Starting phenix.real_space_refine on Tue Jun 10 06:57:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cj7_45624/06_2025/9cj7_45624.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cj7_45624/06_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_45624/06_2025/9cj7_45624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cj7_45624/06_2025/9cj7_45624.map" model { file = "/net/cci-nas-00/data/ceres_data/9cj7_45624/06_2025/9cj7_45624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cj7_45624/06_2025/9cj7_45624.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.29, per 1000 atoms: 0.63 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: 4.31 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.50 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: 3.10 Time building geometry restraints manager: 4.81 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 420 or resid 701 thro \ ugh 702)) selection = (chain 'c' and (resid 260 through 268 or resid 276 through 420 or resid 701 thro \ ugh 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.130 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.630 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.23), 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 TRP 0.013 0.002 TRP H 47 HIS 0.007 0.001 HIS B 141 PHE 0.023 0.002 PHE c 399 TYR 0.019 0.002 TYR b 366 ARG 0.016 0.001 ARG C 250 Details of bonding type rmsd link_NAG-ASN : bond 0.01686 ( 33) link_NAG-ASN : angle 2.84710 ( 99) 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_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) hydrogen bonds : bond 0.17578 ( 452) hydrogen bonds : angle 6.58555 ( 1164) link_BETA1-6 : bond 0.00745 ( 5) link_BETA1-6 : angle 1.62917 ( 15) SS BOND : bond 0.00451 ( 23) SS BOND : angle 1.54400 ( 46) covalent geometry : bond 0.00598 (11729) covalent geometry : angle 0.94980 (15893) *********************** 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 : 1.173 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: 1.5865 time to fit residues: 429.4745 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 : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 3.9990 chunk 95 optimal weight: 0.0870 chunk 52 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- 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 = 0.3355 r_free = 0.3355 target = 0.077418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.061304 restraints weight = 26850.453| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.50 r_work: 0.2864 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11841 Z= 0.164 Angle : 0.725 9.448 16206 Z= 0.343 Chirality : 0.045 0.388 2015 Planarity : 0.004 0.052 1874 Dihedral : 12.496 82.861 3209 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.25 % Allowed : 9.97 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.23), residues: 1269 helix: 0.97 (0.28), residues: 350 sheet: 0.55 (0.34), residues: 223 loop : -0.19 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 283 HIS 0.006 0.001 HIS B 141 PHE 0.013 0.001 PHE c 399 TYR 0.018 0.001 TYR b 419 ARG 0.003 0.001 ARG C 256 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 33) link_NAG-ASN : angle 2.23592 ( 99) link_ALPHA1-6 : bond 0.00465 ( 5) link_ALPHA1-6 : angle 1.81744 ( 15) link_BETA1-4 : bond 0.00622 ( 38) link_BETA1-4 : angle 2.08779 ( 114) link_ALPHA1-2 : bond 0.00739 ( 3) link_ALPHA1-2 : angle 2.44397 ( 9) link_ALPHA1-3 : bond 0.01394 ( 5) link_ALPHA1-3 : angle 2.78543 ( 15) hydrogen bonds : bond 0.04671 ( 452) hydrogen bonds : angle 5.15422 ( 1164) link_BETA1-6 : bond 0.00274 ( 5) link_BETA1-6 : angle 1.75500 ( 15) SS BOND : bond 0.00506 ( 23) SS BOND : angle 1.04642 ( 46) covalent geometry : bond 0.00363 (11729) covalent geometry : angle 0.67311 (15893) *********************** 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 214 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 125 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7961 (ttpt) REVERT: C 156 ASP cc_start: 0.7936 (t0) cc_final: 0.7564 (t0) REVERT: A 214 MET cc_start: 0.6716 (mmm) cc_final: 0.6513 (mmm) REVERT: B 122 ASP cc_start: 0.8245 (t0) cc_final: 0.8034 (t0) REVERT: B 192 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8243 (ttt) REVERT: B 211 ASP cc_start: 0.9078 (m-30) cc_final: 0.8823 (m-30) REVERT: B 247 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8225 (mp10) REVERT: c 331 GLN cc_start: 0.7688 (mp10) cc_final: 0.7433 (mp10) REVERT: c 405 GLN cc_start: 0.8455 (tm130) cc_final: 0.8023 (tm-30) REVERT: c 420 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.6799 (mpt) REVERT: a 307 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7431 (mm-30) REVERT: a 308 GLU