Starting phenix.real_space_refine on Wed Sep 17 21:18:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cj7_45624/09_2025/9cj7_45624.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cj7_45624/09_2025/9cj7_45624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cj7_45624/09_2025/9cj7_45624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cj7_45624/09_2025/9cj7_45624.map" model { file = "/net/cci-nas-00/data/ceres_data/9cj7_45624/09_2025/9cj7_45624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cj7_45624/09_2025/9cj7_45624.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.031 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 103 5.16 5 C 7165 2.51 5 N 1800 2.21 5 O 2433 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11501 Number of models: 1 Model: "" Number of chains: 38 Chain: "C" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1548 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 189} Chain breaks: 1 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1536 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 188} Chain breaks: 1 Chain: "B" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1549 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 190} Chain breaks: 1 Chain: "c" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1306 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 4, 'TRANS': 156} Chain: "a" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1256 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 3, 'TRANS': 150} Chain breaks: 1 Chain: "b" Number of atoms: 1269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1269 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 1 Chain: "H" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1081 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'TYS:plan-2': 3} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 802 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" 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: "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 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: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "J" 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: "K" 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: "M" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "N" 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: "O" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 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: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "d" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.42, per 1000 atoms: 0.30 Number of scatterers: 11501 At special positions: 0 Unit cell: (94.05, 95.095, 128.535, 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 103 16.00 O 2433 8.00 N 1800 7.00 C 7165 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 360 " distance=2.03 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.03 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.03 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.02 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.03 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.02 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.03 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.03 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN d 4 " - " MAN d 5 " " MAN f 4 " - " MAN f 5 " " MAN h 4 " - " MAN h 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA M 3 " - " MAN M 4 " " BMA d 3 " - " MAN d 4 " " BMA f 3 " - " MAN f 4 " " BMA h 3 " - " MAN h 4 " ALPHA1-6 " BMA D 3 " - " MAN D 5 " " BMA M 3 " - " MAN M 5 " " BMA d 3 " - " MAN d 6 " " BMA f 3 " - " MAN f 6 " " BMA h 3 " - " MAN h 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " BETA1-6 " NAG D 1 " - " FUC D 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG I 1 " - " FUC I 3 " " NAG M 1 " - " FUC M 6 " " NAG W 1 " - " FUC W 4 " " NAG Z 1 " - " FUC Z 4 " NAG-ASN " NAG D 1 " - " ASN C 119 " " NAG E 1 " - " ASN C 79 " " NAG F 1 " - " ASN C 89 " " NAG G 1 " - " ASN C 99 " " NAG I 1 " - " ASN C 109 " " NAG J 1 " - " ASN C 167 " " NAG K 1 " - " ASN C 224 " " NAG M 1 " - " ASN A 119 " " NAG N 1 " - " ASN A 79 " " NAG O 1 " - " ASN A 89 " " NAG P 1 " - " ASN A 99 " " NAG Q 1 " - " ASN A 109 " " NAG R 1 " - " ASN A 167 " " NAG S 1 " - " ASN A 224 " " NAG T 1 " - " ASN B 79 " " NAG U 1 " - " ASN B 89 " " NAG V 1 " - " ASN B 99 " " NAG W 1 " - " ASN B 109 " " NAG X 1 " - " ASN B 167 " " NAG Y 1 " - " ASN B 224 " " NAG Z 1 " - " ASN B 119 " " NAG a 701 " - " ASN a 395 " " NAG a 702 " - " ASN a 390 " " NAG b 701 " - " ASN b 390 " " NAG b 702 " - " ASN b 395 " " NAG c 701 " - " ASN c 395 " " NAG c 702 " - " ASN c 390 " " NAG d 1 " - " ASN c 365 " " NAG e 1 " - " ASN c 373 " " NAG f 1 " - " ASN a 365 " " NAG g 1 " - " ASN a 373 " " NAG h 1 " - " ASN b 365 " " NAG i 1 " - " ASN b 373 " Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 560.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2432 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 17 sheets defined 36.8% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'C' and resid 74 through 79 Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.694A pdb=" N ALA C 123 " --> pdb=" O ASN C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.878A pdb=" N LYS C 161 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 198 through 202 removed outlier: 3.734A pdb=" N ILE C 201 " --> pdb=" O GLY C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 247 removed outlier: 4.010A pdb=" N SER C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN C 247 " --> pdb=" O GLY C 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.839A pdb=" N THR A 77 " --> pdb=" O ASN A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.549A pdb=" N GLY A 160 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 238 through 247 removed outlier: 4.040A pdb=" N SER A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN A 247 " --> pdb=" O GLY A 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 81 removed outlier: 3.787A pdb=" N THR B 77 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N MET B 80 " --> pdb=" O THR B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.774A pdb=" N ALA B 123 " --> pdb=" O ASN B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 143 Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 182 through 195 removed outlier: 3.832A pdb=" N GLY B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 238 through 246 removed outlier: 4.088A pdb=" N SER B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing helix chain 'c' and resid 281 through 285 Processing helix chain 'c' and resid 294 through 299 Processing helix chain 'c' and resid 300 through 303 Processing helix chain 'c' and resid 307 through 326 Processing helix chain 'c' and resid 334 through 345 removed outlier: 6.042A pdb=" N ASN c 342 " --> pdb=" O ASN c 338 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ALA c 343 " --> pdb=" O LYS c 339 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.609A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 399 through 420 removed outlier: 3.713A pdb=" N ILE c 403 " --> pdb=" O PHE c 399 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN c 416 " --> pdb=" O THR c 412 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS c 417 " --> pdb=" O GLU c 413 " (cutoff:3.500A) Processing helix chain 'a' and resid 281 through 285 Processing helix chain 'a' and resid 294 through 299 Processing helix chain 'a' and resid 300 through 303 Processing helix chain 'a' and resid 307 through 326 Processing helix chain 'a' and resid 334 through 345 removed outlier: 5.762A pdb=" N ASN a 342 " --> pdb=" O ASN a 338 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ALA a 343 " --> pdb=" O LYS a 339 " (cutoff:3.500A) Processing helix chain 'a' and resid 346 through 359 removed outlier: 3.632A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 396 through 398 No H-bonds generated for 'chain 'a' and resid 396 through 398' Processing helix chain 'a' and resid 399 through 420 removed outlier: 3.506A pdb=" N GLN a 405 " --> pdb=" O ASP a 401 " (cutoff:3.500A) Processing helix chain 'b' and resid 294 through 299 Processing helix chain 'b' and resid 300 through 303 Processing helix chain 'b' and resid 307 through 326 removed outlier: 3.575A pdb=" N GLN b 324 " --> pdb=" O LYS b 320 " (cutoff:3.500A) Processing helix chain 'b' and resid 335 through 345 removed outlier: 5.746A pdb=" N ASN b 342 " --> pdb=" O ASN b 338 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ALA b 343 " --> pdb=" O LYS b 339 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 359 removed outlier: 3.586A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 395 through 398 Processing helix chain 'b' and resid 399 through 420 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 99 through 100F Processing helix chain 'H' and resid 100F through 100K Processing helix chain 'L' and resid 26 through 30C removed outlier: 4.123A pdb=" N ILE L 30 " --> pdb=" O ASN L 27 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N GLY L 30A" --> pdb=" O SER L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AA2, first strand: chain 'C' and resid 84 through 87 Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 62 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 87 removed outlier: 3.566A pdb=" N GLY A 102 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AA6, first strand: chain 'B' and resid 84 through 87 removed outlier: 4.030A pdb=" N THR B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'c' and resid 278 through 280 Processing sheet with id=AA8, first strand: chain 'c' and resid 388 through 389 Processing sheet with id=AA9, first strand: chain 'a' and resid 278 through 280 Processing sheet with id=AB1, first strand: chain 'a' and resid 388 through 389 Processing sheet with id=AB2, first strand: chain 'b' and resid 278 through 280 Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.329A pdb=" N TRP H 35 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASN H 50 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB6, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.761A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP L 35 " --> pdb=" O MET L 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.761A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 19 through 24 459 hydrogen bonds defined for protein. 1164 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: 1.97 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3074 1.34 - 1.46: 2927 1.46 - 1.58: 5571 1.58 - 1.70: 3 1.70 - 1.82: 154 Bond restraints: 11729 Sorted by residual: bond pdb=" N SER b 381 " pdb=" CA SER b 381 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.17e-02 7.31e+03 9.21e+00 bond pdb=" N ASN a 365 " pdb=" CA ASN a 365 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.32e-02 5.74e+03 6.76e+00 bond pdb=" N TYR c 366 " pdb=" CA TYR c 366 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.66e+00 bond pdb=" N ASN c 365 " pdb=" CA ASN c 365 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.33e+00 bond pdb=" N ASN C 79 " pdb=" CA ASN C 79 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.18e+00 ... (remaining 11724 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 14401 1.47 - 2.94: 1146 2.94 - 4.41: 273 4.41 - 5.88: 62 5.88 - 7.35: 11 Bond angle restraints: 15893 Sorted by residual: angle pdb=" N ASN a 365 " pdb=" CA ASN a 365 " pdb=" C ASN a 365 " ideal model delta sigma weight residual 113.16 108.13 5.03 1.24e+00 6.50e-01 1.64e+01 angle pdb=" N ASN b 365 " pdb=" CA ASN b 365 " pdb=" C ASN b 365 " ideal model delta sigma weight residual 113.30 108.32 4.98 1.34e+00 5.57e-01 1.38e+01 angle pdb=" CA ASN B 119 " pdb=" C ASN B 119 " pdb=" O ASN B 119 " ideal model delta sigma weight residual 122.44 117.59 4.85 1.32e+00 5.74e-01 1.35e+01 angle pdb=" CA ASN A 119 " pdb=" C ASN A 119 " pdb=" O ASN A 119 " ideal model delta sigma weight residual 122.64 118.25 4.39 1.25e+00 6.40e-01 1.23e+01 angle pdb=" N SER B 237 " pdb=" CA SER B 237 " pdb=" C SER B 237 " ideal model delta sigma weight residual 108.11 112.34 -4.23 1.29e+00 6.01e-01 1.08e+01 ... (remaining 15888 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.30: 7653 21.30 - 42.60: 291 42.60 - 63.90: 35 63.90 - 85.19: 83 85.19 - 106.49: 45 Dihedral angle restraints: 8107 sinusoidal: 4318 harmonic: 3789 Sorted by residual: dihedral pdb=" CB CYS C 207 " pdb=" SG