0.002 PHE C 53 TYR 0.027 0.001 TYR L 50 ARG 0.005 0.000 ARG L 40 ********************** 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 253 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 209 time to evaluate : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7776 (ttp) REVERT: L 62 ARG cc_start: 0.5780 (mtm-85) cc_final: 0.5495 (mtp-110) REVERT: H 46 GLU cc_start: 0.7175 (pt0) cc_final: 0.6889 (pm20) REVERT: C 207 LYS cc_start: 0.8485 (pttt) cc_final: 0.8260 (tmtt) REVERT: M 83 ARG cc_start: 0.8269 (mpp80) cc_final: 0.7962 (mtp180) REVERT: N 60 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.6999 (t0) REVERT: N 83 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7965 (mm-30) REVERT: N 94 ARG cc_start: 0.6260 (mpt180) cc_final: 0.5101 (tpt170) REVERT: F 533 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8417 (mtp) REVERT: F 571 TRP cc_start: 0.7093 (t-100) cc_final: 0.6853 (t60) REVERT: J 31 ASN cc_start: 0.8512 (OUTLIER) cc_final: 0.8302 (m110) REVERT: J 83 GLU cc_start: 0.7368 (pp20) cc_final: 0.6923 (pt0) REVERT: J 94 ARG cc_start: 0.6856 (mpt180) cc_final: 0.5336 (tpt170) outliers start: 44 outliers final: 35 residues processed: 233 average time/residue: 0.3746 time to fit residues: 130.3228 Evaluate side-chains 242 residues out of total 2202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 203 time to evaluate : 2.352 ------------------------------------------------------------------------------- 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 434 MET Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 100 ASP 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 265 LEU Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain M residue 6 GLU Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 31 ASN Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 70 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 202 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 173 optimal weight: 0.5980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 3 GLN ** 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 = 0.3466 r_free = 0.3466 target = 0.089492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.066179 restraints weight = 51112.579| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.28 r_work: 0.2872 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 21616 Z= 0.187 Angle : 0.567 10.978 29323 Z= 0.293 Chirality : 0.045 0.472 3549 Planarity : 0.004 0.036 3610 Dihedral : 5.753 55.359 4755 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.16 % Favored : 95.71 % Rotamer: Outliers : 1.68 % Allowed : 10.82 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.17), residues: 2497 helix: 0.91 (0.29), residues: 345 sheet: 0.74 (0.20), residues: 740 loop : -0.88 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP L 36 HIS 0.004 0.001 HIS C 105 PHE 0.023 0.001 PHE C 53 TYR 0.029 0.001 TYR L 50 ARG 0.006 0.000 ARG H 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4323.62 seconds wall clock time: 80 minutes 28.73 seconds (4828.73 seconds total)