cc_start: 0.8655 (mp0) cc_final: 0.7841 (mt-10) REVERT: a 323 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8220 (mp) REVERT: a 396 GLU cc_start: 0.8349 (tt0) cc_final: 0.8108 (tt0) REVERT: a 401 ASP cc_start: 0.8268 (m-30) cc_final: 0.7723 (t0) REVERT: a 416 GLN cc_start: 0.7986 (tp40) cc_final: 0.7718 (tp-100) REVERT: b 287 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8062 (tm-30) REVERT: b 332 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7447 (mtm) REVERT: b 408 ASP cc_start: 0.8569 (m-30) cc_final: 0.8368 (m-30) REVERT: L 17 GLN cc_start: 0.8270 (pt0) cc_final: 0.7680 (pt0) outliers start: 26 outliers final: 6 residues processed: 195 average time/residue: 1.4987 time to fit residues: 312.8903 Evaluate side-chains 185 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 173 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain c residue 420 MET Chi-restraints excluded: chain a residue 323 ILE Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain b residue 298 VAL Chi-restraints excluded: chain b residue 332 MET Chi-restraints excluded: chain b residue 347 ASP 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 17 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 1 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 = 0.3319 r_free = 0.3319 target = 0.075471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.059414 restraints weight = 27685.549| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.51 r_work: 0.2823 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11841 Z= 0.202 Angle : 0.706 9.423 16206 Z= 0.331 Chirality : 0.045 0.350 2015 Planarity : 0.004 0.042 1874 Dihedral : 10.283 77.497 3209 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.86 % Allowed : 10.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.23), residues: 1269 helix: 1.08 (0.28), residues: 356 sheet: 0.53 (0.35), residues: 228 loop : -0.34 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 386 HIS 0.006 0.001 HIS B 141 PHE 0.012 0.001 PHE H 78 TYR 0.022 0.001 TYR b 419 ARG 0.004 0.001 ARG b 379 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 33) link_NAG-ASN : angle 2.14767 ( 99) link_ALPHA1-6 : bond 0.00639 ( 5) link_ALPHA1-6 : angle 1.82782 ( 15) link_BETA1-4 : bond 0.00523 ( 38) link_BETA1-4 : angle 1.95388 ( 114) link_ALPHA1-2 : bond 0.00460 ( 3) link_ALPHA1-2 : angle 2.63940 ( 9) link_ALPHA1-3 : bond 0.01223 ( 5) link_ALPHA1-3 : angle 2.53184 ( 15) hydrogen bonds : bond 0.04322 ( 452) hydrogen bonds : angle 4.95156 ( 1164) link_BETA1-6 : bond 0.00284 ( 5) link_BETA1-6 : angle 1.66393 ( 15) SS BOND : bond 0.00500 ( 23) SS BOND : angle 1.06377 ( 46) covalent geometry : bond 0.00461 (11729) covalent geometry : angle 0.65794 (15893) *********************** 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 221 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 3.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8232 (mmtp) REVERT: C 156 ASP cc_start: 0.7980 (t0) cc_final: 0.7663 (t0) REVERT: A 214 MET cc_start: 0.6617 (mmm) cc_final: 0.6417 (mmm) REVERT: B 192 MET cc_start: 0.8687 (ttt) cc_final: 0.8391 (ttt) REVERT: B 211 ASP cc_start: 0.9126 (m-30) cc_final: 0.8921 (m-30) REVERT: c 268 ASP cc_start: 0.7122 (p0) cc_final: 0.6854 (p0) REVERT: c 331 GLN cc_start: 0.7868 (mp10) cc_final: 0.7558 (mp10) REVERT: c 405 GLN cc_start: 0.8536 (tm130) cc_final: 0.8088 (tm-30) REVERT: c 420 MET cc_start: 0.7364 (mpp) cc_final: 0.6672 (mpt) REVERT: a 289 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7574 (tp30) REVERT: a 303 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8398 (mm-30) REVERT: a 308 GLU cc_start: 0.8772 (mp0) cc_final: 0.7871 (mt-10) REVERT: a 401 ASP cc_start: 0.8255 (m-30) cc_final: 0.7692 (t0) REVERT: b 287 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8070 (tm-30) REVERT: b 306 ASP cc_start: 0.9028 (p0) cc_final: 0.8774 (p0) REVERT: b 408 ASP cc_start: 0.8607 (m-30) cc_final: 0.8404 (m-30) REVERT: H 33 TYR cc_start: 0.8713 (m-10) cc_final: 0.8395 (m-10) REVERT: H 75 LYS cc_start: 0.9120 (mtmm) cc_final: 0.8543 (mtmm) REVERT: L 17 GLN cc_start: 0.8292 (pt0) cc_final: 0.7756 (pt0) REVERT: L 45 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8125 (ttpp) outliers start: 33 outliers final: 10 residues processed: 198 average time/residue: 1.7961 time to fit residues: 380.9868 Evaluate side-chains 187 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain b residue 298 VAL Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 396 GLU Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain b residue 413 GLU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain L residue 45 LYS 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 