CYS C 207 " pdb=" SG CYS c 360 " pdb=" CB CYS c 360 " ideal model delta sinusoidal sigma weight residual -86.00 -142.77 56.77 1 1.00e+01 1.00e-02 4.34e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 132.50 -39.50 1 1.00e+01 1.00e-02 2.19e+01 dihedral pdb=" CA GLN a 324 " pdb=" C GLN a 324 " pdb=" N ARG a 325 " pdb=" CA ARG a 325 " ideal model delta harmonic sigma weight residual -180.00 -161.18 -18.82 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 8104 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.211: 1995 0.211 - 0.423: 18 0.423 - 0.634: 1 0.634 - 0.845: 0 0.845 - 1.056: 1 Chirality restraints: 2015 Sorted by residual: chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.77e+02 chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.36e+02 chirality pdb=" C1 BMA N 3 " pdb=" O4 NAG N 2 " pdb=" C2 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.26e+02 ... (remaining 2012 not shown) Planarity restraints: 1907 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 1 " -0.317 2.00e-02 2.50e+03 2.67e-01 8.94e+02 pdb=" C7 NAG T 1 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG T 1 " -0.186 2.00e-02 2.50e+03 pdb=" N2 NAG T 1 " 0.463 2.00e-02 2.50e+03 pdb=" O7 NAG T 1 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " -0.282 2.00e-02 2.50e+03 2.36e-01 6.95e+02 pdb=" C7 NAG E 1 " 0.074 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " -0.183 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " 0.399 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " 0.280 2.00e-02 2.50e+03 2.33e-01 6.78e+02 pdb=" C7 NAG N 1 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " 0.186 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " -0.391 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " 0.000 2.00e-02 2.50e+03 ... (remaining 1904 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 226 2.67 - 3.22: 10954 3.22 - 3.78: 17866 3.78 - 4.34: 25408 4.34 - 4.90: 40790 Nonbonded interactions: 95244 Sorted by model distance: nonbonded pdb=" OG1 THR A 81 " pdb=" OD1 ASN a 319 " model vdw 2.107 3.040 nonbonded pdb=" OG1 THR C 81 " pdb=" OD1 ASN c 319 " model vdw 2.131 3.040 nonbonded pdb=" OG1 THR B 81 " pdb=" OD1 ASN b 319 " model vdw 2.134 3.040 nonbonded pdb=" O GLY C 197 " pdb=" OG SER C 234 " model vdw 2.164 3.040 nonbonded pdb=" OH TYR A 62 " pdb=" OE2 GLU a 396 " model vdw 2.190 3.040 ... (remaining 95239 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 60 through 171 or resid 179 through 259)) selection = (chain 'C' and (resid 60 through 171 or resid 179 through 259)) } ncs_group { reference = (chain 'D' and resid 1 through 5) selection = (chain 'M' and resid 1 through 5) selection = (chain 'd' and resid 1 through 5) selection = (chain 'f' and resid 1 through 5) selection = (chain 'h' and resid 1 through 5) } ncs_group { reference = (chain 'E' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'e' selection = chain 'g' selection = chain 'i' } ncs_group { reference = chain 'W' selection = chain 'Z' } ncs_group { reference = chain 'a' selection = (chain 'b' and (resid 260 through 268 or resid 276 through 702)) selection = (chain 'c' and (resid 260 through 268 or resid 276 through 702)) } 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: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.660 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 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 : 0.006 0.092 11841 Z= 0.297 Angle : 0.989 14.907 16206 Z= 0.495 Chirality : 0.059 1.056 2015 Planarity : 0.015 0.267 1874 Dihedral : 16.203 106.492 5606 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.23), residues: 1269 helix: 0.44 (0.28), residues: 346 sheet: -0.03 (0.35), residues: 194 loop : -0.28 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 250 TYR 0.019 0.002 TYR b 366 PHE 0.023 0.002 PHE c 399 TRP 0.013 0.002 TRP H 47 HIS 0.007 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00598 (11729) covalent geometry : angle 0.94980 (15893) SS BOND : bond 0.00451 ( 23) SS BOND : angle 1.54400 ( 46) hydrogen bonds : bond 0.17578 ( 452) hydrogen bonds : angle 6.58555 ( 1164) link_ALPHA1-2 : bond 0.00523 ( 3) link_ALPHA1-2 : angle 2.70012 ( 9) link_ALPHA1-3 : bond 0.00482 ( 5) link_ALPHA1-3 : angle 1.88930 ( 15) link_ALPHA1-6 : bond 0.00397 ( 5) link_ALPHA1-6 : angle 0.64082 ( 15) link_BETA1-4 : bond 0.00520 ( 38) link_BETA1-4 : angle 1.99205 ( 114) link_BETA1-6 : bond 0.00745 ( 5) link_BETA1-6 : angle 1.62917 ( 15) link_NAG-ASN : bond 0.01686 ( 33) link_NAG-ASN : angle 2.84710 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: c 405 GLN cc_start: 0.8055 (tm130) cc_final: 0.7679 (tm-30) REVERT: a 308 GLU cc_start: 0.8394 (mp0) cc_final: 0.8095 (mt-10) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.8262 time to fit residues: 223.5547 Evaluate side-chains 178 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.0770 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 HIS C 93 HIS A 90 ASN A 93 HIS ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 HIS B 149 GLN c 342 ASN ** c 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 335 GLN a 405 GLN a 416 GLN b 354 HIS H 50 ASN L 60 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.077016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.061201 restraints weight = 27124.895| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.49 r_work: 0.2873 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11841 Z= 0.159 Angle : 0.728 9.548 16206 Z= 0.344 Chirality : 0.045 0.334 2015 Planarity : 0.004 0.053 1874 Dihedral : 12.610 83.310 3209 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.99 % Allowed : 10.15 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.23), residues: 1269 helix: 0.99 (0.29), residues: 350 sheet: 0.57 (0.34), residues: 217 loop : -0.21 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 250 TYR 0.019 0.001 TYR b 419 PHE 0.013 0.001 PHE c 399 TRP 0.009 0.001 TRP b 283 HIS 0.007 0.001 HIS C 179 Details of bonding type rmsd covalent geometry : bond 0.00355 (11729) covalent geometry : angle 0.67754 (15893) SS BOND : bond 0.00488 ( 23) SS BOND : angle 0.87098 ( 46) hydrogen bonds : bond 0.04597 ( 452) hydrogen bonds : angle 5.16023 ( 1164) link_ALPHA1-2 : bond 0.00704 ( 3) link_ALPHA1-2 : angle 2.46376 ( 9) link_ALPHA1-3 : bond 0.01213 ( 5) link_ALPHA1-3 : angle 2.72069 ( 15) link_ALPHA1-6 : bond 0.00473 ( 5) link_ALPHA1-6 : angle 1.93216 ( 15) link_BETA1-4 : bond 0.00631 ( 38) link_BETA1-4 : angle 2.07845 ( 114) link_BETA1-6 : bond 0.00195 ( 5) link_BETA1-6 : angle 1.78130 ( 15) link_NAG-ASN : bond 0.00253 ( 33) link_NAG-ASN : angle 2.22093 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 125 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7980 (ttpt) REVERT: C 156 ASP cc_start: 0.7966 (t0) cc_final: 0.7619 (t0) REVERT: A 214 MET cc_start: 0.6746 (mmm) cc_final: 0.6518 (mmm) REVERT: B 122 ASP cc_start: 0.8246 (t0) cc_final: 0.8044 (t0) REVERT: B 192 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8274 (ttt) REVERT: B 211 ASP cc_start: 0.9066 (m-30) cc_final: 0.8809 (m-30) REVERT: c 331 GLN cc_start: 0.7709 (mp10) cc_final: 0.7455 (mp10) REVERT: c 405 GLN cc_start: 0.8430 (tm130) cc_final: 0.7966 (tm-30) REVERT: c 408 ASP cc_start: 0.8959 (m-30) cc_final: 0.8749 (m-30) REVERT: c 420 MET cc_start: 0.7406 (mpp) cc_final: 0.6700 (mpt) REVERT: a 308 GLU cc_start: 0.8683 (mp0) cc_final: 0.7803 (mt-10) REVERT: a 323 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8253 (mp) REVERT: a 396 GLU cc_start: 0.8347 (tt0) cc_final: 0.8106 (tt0) REVERT: a 401 ASP cc_start: 0.8262 (m-30) cc_final: 0.7724 (t0) REVERT: a 416 GLN cc_start: 0.7997 (tp40) cc_final: 0.7728 (tp-100) REVERT: b 287 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8094 (tm-30) REVERT: b 332 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.7440 (mtm) REVERT: H 100 ASP cc_start: 0.8146 (m-30) cc_final: 0.7933 (m-30) REVERT: L 17 GLN cc_start: 0.8220 (pt0) cc_final: 0.7651 (pt0) outliers start: 23 outliers final: 4 residues processed: 194 average time/residue: 0.7619 time to fit residues: 157.7452 Evaluate side-chains 181 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 173 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain a residue 323 ILE Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain b residue 332 MET Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 50 ASN Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 65 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 54 optimal weight: 0.0030 chunk 119 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 335 GLN a 405 GLN L 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.077365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.061395 restraints weight = 27445.693| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.56 r_work: 0.2865 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11841 Z= 0.139 Angle : 0.663 9.686 16206 Z= 0.311 Chirality : 0.043 0.311 2015 Planarity : 0.004 0.039 1874 Dihedral : 10.113 77.456 3209 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.34 % Allowed : 10.93 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.23), residues: 1269 helix: 1.19 (0.28), residues: 357 sheet: 0.83 (0.36), residues: 208 loop : -0.34 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 379 TYR 0.023 0.001 TYR b 419 PHE 0.012 0.001 PHE H 78 TRP 0.008 0.001 TRP b 283 HIS 0.005 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00306 (11729) covalent geometry : angle 0.61572 (15893) SS BOND : bond 0.00485 ( 23) SS BOND : angle 0.92647 ( 46) hydrogen bonds : bond 0.04029 ( 452) hydrogen bonds : angle 4.84173 ( 1164) link_ALPHA1-2 : bond 0.00596 ( 3) link_ALPHA1-2 : angle 2.55054 ( 9) link_ALPHA1-3 : bond 0.01173 ( 5) link_ALPHA1-3 : angle 2.50539 ( 15) link_ALPHA1-6 : bond 0.00712 ( 5) link_ALPHA1-6 : angle 1.78626 ( 15) link_BETA1-4 : bond 0.00568 ( 38) link_BETA1-4 : angle 1.88577 ( 114) link_BETA1-6 : bond 0.00190 ( 5) link_BETA1-6 : angle 1.52743 ( 15) link_NAG-ASN : bond 0.00218 ( 33) link_NAG-ASN : angle 2.03854 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8170 (mmtp) REVERT: C 125 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7976 (ttpt) REVERT: C 156 ASP cc_start: 0.7935 (t0) cc_final: 0.7608 (t0) REVERT: C 189 GLN cc_start: 0.8808 (mt0) cc_final: 0.8592 (mt0) REVERT: B 192 MET cc_start: 0.8624 (ttt) cc_final: 0.8305 (ttt) REVERT: B 211 ASP cc_start: 0.9107 (m-30) cc_final: 0.8859 (m-30) REVERT: B 214 MET cc_start: 0.7669 (mmm) cc_final: 0.7466 (mmt) REVERT: B 228 GLU cc_start: 0.8475 (tp30) cc_final: 0.8263 (tp30) REVERT: c 331 GLN cc_start: 0.7860 (mp10) cc_final: 0.7520 (mp10) REVERT: c 405 GLN cc_start: 0.8538 (tm130) cc_final: 0.8063 (tm-30) REVERT: c 420 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.6717 (mpt) REVERT: a 289 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7549 (tp30) REVERT: a 303 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8384 (mm-30) REVERT: a 308 GLU cc_start: 0.8714 (mp0) cc_final: 0.7809 (mt-10) REVERT: a 401 ASP cc_start: 0.8206 (m-30) cc_final: 0.7652 (t0) REVERT: b 287 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8071 (tm-30) REVERT: b 306 ASP cc_start: 0.9044 (p0) cc_final: 0.8756 (p0) REVERT: b 408 ASP cc_start: 0.8540 (m-30) cc_final: 0.8249 (m-30) REVERT: H 75 LYS cc_start: 0.9135 (mtmm) cc_final: 0.8583 (mtmm) REVERT: H 100 ASP cc_start: 0.8213 (m-30) cc_final: 0.7952 (t0) REVERT: L 17 GLN cc_start: 0.8194 (pt0) cc_final: 0.7607 (pt0) outliers start: 27 outliers final: 7 residues processed: 200 average time/residue: 0.7824 time to fit residues: 166.6815 Evaluate side-chains 187 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 177 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain c residue 420 MET Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain b residue 298 VAL Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 10 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 58 optimal weight: 0.0030 chunk 50 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 95 optimal weight: 0.2980 chunk 65 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 405 GLN H 50 ASN L 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.076299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.059869 restraints weight = 27587.411| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.72 r_work: 0.2843 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11841 Z= 0.119 Angle : 0.636 9.583 16206 Z= 0.299 Chirality : 0.042 