98 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 21 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 354 HIS ** c 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 405 GLN H 1 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 = 0.3327 r_free = 0.3327 target = 0.075584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.059176 restraints weight = 27577.162| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 3.69 r_work: 0.2824 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11841 Z= 0.122 Angle : 0.645 9.598 16206 Z= 0.303 Chirality : 0.042 0.289 2015 Planarity : 0.004 0.034 1874 Dihedral : 8.972 75.270 3209 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.25 % Allowed : 11.71 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.23), residues: 1269 helix: 1.35 (0.29), residues: 357 sheet: 0.82 (0.36), residues: 206 loop : -0.36 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP b 283 HIS 0.003 0.001 HIS C 141 PHE 0.013 0.001 PHE H 78 TYR 0.022 0.001 TYR b 419 ARG 0.005 0.000 ARG a 379 Details of bonding type rmsd link_NAG-ASN : bond 0.00211 ( 33) link_NAG-ASN : angle 1.93310 ( 99) link_ALPHA1-6 : bond 0.00799 ( 5) link_ALPHA1-6 : angle 1.84904 ( 15) link_BETA1-4 : bond 0.00559 ( 38) link_BETA1-4 : angle 1.73510 ( 114) link_ALPHA1-2 : bond 0.00561 ( 3) link_ALPHA1-2 : angle 2.56453 ( 9) link_ALPHA1-3 : bond 0.01194 ( 5) link_ALPHA1-3 : angle 2.58739 ( 15) hydrogen bonds : bond 0.03630 ( 452) hydrogen bonds : angle 4.74402 ( 1164) link_BETA1-6 : bond 0.00216 ( 5) link_BETA1-6 : angle 1.43660 ( 15) SS BOND : bond 0.00627 ( 23) SS BOND : angle 1.53306 ( 46) covalent geometry : bond 0.00263 (11729) covalent geometry : angle 0.59755 (15893) *********************** 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 210 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8294 (mmtp) REVERT: C 156 ASP cc_start: 0.8153 (t0) cc_final: 0.7755 (t0) REVERT: B 192 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8417 (ttt) REVERT: c 268 ASP cc_start: 0.7083 (p0) cc_final: 0.6812 (p0) REVERT: c 331 GLN cc_start: 0.8028 (mp10) cc_final: 0.7699 (mp10) REVERT: c 405 GLN cc_start: 0.8608 (tm130) cc_final: 0.8078 (tm-30) REVERT: c 420 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.6791 (mpt) REVERT: a 286 ILE cc_start: 0.8733 (mm) cc_final: 0.8508 (mm) REVERT: a 303 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8389 (mm-30) REVERT: a 308 GLU cc_start: 0.8870 (mp0) cc_final: 0.8011 (mt-10) REVERT: a 396 GLU cc_start: 0.8672 (tt0) cc_final: 0.8388 (tt0) REVERT: b 306 ASP cc_start: 0.9188 (p0) cc_final: 0.8923 (p0) REVERT: b 317 ASP cc_start: 0.8893 (t70) cc_final: 0.8676 (t0) REVERT: L 17 GLN cc_start: 0.8415 (pt0) cc_final: 0.7912 (pt0) outliers start: 26 outliers final: 7 residues processed: 193 average time/residue: 1.8845 time to fit residues: 388.2872 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 : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 116 LYS 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 b residue 401 ASP Chi-restraints excluded: chain b residue 411 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 0.0970 chunk 65 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 354 HIS ** c 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 405 GLN H 1 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.075557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.058782 restraints weight = 27165.753| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.77 r_work: 0.2805 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2589 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= 0.137 Angle : 0.641 9.547 16206 Z= 0.300 Chirality : 0.042 0.278 2015 Planarity : 0.003 0.033 1874 Dihedral : 8.631 75.695 3209 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.78 % Allowed : 11.97 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.23), residues: 1269 helix: 1.43 (0.29), residues: 357 sheet: 0.94 (0.36), residues: 204 loop : -0.38 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP b 283 HIS 0.003 0.001 HIS C 141 PHE 0.012 0.001 PHE H 78 TYR 0.018 0.001 TYR b 419 ARG 0.004 0.000 ARG b 379 Details of bonding type rmsd link_NAG-ASN : bond 0.00210 ( 33) link_NAG-ASN : angle 1.90071 ( 99) link_ALPHA1-6 : bond 0.00796 ( 5) link_ALPHA1-6 : angle 1.82676 ( 15) link_BETA1-4 : bond 0.00503 ( 38) link_BETA1-4 : angle 1.67592 ( 114) link_ALPHA1-2 : bond 0.00442 ( 3) link_ALPHA1-2 : angle 2.58005 ( 9) link_ALPHA1-3 : bond 0.01158 ( 5) link_ALPHA1-3 : angle 2.55300 ( 15) hydrogen bonds : bond 0.03599 ( 452) hydrogen bonds : angle 4.65193 ( 1164) link_BETA1-6 : bond 0.00154 ( 5) link_BETA1-6 : angle 1.47977 ( 15) SS BOND : bond 0.00419 ( 