0.286 2015 Planarity : 0.004 0.033 1874 Dihedral : 8.884 77.045 3209 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.60 % Allowed : 11.19 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.23), residues: 1269 helix: 1.34 (0.29), residues: 357 sheet: 0.98 (0.35), residues: 212 loop : -0.33 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 379 TYR 0.022 0.001 TYR b 419 PHE 0.012 0.001 PHE H 78 TRP 0.007 0.001 TRP b 283 HIS 0.003 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00257 (11729) covalent geometry : angle 0.58802 (15893) SS BOND : bond 0.00385 ( 23) SS BOND : angle 1.61631 ( 46) hydrogen bonds : bond 0.03565 ( 452) hydrogen bonds : angle 4.69140 ( 1164) link_ALPHA1-2 : bond 0.00615 ( 3) link_ALPHA1-2 : angle 2.50018 ( 9) link_ALPHA1-3 : bond 0.01139 ( 5) link_ALPHA1-3 : angle 2.56345 ( 15) link_ALPHA1-6 : bond 0.00802 ( 5) link_ALPHA1-6 : angle 1.85060 ( 15) link_BETA1-4 : bond 0.00547 ( 38) link_BETA1-4 : angle 1.72350 ( 114) link_BETA1-6 : bond 0.00210 ( 5) link_BETA1-6 : angle 1.43691 ( 15) link_NAG-ASN : bond 0.00204 ( 33) link_NAG-ASN : angle 1.90282 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8308 (mmtp) REVERT: C 125 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8129 (ttpt) REVERT: C 156 ASP cc_start: 0.8153 (t0) cc_final: 0.7761 (t0) REVERT: A 251 ASP cc_start: 0.7575 (m-30) cc_final: 0.6926 (m-30) REVERT: B 192 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8405 (ttt) REVERT: B 211 ASP cc_start: 0.9054 (m-30) cc_final: 0.8815 (m-30) REVERT: c 317 ASP cc_start: 0.8368 (t70) cc_final: 0.8130 (t70) REVERT: c 331 GLN cc_start: 0.7989 (mp10) cc_final: 0.7635 (mp10) REVERT: c 405 GLN cc_start: 0.8544 (tm130) cc_final: 0.8006 (tm-30) REVERT: c 417 LYS cc_start: 0.8830 (tmmt) cc_final: 0.8589 (tmmt) REVERT: c 420 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.6654 (mpt) REVERT: a 286 ILE cc_start: 0.8727 (mm) cc_final: 0.8507 (mm) REVERT: a 289 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7518 (tp30) REVERT: a 303 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8411 (mm-30) REVERT: a 308 GLU cc_start: 0.8872 (mp0) cc_final: 0.7985 (mt-10) REVERT: b 306 ASP cc_start: 0.9198 (p0) cc_final: 0.8916 (p0) REVERT: b 317 ASP cc_start: 0.8896 (t70) cc_final: 0.8683 (t0) REVERT: H 100 ASP cc_start: 0.8152 (m-30) cc_final: 0.7886 (t0) REVERT: L 17 GLN cc_start: 0.8442 (pt0) cc_final: 0.7939 (pt0) outliers start: 30 outliers final: 8 residues processed: 198 average time/residue: 0.7848 time to fit residues: 165.6119 Evaluate side-chains 189 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 177 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain c residue 420 MET Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain b residue 401 ASP Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 54 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN c 305 HIS c 342 ASN c 409 ASN a 335 GLN a 405 GLN H 50 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.074829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.058061 restraints weight = 27492.133| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 3.57 r_work: 0.2794 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 11841 Z= 0.247 Angle : 0.720 9.506 16206 Z= 0.339 Chirality : 0.045 0.356 2015 Planarity : 0.004 0.038 1874 Dihedral : 8.754 68.705 3209 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.38 % Allowed : 11.54 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.23), residues: 1269 helix: 1.21 (0.28), residues: 356 sheet: 0.59 (0.34), residues: 230 loop : -0.29 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 256 TYR 0.019 0.002 TYR b 419 PHE 0.014 0.002 PHE H 78 TRP 0.011 0.001 TRP a 386 HIS 0.008 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00573 (11729) covalent geometry : angle 0.67445 (15893) SS BOND : bond 0.00543 ( 23) SS BOND : angle 1.57389 ( 46) hydrogen bonds : bond 0.04163 ( 452) hydrogen bonds : angle 4.80469 ( 1164) link_ALPHA1-2 : bond 0.00280 ( 3) link_ALPHA1-2 : angle 2.67556 ( 9) link_ALPHA1-3 : bond 0.00974 ( 5) link_ALPHA1-3 : angle 2.55898 ( 15) link_ALPHA1-6 : bond 0.00690 ( 5) link_ALPHA1-6 : angle 1.84677 ( 15) link_BETA1-4 : bond 0.00439 ( 38) link_BETA1-4 : angle 1.78921 ( 114) link_BETA1-6 : bond 0.00329 ( 5) link_BETA1-6 : angle 1.76391 ( 15) link_NAG-ASN : bond 0.00368 ( 33) link_NAG-ASN : angle 2.10209 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8229 (mmtp) REVERT: C 125 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7971 (ttpt) REVERT: C 156 ASP cc_start: 0.8159 (t0) cc_final: 0.7855 (t0) REVERT: B 192 MET cc_start: 0.8710 (ttt) cc_final: 0.8350 (ttt) REVERT: c 331 GLN cc_start: 0.7913 (mp10) cc_final: 0.7567 (mp10) REVERT: c 405 GLN cc_start: 0.8584 (tm130) cc_final: 0.8070 (tm-30) REVERT: c 420 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.6641 (mpt) REVERT: a 289 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7552 (tp30) REVERT: a 303 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8400 (mm-30) REVERT: a 308 GLU cc_start: 0.8705 (mp0) cc_final: 0.7897 (mt-10) REVERT: a 396 GLU cc_start: 0.8648 (tt0) cc_final: 0.8038 (tm-30) REVERT: b 306 ASP cc_start: 0.9128 (p0) cc_final: 0.8898 (p0) REVERT: b 409 ASN cc_start: 0.8440 (m-40) cc_final: 0.8226 (m-40) REVERT: b 413 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8571 (pt0) REVERT: H 33 TYR cc_start: 0.8829 (m-10) cc_final: 0.8538 (m-10) REVERT: H 75 LYS cc_start: 0.9085 (mtmm) cc_final: 0.8574 (mtmm) REVERT: H 100 ASP cc_start: 0.8283 (m-30) cc_final: 0.8040 (t0) REVERT: L 17 GLN cc_start: 0.8387 (pt0) cc_final: 0.7943 (pt0) REVERT: L 45 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8156 (ttpp) outliers start: 39 outliers final: 15 residues processed: 193 average time/residue: 0.7980 time to fit residues: 163.9299 Evaluate side-chains 190 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain c residue 420 MET Chi-restraints excluded: chain a residue 298 VAL Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain b residue 298 VAL Chi-restraints excluded: chain b residue 401 ASP Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain b residue 413 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 50 ASN Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 64 optimal weight: 0.0270 chunk 106 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 overall best weight: 1.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN c 342 ASN a 405 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.074552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.057532 restraints weight = 27619.286| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.78 r_work: 0.2775 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11841 Z= 0.150 Angle : 0.667 10.189 16206 Z= 0.312 Chirality : 0.042 0.286 2015 Planarity : 0.003 0.033 1874 Dihedral : 8.426 68.794 3209 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.69 % Allowed : 12.92 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.23), residues: 1269 helix: 1.31 (0.29), residues: 357 sheet: 0.55 (0.35), residues: 230 loop : -0.30 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG c 379 TYR 0.016 0.001 TYR b 419 PHE 0.013 0.001 PHE H 78 TRP 0.010 0.001 TRP b 283 HIS 0.004 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00341 (11729) covalent geometry : angle 0.62581 (15893) SS BOND : bond 0.00415 ( 23) SS BOND : angle 1.08960 ( 46) hydrogen bonds : bond 0.03718 ( 452) hydrogen bonds : angle 4.68553 ( 1164) link_ALPHA1-2 : bond 0.00384 ( 3) link_ALPHA1-2 : angle 2.66336 ( 9) link_ALPHA1-3 : bond 0.01065 ( 5) link_ALPHA1-3 : angle 2.52481 ( 15) link_ALPHA1-6 : bond 0.00816 ( 5) link_ALPHA1-6 : angle 1.83827 ( 15) link_BETA1-4 : bond 0.00474 ( 38) link_BETA1-4 : angle 1.63586 ( 114) link_BETA1-6 : bond 0.00142 ( 5) link_BETA1-6 : angle 1.51570 ( 15) link_NAG-ASN : bond 0.00226 ( 33) link_NAG-ASN : angle 1.95960 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 0.447 Fit side-chains REVERT: C 116 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8353 (mmtp) REVERT: B 192 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8466 (ttt) REVERT: c 331 GLN cc_start: 0.8012 (mp10) cc_final: 0.7671 (mp10) REVERT: c 405 GLN cc_start: 0.8598 (tm130) cc_final: 0.8213 (tm-30) REVERT: c 420 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.6729 (mpt) REVERT: a 303 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8413 (mm-30) REVERT: a 308 GLU cc_start: 0.8890 (mp0) cc_final: 0.8058 (mt-10) REVERT: a 396 GLU cc_start: 0.8683 (tt0) cc_final: 0.8071 (tm-30) REVERT: b 306 ASP cc_start: 0.9158 (p0) cc_final: 0.8921 (p0) REVERT: b 317 ASP cc_start: 0.8921 (t70) cc_final: 0.8704 (t0) REVERT: b 413 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8588 (pt0) REVERT: H 16 GLU cc_start: 0.7649 (mp0) cc_final: 0.7410 (mp0) REVERT: H 33 TYR cc_start: 0.8861 (m-10) cc_final: 0.8524 (m-10) REVERT: L 17 GLN cc_start: 0.8564 (pt0) cc_final: 0.8108 (pt0) outliers start: 31 outliers final: 13 residues processed: 184 average time/residue: 0.7614 time to fit residues: 149.6149 Evaluate side-chains 183 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain c residue 420 MET Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain b residue 298 VAL Chi-restraints excluded: chain b residue 401 ASP Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain b residue 413 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 50 ASN Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 115 optimal weight: 0.9980 chunk 108 optimal weight: 0.5980 chunk 11 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 121 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN a 405 GLN H 50 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.075176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.058442 restraints weight = 27474.697| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.73 r_work: 0.2806 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11841 Z= 0.123 Angle : 0.640 10.733 16206 Z= 0.301 Chirality : 0.042 0.283 2015 Planarity : 0.003 0.031 1874 Dihedral : 8.124 78.297 3209 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.34 % Allowed : 14.05 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.23), residues: 1269 helix: 1.44 (0.29), residues: 356 sheet: 0.90 (0.36), residues: 216 loop : -0.34 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG b 379 TYR 0.014 0.001 TYR a 366 PHE 0.012 0.001 PHE H 78 TRP 0.008 0.001 TRP b 283 HIS 0.003 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00275 (11729) covalent geometry : angle 0.60103 (15893) SS BOND : bond 0.00362 ( 23) SS BOND : angle 0.92774 ( 46) hydrogen bonds : bond 0.03471 ( 452) hydrogen bonds : angle 4.59088 ( 1164) link_ALPHA1-2 : bond 0.00429 ( 3) link_ALPHA1-2 : angle 2.57949 ( 9) link_ALPHA1-3 : bond 0.01102 ( 5) link_ALPHA1-3 : angle 2.53289 ( 15) link_ALPHA1-6 : bond 0.00865 ( 5) link_ALPHA1-6 : angle 1.79923 ( 15) link_BETA1-4 : bond 0.00496 ( 38) link_BETA1-4 : angle 1.56326 ( 114) link_BETA1-6 : bond 0.00172 ( 5) link_BETA1-6 : angle 1.42398 ( 15) link_NAG-ASN : bond 0.00194 ( 33) link_NAG-ASN : angle 1.86764 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 178 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: B 192 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8427 (ttt) REVERT: c 331 GLN cc_start: 0.8041 (mp10) cc_final: 0.7657 (mp10) REVERT: c 405 GLN cc_start: 0.8611 (tm130) cc_final: 0.7984 (tm-30) REVERT: c 420 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.6810 (mpt) REVERT: a 286 ILE cc_start: 0.8833 (mm) cc_final: 0.8577 (mm) REVERT: a 303 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8389 (mm-30) REVERT: a 308 GLU cc_start: 0.8910 (mp0) cc_final: 0.8149 (mt-10) REVERT: a 396 GLU cc_start: 0.8659 (tt0) cc_final: 0.8150 (tm-30) REVERT: b 306 ASP cc_start: 0.9147 (p0) cc_final: 0.8936 (p0) REVERT: b 317 ASP cc_start: 0.8918 (t70) cc_final: 0.8713 (t0) REVERT: b 379 ARG cc_start: 0.8463 (ttm-80) cc_final: 0.7866 (mmm-85) REVERT: H 16 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7370 (mp0) REVERT: H 75 LYS cc_start: 0.9067 (mtmm) cc_final: 0.8621 (mtmm) REVERT: L 17 GLN cc_start: 0.8597 (pt0) cc_final: 0.8148 (pt0) outliers start: 27 outliers final: 13 residues processed: 186 average time/residue: 0.7957 time to fit residues: 157.6285 Evaluate side-chains 186 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain c residue 420 MET Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain b residue 401 