23) SS BOND : angle 1.28822 ( 46) covalent geometry : bond 0.00310 (11729) covalent geometry : angle 0.59667 (15893) *********************** 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 215 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8338 (mmtp) REVERT: C 156 ASP cc_start: 0.8210 (t0) cc_final: 0.7800 (t0) REVERT: B 192 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8453 (ttt) REVERT: B 247 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8325 (mp10) REVERT: c 331 GLN cc_start: 0.8053 (mp10) cc_final: 0.7697 (mp10) REVERT: c 405 GLN cc_start: 0.8597 (tm130) cc_final: 0.8005 (tm-30) REVERT: c 420 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.6708 (mpt) REVERT: a 286 ILE cc_start: 0.8780 (mm) cc_final: 0.8549 (mm) REVERT: a 308 GLU cc_start: 0.8878 (mp0) cc_final: 0.8024 (mt-10) REVERT: a 396 GLU cc_start: 0.8671 (tt0) cc_final: 0.8381 (tt0) REVERT: b 306 ASP cc_start: 0.9190 (p0) cc_final: 0.8944 (p0) REVERT: b 317 ASP cc_start: 0.8906 (t70) cc_final: 0.8689 (t0) REVERT: b 408 ASP cc_start: 0.8626 (m-30) cc_final: 0.8398 (m-30) REVERT: b 413 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8535 (pt0) REVERT: H 33 TYR cc_start: 0.8736 (m-10) cc_final: 0.8460 (m-10) REVERT: H 75 LYS cc_start: 0.9164 (mtmm) cc_final: 0.8633 (mtmm) REVERT: L 17 GLN cc_start: 0.8474 (pt0) cc_final: 0.7977 (pt0) outliers start: 32 outliers final: 10 residues processed: 194 average time/residue: 1.6346 time to fit residues: 337.9434 Evaluate side-chains 189 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 174 time to evaluate : 1.194 ------------------------------------------------------------------------------- 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 B residue 247 GLN Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain c residue 420 MET 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 100 MET 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 76 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 89 optimal weight: 0.0470 overall best weight: 0.9082 ------------------------------------------------------------------------------- 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 354 HIS ** c 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3325 r_free = 0.3325 target = 0.075757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.058802 restraints weight = 27646.138| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 3.82 r_work: 0.2812 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 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 0.037 11841 Z= 0.132 Angle : 0.635 9.666 16206 Z= 0.297 Chirality : 0.042 0.285 2015 Planarity : 0.003 0.032 1874 Dihedral : 8.232 79.860 3209 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.60 % Allowed : 13.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.23), residues: 1269 helix: 1.49 (0.29), residues: 355 sheet: 1.10 (0.36), residues: 204 loop : -0.31 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP b 283 HIS 0.004 0.001 HIS C 141 PHE 0.013 0.001 PHE H 78 TYR 0.016 0.001 TYR b 419 ARG 0.007 0.000 ARG c 379 Details of bonding type rmsd link_NAG-ASN : bond 0.00198 ( 33) link_NAG-ASN : angle 1.86401 ( 99) link_ALPHA1-6 : bond 0.00836 ( 5) link_ALPHA1-6 : angle 1.82612 ( 15) link_BETA1-4 : bond 0.00496 ( 38) link_BETA1-4 : angle 1.58979 ( 114) link_ALPHA1-2 : bond 0.00425 ( 3) link_ALPHA1-2 : angle 2.54230 ( 9) link_ALPHA1-3 : bond 0.01146 ( 5) link_ALPHA1-3 : angle 2.54426 ( 15) hydrogen bonds : bond 0.03496 ( 452) hydrogen bonds : angle 4.55864 ( 1164) link_BETA1-6 : bond 0.00159 ( 5) link_BETA1-6 : angle 1.44904 ( 15) SS BOND : bond 0.00402 ( 23) SS BOND : angle 1.04877 ( 46) covalent geometry : bond 0.00297 (11729) covalent geometry : angle 0.59431 (15893) *********************** 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 211 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 3.405 Fit side-chains revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8332 (mmtp) REVERT: C 156 ASP cc_start: 0.8233 (t0) cc_final: 0.7792 (t0) REVERT: B 192 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8457 (ttt) REVERT: B 214 MET cc_start: 0.8094 (mmt) cc_final: 0.7864 (mmm) REVERT: c 331 GLN cc_start: 0.8064 (mp10) cc_final: 0.7709 (mp10) REVERT: c 405 GLN cc_start: 0.8589 (tm130) cc_final: 0.7996 (tm-30) REVERT: c 420 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.6690 (mpt) REVERT: a 286 ILE cc_start: 0.8824 (mm) cc_final: 0.8593 (mm) REVERT: a 308 GLU cc_start: 0.8876 (mp0) cc_final: 0.8068 (mt-10) REVERT: a 396 GLU cc_start: 0.8703 (tt0) cc_final: 0.8414 (tt0) REVERT: b 306 ASP cc_start: 0.9185 (p0) cc_final: 0.8963 (p0) REVERT: b 317 ASP cc_start: 0.8921 (t70) cc_final: 