ASP Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain b residue 413 GLU Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 51 optimal weight: 7.9990 chunk 107 optimal weight: 0.3980 chunk 74 optimal weight: 8.9990 chunk 112 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN a 335 GLN a 405 GLN H 50 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.074805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.058515 restraints weight = 27487.486| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.65 r_work: 0.2809 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11841 Z= 0.129 Angle : 0.650 11.536 16206 Z= 0.303 Chirality : 0.042 0.286 2015 Planarity : 0.004 0.100 1874 Dihedral : 7.852 82.893 3209 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.52 % Allowed : 14.31 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.23), residues: 1269 helix: 1.45 (0.29), residues: 354 sheet: 1.01 (0.35), residues: 224 loop : -0.31 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG c 379 TYR 0.025 0.001 TYR c 419 PHE 0.012 0.001 PHE H 78 TRP 0.009 0.001 TRP b 283 HIS 0.003 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00292 (11729) covalent geometry : angle 0.61285 (15893) SS BOND : bond 0.00374 ( 23) SS BOND : angle 0.91325 ( 46) hydrogen bonds : bond 0.03437 ( 452) hydrogen bonds : angle 4.53360 ( 1164) link_ALPHA1-2 : bond 0.00415 ( 3) link_ALPHA1-2 : angle 2.51180 ( 9) link_ALPHA1-3 : bond 0.01104 ( 5) link_ALPHA1-3 : angle 2.53594 ( 15) link_ALPHA1-6 : bond 0.00886 ( 5) link_ALPHA1-6 : angle 1.76746 ( 15) link_BETA1-4 : bond 0.00487 ( 38) link_BETA1-4 : angle 1.53231 ( 114) link_BETA1-6 : bond 0.00153 ( 5) link_BETA1-6 : angle 1.43349 ( 15) link_NAG-ASN : bond 0.00195 ( 33) link_NAG-ASN : angle 1.83110 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8320 (mmtp) REVERT: B 76 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8389 (tt0) REVERT: B 192 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8412 (ttt) REVERT: B 247 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7620 (tp40) REVERT: c 331 GLN cc_start: 0.7973 (mp10) cc_final: 0.7384 (pm20) REVERT: c 420 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.6841 (mpt) REVERT: a 286 ILE cc_start: 0.8787 (mm) cc_final: 0.8547 (mm) REVERT: a 303 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8421 (mm-30) REVERT: a 308 GLU cc_start: 0.8895 (mp0) cc_final: 0.8049 (mt-10) REVERT: a 413 GLU cc_start: 0.8416 (tt0) cc_final: 0.7947 (tm-30) REVERT: b 306 ASP cc_start: 0.9128 (p0) cc_final: 0.8898 (p0) REVERT: b 317 ASP cc_start: 0.8909 (t70) cc_final: 0.8701 (t0) REVERT: b 404 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8400 (mm-30) REVERT: b 408 ASP cc_start: 0.8682 (m-30) cc_final: 0.8479 (m-30) REVERT: b 413 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8552 (pt0) REVERT: H 16 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: H 33 TYR cc_start: 0.8818 (m-10) cc_final: 0.8609 (m-10) REVERT: H 75 LYS cc_start: 0.9096 (mtmm) cc_final: 0.8729 (mtmm) REVERT: L 17 GLN cc_start: 0.8601 (pt0) cc_final: 0.8161 (pt0) outliers start: 29 outliers final: 13 residues processed: 187 average time/residue: 0.8097 time to fit residues: 160.9550 Evaluate side-chains 192 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain c residue 410 MET Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain c residue 420 MET Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain b residue 298 VAL Chi-restraints excluded: chain b residue 401 ASP Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain b residue 413 GLU Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 50 ASN Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 51 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN a 335 GLN a 405 GLN H 1 GLN H 50 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.075018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.058415 restraints weight = 27208.400| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 3.70 r_work: 0.2801 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11841 Z= 0.139 Angle : 0.657 12.142 16206 Z= 0.307 Chirality : 0.042 0.286 2015 Planarity : 0.004 0.046 1874 Dihedral : 7.712 84.918 3209 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.25 % Allowed : 14.92 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.23), residues: 1269 helix: 1.49 (0.29), residues: 355 sheet: 1.10 (0.37), residues: 210 loop : -0.28 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG c 379 TYR 0.018 0.001 TYR a 366 PHE 0.012 0.001 PHE H 78 TRP 0.007 0.001 TRP b 283 HIS 0.003 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00316 (11729) covalent geometry : angle 0.62156 (15893) SS BOND : bond 0.00388 ( 23) SS BOND : angle 0.87789 ( 46) hydrogen bonds : bond 0.03418 ( 452) hydrogen bonds : angle 4.53613 ( 1164) link_ALPHA1-2 : bond 0.00402 ( 3) link_ALPHA1-2 : angle 2.48373 ( 9) link_ALPHA1-3 : bond 0.01089 ( 5) link_ALPHA1-3 : angle 2.52516 ( 15) link_ALPHA1-6 : bond 0.00884 ( 5) link_ALPHA1-6 : angle 1.74807 ( 15) link_BETA1-4 : bond 0.00473 ( 38) link_BETA1-4 : angle 1.52565 ( 114) link_BETA1-6 : bond 0.00138 ( 5) link_BETA1-6 : angle 1.44881 ( 15) link_NAG-ASN : bond 0.00200 ( 33) link_NAG-ASN : angle 1.82912 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8330 (mmtp) REVERT: B 76 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8535 (tt0) REVERT: B 192 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8411 (ttt) REVERT: B 247 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7615 (tp40) REVERT: c 331 GLN cc_start: 0.8031 (mp10) cc_final: 0.7452 (pm20) REVERT: c 405 GLN cc_start: 0.8854 (tm-30) cc_final: 0.8061 (tm-30) REVERT: c 420 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.6882 (mpt) REVERT: a 286 ILE cc_start: 0.8807 (mm) cc_final: 0.8549 (mm) REVERT: a 287 GLU cc_start: 0.8932 (tt0) cc_final: 0.8726 (tt0) REVERT: a 303 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8411 (mm-30) REVERT: a 308 GLU cc_start: 0.8853 (mp0) cc_final: 0.8027 (mt-10) REVERT: a 396 GLU cc_start: 0.8665 (tt0) cc_final: 0.8058 (tm-30) REVERT: a 413 GLU cc_start: 0.8371 (tt0) cc_final: 0.7961 (tm-30) REVERT: b 317 ASP cc_start: 0.8911 (t70) cc_final: 0.8696 (t0) REVERT: b 404 