0.8717 (t0) REVERT: b 379 ARG cc_start: 0.8486 (ttm-80) cc_final: 0.7965 (mmm-85) REVERT: b 413 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8205 (pt0) REVERT: H 16 GLU cc_start: 0.7620 (mp0) cc_final: 0.7373 (mp0) REVERT: H 75 LYS cc_start: 0.9146 (mtmm) cc_final: 0.8593 (mtmm) REVERT: L 17 GLN cc_start: 0.8600 (pt0) cc_final: 0.8100 (pt0) outliers start: 30 outliers final: 11 residues processed: 189 average time/residue: 1.5547 time to fit residues: 315.8040 Evaluate side-chains 187 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 1.158 ------------------------------------------------------------------------------- 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 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 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 87 optimal weight: 9.9990 chunk 107 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 116 optimal weight: 0.0000 chunk 33 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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 354 HIS ** c 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3327 r_free = 0.3327 target = 0.075621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.059292 restraints weight = 27828.408| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.69 r_work: 0.2830 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2873 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= 0.118 Angle : 0.626 10.832 16206 Z= 0.294 Chirality : 0.042 0.288 2015 Planarity : 0.004 0.044 1874 Dihedral : 7.864 74.828 3209 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.52 % Allowed : 14.05 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.23), residues: 1269 helix: 1.56 (0.29), residues: 354 sheet: 1.25 (0.37), residues: 198 loop : -0.28 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 283 HIS 0.003 0.001 HIS C 141 PHE 0.011 0.001 PHE H 78 TYR 0.024 0.001 TYR c 419 ARG 0.010 0.001 ARG c 379 Details of bonding type rmsd link_NAG-ASN : bond 0.00191 ( 33) link_NAG-ASN : angle 1.80893 ( 99) link_ALPHA1-6 : bond 0.00887 ( 5) link_ALPHA1-6 : angle 1.78832 ( 15) link_BETA1-4 : bond 0.00502 ( 38) link_BETA1-4 : angle 1.53092 ( 114) link_ALPHA1-2 : bond 0.00450 ( 3) link_ALPHA1-2 : angle 2.47627 ( 9) link_ALPHA1-3 : bond 0.01165 ( 5) link_ALPHA1-3 : angle 2.53692 ( 15) hydrogen bonds : bond 0.03339 ( 452) hydrogen bonds : angle 4.49482 ( 1164) link_BETA1-6 : bond 0.00185 ( 5) link_BETA1-6 : angle 1.40642 ( 15) SS BOND : bond 0.00428 ( 23) SS BOND : angle 0.89828 ( 46) covalent geometry : bond 0.00263 (11729) covalent geometry : angle 0.58805 (15893) *********************** 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 208 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8316 (mmtp) REVERT: C 156 ASP cc_start: 0.8313 (t0) cc_final: 0.7826 (t0) REVERT: B 161 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7469 (ptpt) REVERT: B 192 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8434 (ttt) REVERT: B 214 MET cc_start: 0.8084 (mmt) cc_final: 0.7862 (mmm) REVERT: c 317 ASP cc_start: 0.8426 (t70) cc_final: 0.8223 (t70) REVERT: c 331 GLN cc_start: 0.8024 (mp10) cc_final: 0.7404 (pm20) REVERT: c 405 GLN cc_start: 0.8569 (tm130) cc_final: 0.7928 (tm-30) REVERT: c 420 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.6701 (mpt) REVERT: a 286 ILE cc_start: 0.8830 (mm) cc_final: 0.8603 (mm) REVERT: a 303 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8424 (mm-30) REVERT: a 308 GLU cc_start: 0.8884 (mp0) cc_final: 0.8143 (mt-10) REVERT: a 396 GLU cc_start: 0.8691 (tt0) cc_final: 0.8392 (tt0) REVERT: b 317 ASP cc_start: 0.8924 (t70) cc_final: 0.8713 (t0) REVERT: b 379 ARG cc_start: 0.8510 (ttm-80) cc_final: 0.8034 (mmm-85) REVERT: b 404 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8682 (mm-30) REVERT: b 413 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8276 (pt0) REVERT: H 6 GLU cc_start: 0.7755 (mp0) cc_final: 0.7449 (mp0) REVERT: H 16 GLU cc_start: 0.7681 (mp0) cc_final: 0.7401 (mp0) REVERT: H 33 TYR cc_start: 0.8777 (m-10) cc_final: 0.8564 (m-10) REVERT: H 75 LYS cc_start: 0.9161 (mtmm) cc_final: 0.8607 (mtmm) REVERT: L 17 GLN cc_start: 0.8565 (pt0) cc_final: 0.8091 (pt0) outliers start: 29 outliers final: 13 residues processed: 189 average time/residue: 1.6773 time to fit residues: 340.6167 Evaluate side-chains 192 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 161 LYS 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 1 GLN 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 51 VAL 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 14 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 35 optimal weight: 0.0470 chunk 99 optimal weight: 0.0470 chunk 