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8511 (mm-30) REVERT: b 413 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8434 (pt0) REVERT: H 16 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7321 (mp0) REVERT: H 33 TYR cc_start: 0.8830 (m-10) cc_final: 0.8609 (m-10) REVERT: H 75 LYS cc_start: 0.9109 (mtmm) cc_final: 0.8732 (mtmm) REVERT: L 17 GLN cc_start: 0.8622 (pt0) cc_final: 0.8182 (pt0) outliers start: 26 outliers final: 14 residues processed: 187 average time/residue: 0.7955 time to fit residues: 158.4553 Evaluate side-chains 192 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain c residue 410 MET Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain c residue 420 MET Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain b residue 298 VAL Chi-restraints excluded: chain b residue 401 ASP Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain b residue 413 GLU Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 50 ASN Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 117 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN a 335 GLN a 405 GLN H 50 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.074757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.058529 restraints weight = 27547.410| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.68 r_work: 0.2813 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11841 Z= 0.135 Angle : 0.662 12.404 16206 Z= 0.309 Chirality : 0.042 0.286 2015 Planarity : 0.004 0.042 1874 Dihedral : 7.537 78.721 3209 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.17 % Allowed : 14.83 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.24), residues: 1269 helix: 1.54 (0.29), residues: 355 sheet: 1.06 (0.36), residues: 221 loop : -0.28 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG c 379 TYR 0.025 0.001 TYR c 419 PHE 0.012 0.001 PHE H 78 TRP 0.007 0.001 TRP b 283 HIS 0.003 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00306 (11729) covalent geometry : angle 0.62718 (15893) SS BOND : bond 0.00390 ( 23) SS BOND : angle 0.90972 ( 46) hydrogen bonds : bond 0.03389 ( 452) hydrogen bonds : angle 4.52458 ( 1164) link_ALPHA1-2 : bond 0.00410 ( 3) link_ALPHA1-2 : angle 2.47565 ( 9) link_ALPHA1-3 : bond 0.01079 ( 5) link_ALPHA1-3 : angle 2.50818 ( 15) link_ALPHA1-6 : bond 0.00908 ( 5) link_ALPHA1-6 : angle 1.70025 ( 15) link_BETA1-4 : bond 0.00479 ( 38) link_BETA1-4 : angle 1.50381 ( 114) link_BETA1-6 : bond 0.00155 ( 5) link_BETA1-6 : angle 1.44429 ( 15) link_NAG-ASN : bond 0.00191 ( 33) link_NAG-ASN : angle 1.81488 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: C 75 MET cc_start: 0.8393 (mtm) cc_final: 0.8185 (ttm) REVERT: C 116 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8343 (mmtp) REVERT: B 76 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8561 (tt0) REVERT: B 192 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8421 (ttt) REVERT: B 247 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.7675 (tp40) REVERT: c 331 GLN cc_start: 0.8028 (mp10) cc_final: 0.7487 (pm20) REVERT: c 405 GLN cc_start: 0.8866 (tm-30) cc_final: 0.8077 (tm-30) REVERT: c 420 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.6835 (mpt) REVERT: a 286 ILE cc_start: 0.8834 (mm) cc_final: 0.8577 (mm) REVERT: a 287 GLU cc_start: 0.8948 (tt0) cc_final: 0.8737 (tt0) REVERT: a 303 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8399 (mm-30) REVERT: a 308 GLU cc_start: 0.8861 (mp0) cc_final: 0.8065 (mt-10) REVERT: a 396 GLU cc_start: 0.8673 (tt0) cc_final: 0.8067 (tm-30) REVERT: a 413 GLU cc_start: 0.8366 (tt0) cc_final: 0.7946 (tm-30) REVERT: b 317 ASP cc_start: 0.8932 (t70) cc_final: 0.8717 (t0) REVERT: b 404 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8488 (mm-30) REVERT: H 16 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7379 (mp0) REVERT: H 33 TYR cc_start: 0.8818 (m-10) cc_final: 0.8591 (m-10) REVERT: H 75 LYS cc_start: 0.9127 (mtmm) cc_final: 0.8748 (mtmm) REVERT: L 17 GLN cc_start: 0.8643 (pt0) cc_final: 0.8202 (pt0) outliers start: 25 outliers final: 13 residues processed: 187 average time/residue: 0.7966 time to fit residues: 158.8611 Evaluate side-chains 192 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain c residue 410 MET Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain c residue 420 MET Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain b residue 298 VAL Chi-restraints excluded: chain b residue 401 ASP Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain H residue 5 ARG Chi-restraints excluded: chain H residue 16 GLU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 79 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN a 335 GLN H 50 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.074501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.057812 restraints weight = 27604.235| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.75 r_work: 0.2782 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11841 Z= 0.162 Angle : 0.683 12.548 16206 Z= 0.318 Chirality : 0.043 0.292 2015 Planarity : 0.004 0.042 1874 Dihedral : 7.435 78.848 3209 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.82 % Allowed : 15.78 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.24), residues: 1269 helix: 1.53 (0.29), residues: 356 sheet: 1.11 (0.37), residues: 210 loop : -0.29 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG c 379 TYR 0.019 0.001 TYR a 366 PHE 0.012 0.001 PHE H 78 TRP 0.009 0.001 TRP H 47 HIS 0.004 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00371 (11729) covalent geometry : angle 0.64828 (15893) SS BOND : bond 0.00436 ( 23) SS BOND : angle 1.02266 ( 46) hydrogen bonds : bond 0.03541 ( 452) hydrogen bonds : angle 4.55069 ( 1164) link_ALPHA1-2 : bond 0.00355 ( 3) link_ALPHA1-2 : angle 2.47232 ( 9) link_ALPHA1-3 : bond 0.01059 ( 5) link_ALPHA1-3 : angle 2.51320 ( 15) link_ALPHA1-6 : bond 0.00896 ( 5) link_ALPHA1-6 : angle 1.65447 ( 15) link_BETA1-4 : bond 0.00451 ( 38) link_BETA1-4 : angle 1.52983 ( 114) link_BETA1-6 : bond 0.00133 ( 5) link_BETA1-6 : angle 1.51017 ( 15) link_NAG-ASN : bond 0.00220 ( 33) link_NAG-ASN : angle 1.87974 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3932.69 seconds wall clock time: 68 minutes 28.31 seconds (4108.31 seconds total)