47 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 67 optimal weight: 0.0980 chunk 26 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 overall best weight: 0.3976 ------------------------------------------------------------------------------- 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 354 HIS ** c 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3341 r_free = 0.3341 target = 0.076543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.059853 restraints weight = 27510.139| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.78 r_work: 0.2841 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11841 Z= 0.111 Angle : 0.628 11.409 16206 Z= 0.294 Chirality : 0.041 0.290 2015 Planarity : 0.003 0.039 1874 Dihedral : 7.629 83.191 3209 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.52 % Allowed : 14.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.24), residues: 1269 helix: 1.61 (0.29), residues: 354 sheet: 1.23 (0.37), residues: 208 loop : -0.26 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP b 283 HIS 0.003 0.001 HIS C 230 PHE 0.011 0.001 PHE H 78 TYR 0.017 0.001 TYR H 27 ARG 0.009 0.001 ARG c 379 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 33) link_NAG-ASN : angle 1.76112 ( 99) link_ALPHA1-6 : bond 0.00929 ( 5) link_ALPHA1-6 : angle 1.73873 ( 15) link_BETA1-4 : bond 0.00515 ( 38) link_BETA1-4 : angle 1.48703 ( 114) link_ALPHA1-2 : bond 0.00467 ( 3) link_ALPHA1-2 : angle 2.43794 ( 9) link_ALPHA1-3 : bond 0.01122 ( 5) link_ALPHA1-3 : angle 2.52768 ( 15) hydrogen bonds : bond 0.03225 ( 452) hydrogen bonds : angle 4.43557 ( 1164) link_BETA1-6 : bond 0.00222 ( 5) link_BETA1-6 : angle 1.36917 ( 15) SS BOND : bond 0.00329 ( 23) SS BOND : angle 0.81126 ( 46) covalent geometry : bond 0.00243 (11729) covalent geometry : angle 0.59246 (15893) *********************** 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 211 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 1.238 Fit side-chains REVERT: C 116 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8302 (mmtp) REVERT: C 156 ASP cc_start: 0.8293 (t0) cc_final: 0.7798 (t0) REVERT: A 214 MET cc_start: 0.6796 (mmm) cc_final: 0.6519 (mmm) REVERT: A 251 ASP cc_start: 0.7569 (m-30) cc_final: 0.6851 (m-30) REVERT: B 76 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8358 (tt0) REVERT: B 161 LYS cc_start: 0.7771 (ttpt) cc_final: 0.7553 (ptpt) REVERT: B 192 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8398 (ttt) REVERT: B 214 MET cc_start: 0.8099 (mmt) cc_final: 0.7874 (mmm) REVERT: c 317 ASP cc_start: 0.8421 (t70) cc_final: 0.8171 (t70) REVERT: c 331 GLN cc_start: 0.8035 (mp10) cc_final: 0.7455 (pm20) REVERT: c 405 GLN cc_start: 0.8557 (tm130) cc_final: 0.7931 (tm-30) REVERT: c 420 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.6769 (mpt) REVERT: a 286 ILE cc_start: 0.8840 (mm) cc_final: 0.8622 (mm) REVERT: a 303 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8417 (mm-30) REVERT: a 308 GLU cc_start: 0.8873 (mp0) cc_final: 0.8003 (mt-10) REVERT: a 379 ARG cc_start: 0.7985 (mmm-85) cc_final: 0.7757 (mmm160) REVERT: a 396 GLU cc_start: 0.8667 (tt0) cc_final: 0.8341 (tt0) REVERT: b 379 ARG cc_start: 0.8498 (ttm-80) cc_final: 0.8020 (mmm-85) REVERT: b 404 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8635 (mm-30) REVERT: b 413 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8112 (pt0) REVERT: H 16 GLU cc_start: 0.7687 (mp0) cc_final: 0.7367 (mp0) REVERT: H 33 TYR cc_start: 0.8738 (m-10) cc_final: 0.8514 (m-10) REVERT: L 17 GLN cc_start: 0.8569 (pt0) cc_final: 0.8095 (pt0) outliers start: 29 outliers final: 13 residues processed: 192 average time/residue: 1.4804 time to fit residues: 303.5993 Evaluate side-chains 188 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 116 LYS 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 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 18 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 50 ASN Chi-restraints excluded: chain L residue 51 VAL 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 121 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 24 optimal weight: 0.0570 chunk 100 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- 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 c 354 HIS ** c 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 335 GLN a 405 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 = 0.3326 r_free = 0.3326 target = 0.075573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.059440 restraints weight = 27761.254| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.65 r_work: 0.2837 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11841 Z= 0.125 Angle : 0.641 11.679 16206 Z= 0.300 Chirality : 0.042 0.289 2015 Planarity : 0.004 0.041 1874 Dihedral : 7.518 87.255 3209 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.17 % Allowed : 15.70 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.24), residues: 1269 helix: 1.58 (0.29), residues: 354 sheet: 1.34 (0.36), residues: 216 loop : -0.26 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP b 283 HIS 0.003 0.001 HIS C 230 PHE 0.012 0.001 PHE H 78 TYR 0.025 0.001 TYR c 419 ARG 0.009 0.001 ARG c 379 Details of bonding type rmsd link_NAG-ASN : bond 0.00189 ( 33) link_NAG-ASN : angle 1.76528 ( 99) link_ALPHA1-6 : bond 0.00911 ( 5) link_ALPHA1-6 : angle 1.72201 ( 15) link_BETA1-4 : bond 0.00494 ( 38) link_BETA1-4 : angle 1.48920 ( 114) link_ALPHA1-2 : bond 0.00435 ( 3) link_ALPHA1-2 : angle 2.39663 ( 9) link_ALPHA1-3 : bond 0.01109 ( 5) link_ALPHA1-3 : angle 2.52106 ( 15) hydrogen bonds : bond 0.03303 ( 452) hydrogen bonds : angle 4.42729 ( 1164) link_BETA1-6 : bond 0.00165 ( 5) link_BETA1-6 : angle 1.40103 ( 15) SS BOND : bond 0.00369 ( 23) SS BOND : angle 0.85086 ( 46) covalent geometry : bond 0.00282 (11729) covalent geometry : angle 0.60625 (15893) *********************** 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 199 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 1.211 Fit side-chains REVERT: C 116 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8334 (mmtp) REVERT: C 156 ASP cc_start: 0.8323 (t0) cc_final: 0.7829 (t0) REVERT: A 251 ASP cc_start: 0.7468 (m-30) cc_final: 0.7218 (m-30) REVERT: B 76 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8414 (tt0) REVERT: B 192 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8417 (ttt) REVERT: B 214 MET cc_start: 0.8127 (mmt) cc_final: 0.7900 (mmm) REVERT: c 317 ASP cc_start: 0.8460 (t70) cc_final: 0.8213 (t70) REVERT: c 331 GLN cc_start: 0.8015 (mp10) cc_final: 0.7461 (pm20) REVERT: c 405 GLN cc_start: 0.8554 (tm130) cc_final: 0.7974 (tm-30) REVERT: c 420 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.6750 (mpt) REVERT: a 286 ILE cc_start: 0.8888 (mm) cc_final: 0.8667 (mm) REVERT: a 303 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8432 (mm-30) REVERT: a 308 GLU cc_start: 0.8883 (mp0) cc_final: 0.8041 (mt-10) REVERT: a 347 ASP cc_start: 0.8601 (m-30) cc_final: 0.8375 (t0) REVERT: a 379 ARG cc_start: 0.8082 (mmm-85) cc_final: 0.7698 (mtp-110) REVERT: a 396 GLU cc_start: 0.8721 (tt0) cc_final: 0.8424 (tt0) REVERT: b 379 ARG cc_start: 0.8541 (ttm-80) cc_final: 0.8071 (mmm-85) REVERT: b 404 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8575 (mm-30) REVERT: b 413 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8184 (pt0) REVERT: H 16 GLU cc_start: 0.7676 (mp0) cc_final: 0.7309 (mp0) REVERT: H 33 TYR cc_start: 0.8773 (m-10) cc_final: 0.8521 (m-10) REVERT: L 17 GLN cc_start: 0.8626 (pt0) cc_final: 0.8191 (pt0) outliers start: 25 outliers final: 14 residues processed: 184 average time/residue: 1.5757 time to fit residues: 309.3735 Evaluate side-chains 191 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 116 LYS 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 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 5 ARG 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 51 VAL 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 61 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 chunk 99 optimal weight: 0.2980 chunk 22 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 60 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 c 354 HIS ** c 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 335 GLN a 405 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 = 0.3338 r_free = 0.3338 target = 0.076160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.059918 restraints weight = 27575.139| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.67 r_work: 0.2847 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11841 Z= 0.118 Angle : 0.645 12.336 16206 Z= 0.303 Chirality : 0.042 0.289 2015 Planarity : 0.003 0.041 1874 Dihedral : 7.331 80.219 3209 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.99 % Allowed : 15.96 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.24), residues: 1269 helix: 1.59 (0.29), residues: 355 sheet: 1.37 (0.36), residues: 216 loop : -0.28 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.003 0.001 HIS C 230 PHE 0.012 0.001 PHE H 78 TYR 0.018 0.001 TYR a 366 ARG 0.009 0.001 ARG c 379 Details of bonding type rmsd link_NAG-ASN : bond 0.00192 ( 33) link_NAG-ASN : angle 1.74185 ( 99) link_ALPHA1-6 : bond 0.00943 ( 5) link_ALPHA1-6 : angle 1.66424 ( 15) link_BETA1-4 : bond 0.00502 ( 38) link_BETA1-4 : angle 1.45489 ( 114) link_ALPHA1-2 : bond 0.00442 ( 3) link_ALPHA1-2 : angle 2.38999 ( 9) link_ALPHA1-3 : bond 0.01108 ( 5) link_ALPHA1-3 : angle 2.51527 ( 15) hydrogen bonds : bond 0.03245 ( 452) hydrogen bonds : angle 4.39488 ( 1164) link_BETA1-6 : bond 0.00202 ( 5) link_BETA1-6 : angle 1.37082 ( 15) SS BOND : bond 0.00365 ( 23) SS BOND : angle 0.82724 ( 46) covalent geometry : bond 0.00264 (11729) covalent geometry : angle 0.61151 (15893) ********************** 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 198 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 1.205 Fit side-chains REVERT: C 116 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8305 (mmtp) REVERT: C 156 ASP cc_start: 0.8312 (t0) cc_final: 0.7795 (t0) REVERT: B 76 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8439 (tt0) REVERT: B 192 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8405 (ttt) REVERT: B 214 MET cc_start: 0.8137 (mmt) cc_final: 0.7907 (mmm) REVERT: c 317 ASP cc_start: 0.8432 (t70) cc_final: 0.8171 (t70) REVERT: c 331 GLN cc_start: 0.7979 (mp10) cc_final: 0.7442 (pm20) REVERT: c 405 GLN cc_start: 0.8552 (tm130) cc_final: 0.8060 (tm-30) REVERT: c 420 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.6845 (mpt) REVERT: a 286 ILE cc_start: 0.8873 (mm) cc_final: 0.8655 (mm) REVERT: a 303 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8426 (mm-30) REVERT: a 308 GLU cc_start: 0.8831 (mp0) cc_final: 0.7997 (mt-10) REVERT: a 347 ASP cc_start: 0.8598 (m-30) cc_final: 0.8386 (t0) REVERT: a 379 ARG cc_start: 0.8015 (mmm-85) cc_final: 0.7560 (mtp-110) REVERT: a 396 GLU cc_start: 0.8717 (tt0) cc_final: 0.8407 (tt0) REVERT: b 303 GLU cc_start: 0.8599 (pm20) cc_final: 0.8383 (pm20) REVERT: b 379 ARG cc_start: 0.8541 (ttm-80) cc_final: 0.8078 (mmm-85) REVERT: b 404 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8512 (mm-30) REVERT: b 413 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8201 (pt0) REVERT: H 11 LEU cc_start: 0.9118 (tp) cc_final: 0.8841 (tp) REVERT: H 16 GLU cc_start: 0.7692 (mp0) cc_final: 0.7319 (mp0) REVERT: H 33 TYR cc_start: 0.8782 (m-10) cc_final: 0.8545 (m-10) REVERT: H 37 ILE cc_start: 0.9434 (mp) cc_final: 0.9223 (mm) REVERT: H 75 LYS cc_start: 0.8987 (mtmm) cc_final: 0.8428 (mtmm) REVERT: L 17 GLN cc_start: 0.8631 (pt0) cc_final: 0.8133 (pt0) outliers start: 23 outliers final: 14 residues processed: 183 average time/residue: 1.6043 time to fit residues: 313.4202 Evaluate side-chains 191 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 116 LYS 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 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 5 ARG 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 51 VAL 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 32 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 97 optimal weight: 0.0770 overall best weight: 0.9940 ------------------------------------------------------------------------------- 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 c 354 HIS ** c 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 335 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 = 0.3327 r_free = 0.3327 target = 0.075913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.059041 restraints weight = 27432.033| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.75 r_work: 0.2823 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3112 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= 0.137 Angle : 0.643 12.422 16206 Z= 0.299 Chirality : 0.042 0.286 2015 Planarity : 0.004 0.041 1874 Dihedral : 7.246 78.697 3209 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.91 % Allowed : 16.22 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.24), residues: 1269 helix: 1.58 (0.29), residues: 355 sheet: 1.36 (0.36), residues: 216 loop : -0.28 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.003 0.001 HIS C 230 PHE 0.012 0.001 PHE H 78 TYR 0.024 0.001 TYR c 419 ARG 0.009 0.001 ARG c 379 Details of bonding type rmsd link_NAG-ASN : bond 0.00196 ( 33) link_NAG-ASN : angle 1.78294 ( 99) link_ALPHA1-6 : bond 0.00914 ( 5) link_ALPHA1-6 : angle 1.64503 ( 15) link_BETA1-4 : bond 0.00467 ( 38) link_BETA1-4 : angle 1.47834 ( 114) link_ALPHA1-2 : bond 0.00403 ( 3) link_ALPHA1-2 : angle 2.36793 ( 9) link_ALPHA1-3 : bond 0.01066 ( 5) link_ALPHA1-3 : angle 2.51498 ( 15) hydrogen bonds : bond 0.03331 ( 452) hydrogen bonds : angle 4.40764 ( 1164) link_BETA1-6 : bond 0.00139 ( 5) link_BETA1-6 : angle 1.43133 ( 15) SS BOND : bond 0.00387 ( 23) SS BOND : angle 0.89105 ( 46) covalent geometry : bond 0.00312 (11729) covalent geometry : angle 0.60800 (15893) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8358.82 seconds wall clock time: 148 minutes 27.78 seconds (8907.78 seconds total)