Starting phenix.real_space_refine on Fri Jan 17 23:02:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cj7_45624/01_2025/9cj7_45624.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cj7_45624/01_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_45624/01_2025/9cj7_45624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cj7_45624/01_2025/9cj7_45624.map" model { file = "/net/cci-nas-00/data/ceres_data/9cj7_45624/01_2025/9cj7_45624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cj7_45624/01_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-5571/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: 7.56, per 1000 atoms: 0.66 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: 4.03 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: 1.51 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: 3.27 Time building geometry restraints manager: 4.27 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: 1.420 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 28.500 Find NCS groups from input model: 0.500 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:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.400 ------------------------------------------------------------------------------- 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 0.050 11729 Z= 0.370 Angle : 0.950 7.353 15893 Z= 0.489 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 *********************** 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 : 1.169 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: 1.6402 time to fit residues: 444.1873 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 : 1.134 ------------------------------------------------------------------------------- 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: 0.8980 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- 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 = 0.3347 r_free = 0.3347 target = 0.076671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.060913 restraints weight = 26732.353| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.44 r_work: 0.2867 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11729 Z= 0.235 Angle : 0.676 9.480 15893 Z= 0.333 Chirality : 0.045 0.381 2015 Planarity : 0.004 0.053 1874 Dihedral : 12.460 82.504 3209 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.52 % Allowed : 9.63 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.32 (0.23), residues: 1269 helix: 0.94 (0.28), residues: 351 sheet: 0.55 (0.34), residues: 223 loop : -0.21 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP b 283 HIS 0.007 0.001 HIS B 141 PHE 0.014 0.001 PHE c 399 TYR 0.018 0.001 TYR b 419 ARG 0.004 0.001 ARG C 250 *********************** 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 218 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 125 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7983 (ttpt) REVERT: C 156 ASP cc_start: 0.8002 (t0) cc_final: 0.7642 (t0) REVERT: A 214 MET cc_start: 0.6759 (mmm) cc_final: 0.6531 (mmm) REVERT: B 122 ASP cc_start: 0.8272 (t0) cc_final: 0.8057 (t0) REVERT: B 192 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8281 (ttt) REVERT: c 331 GLN cc_start: 0.7738 (mp10) cc_final: 0.7482 (mp10) REVERT: c 405 GLN cc_start: 0.8460 (tm130) cc_final: 0.8017 (tm-30) REVERT: c 408 ASP cc_start: 0.8967 (m-30) cc_final: 0.8745 (m-30) REVERT: c 420 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.6809 (mpt) REVERT: a 307 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7492 (mm-30) REVERT: a 308 GLU cc_start: 0.8691 (mp0) cc_final: 0.7883 (mt-10) REVERT: a 323 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8252 (mp) REVERT: a 401 ASP cc_start: 0.8266 (m-30) cc_final: 0.7722 (t0) REVERT: a 416 GLN cc_start: 0.8002 (tp40) cc_final: 0.7728 (tp-100) REVERT: b 287 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8056 (tm-30) REVERT: b 332 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7478 (mtm) REVERT: b 408 ASP cc_start: 0.8590 (m-30) cc_final: 0.8379 (m-30) REVERT: H 100 ASP cc_start: 0.8150 (m-30) cc_final: 0.7820 (t0) REVERT: L 17 GLN cc_start: 0.8322 (pt0) cc_final: 0.7753 (pt0) outliers start: 29 outliers final: 6 residues processed: 196 average time/residue: 1.6043 time to fit residues: 336.4169 Evaluate side-chains 185 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 174 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain B residue 192 MET 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: 2.9990 chunk 6 optimal weight: 0.8980 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: 0.8980 chunk 7 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 247 GLN ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 405 GLN L 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.074633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.058734 restraints weight = 27563.948| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 3.46 r_work: 0.2815 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11729 Z= 0.316 Angle : 0.666 9.797 15893 Z= 0.325 Chirality : 0.045 0.355 2015 Planarity : 0.004 0.042 1874 Dihedral : 10.176 77.075 3209 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.86 % Allowed : 10.32 % Favored : 86.82 % 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: 0.26 (0.23), residues: 1269 helix: 1.06 (0.28), residues: 356 sheet: 0.47 (0.35), residues: 222 loop : -0.35 (0.22), residues: 691 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 0.013 0.001 PHE c 399 TYR 0.022 0.001 TYR b 419 ARG 0.003 0.000 ARG a 282 *********************** 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 222 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8230 (mmtp) REVERT: C 125 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8020 (ttpt) REVERT: C 156 ASP cc_start: 0.8079 (t0) cc_final: 0.7796 (t0) REVERT: A 214 MET cc_start: 0.6675 (mmm) cc_final: 0.6469 (mmm) REVERT: B 192 MET cc_start: 0.8724 (ttt) cc_final: 0.8424 (ttt) REVERT: c 268 ASP cc_start: 0.7161 (p0) cc_final: 0.6894 (p0) REVERT: c 331 GLN cc_start: 0.7907 (mp10) cc_final: 0.7607 (mp10) REVERT: c 405 GLN cc_start: 0.8553 (tm130) cc_final: 0.8097 (tm-30) REVERT: c 420 MET cc_start: 0.7377 (mpp) cc_final: 0.6675 (mpt) REVERT: a 303 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8418 (mm-30) REVERT: a 308 GLU cc_start: 0.8787 (mp0) cc_final: 0.7886 (mt-10) REVERT: a 401 ASP cc_start: 0.8256 (m-30) cc_final: 0.7699 (t0) REVERT: b 287 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8057 (tm-30) REVERT: b 306 ASP cc_start: 0.9162 (p0) cc_final: 0.8918 (p0) REVERT: b 408 ASP cc_start: 0.8618 (m-30) cc_final: 0.8410 (m-30) REVERT: H 75 LYS cc_start: 0.9126 (mtmm) cc_final: 0.8548 (mtmm) REVERT: H 100 ASP cc_start: 0.8306 (m-30) cc_final: 0.8007 (t0) REVERT: L 17 GLN cc_start: 0.8398 (pt0) cc_final: 0.7852 (pt0) REVERT: L 45 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8205 (ttpp) REVERT: L 79 GLN cc_start: 0.7356 (mp10) cc_final: 0.6789 (mp10) outliers start: 33 outliers final: 13 residues processed: 199 average time/residue: 1.6798 time to fit residues: 355.7056 Evaluate side-chains 191 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain a residue 298 VAL Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain b residue 298 VAL Chi-restraints excluded: chain b residue 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: 2.9990 chunk 115 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 21 optimal weight: 0.3980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3330 r_free = 0.3330 target = 0.076157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.059972 restraints weight = 27253.488| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.57 r_work: 0.2837 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11729 Z= 0.206 Angle : 0.614 9.547 15893 Z= 0.300 Chirality : 0.043 0.286 2015 Planarity : 0.004 0.035 1874 Dihedral : 9.087 75.191 3209 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.69 % Allowed : 11.62 % Favored : 85.69 % 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: 0.37 (0.23), residues: 1269 helix: 1.29 (0.29), residues: 357 sheet: 0.70 (0.36), residues: 214 loop : -0.42 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP b 283 HIS 0.004 0.001 HIS C 141 PHE 0.013 0.001 PHE H 78 TYR 0.022 0.001 TYR b 419 ARG 0.004 0.000 ARG b 379 *********************** 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 211 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8197 (mmtp) REVERT: C 125 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7955 (ttpt) REVERT: C 156 ASP cc_start: 0.8067 (t0) cc_final: 0.7726 (t0) REVERT: A 214 MET cc_start: 0.6648 (mmm) cc_final: 0.6402 (mmm) REVERT: B 192 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8324 (ttt) REVERT: B 247 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8307 (mp10) REVERT: c 268 ASP cc_start: 0.7175 (p0) cc_final: 0.6898 (p0) REVERT: c 331 GLN cc_start: 0.7895 (mp10) cc_final: 0.7558 (mp10) REVERT: c 405 GLN cc_start: 0.8557 (tm130) cc_final: 0.8053 (tm-30) REVERT: c 420 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.6735 (mpt) REVERT: a 303 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8383 (mm-30) REVERT: a 308 GLU cc_start: 0.8742 (mp0) cc_final: 0.7888 (mt-10) REVERT: a 396 GLU cc_start: 0.8643 (tt0) cc_final: 0.7936 (tm-30) REVERT: a 401 ASP cc_start: 0.8100 (m-30) cc_final: 0.7478 (t0) REVERT: b 306 ASP cc_start: 0.9107 (p0) cc_final: 0.8873 (p0) REVERT: b 413 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8549 (pt0) REVERT: H 100 ASP cc_start: 0.8393 (m-30) cc_final: 0.8072 (t0) REVERT: L 17 GLN cc_start: 0.8310 (pt0) cc_final: 0.7784 (pt0) REVERT: L 79 GLN cc_start: 0.7338 (mp10) cc_final: 0.6765 (mp10) outliers start: 31 outliers final: 11 residues processed: 191 average time/residue: 1.5821 time to fit residues: 323.1458 Evaluate side-chains 189 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain 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 298 VAL Chi-restraints excluded: chain b residue 347 ASP 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 104 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 65 optimal weight: 0.0040 chunk 10 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 94 optimal weight: 0.0870 chunk 1 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.5570 ------------------------------------------------------------------------------- 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 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 = 0.075891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.059033 restraints weight = 27136.292| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 3.75 r_work: 0.2812 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11729 Z= 0.167 Angle : 0.587 9.610 15893 Z= 0.286 Chirality : 0.042 0.282 2015 Planarity : 0.003 0.033 1874 Dihedral : 8.632 79.254 3209 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.52 % Allowed : 12.14 % Favored : 85.34 % 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: 0.50 (0.23), residues: 1269 helix: 1.43 (0.29), residues: 357 sheet: 0.94 (0.37), residues: 204 loop : -0.41 (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 *********************** 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: 29 poor density : 186 time to evaluate : 1.173 Fit side-chains revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8316 (mmtp) REVERT: C 125 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8126 (ttpt) REVERT: C 156 ASP cc_start: 0.8184 (t0) cc_final: 0.7760 (t0) REVERT: B 192 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8429 (ttt) REVERT: c 331 GLN cc_start: 0.8047 (mp10) cc_final: 0.7711 (mp10) REVERT: c 405 GLN cc_start: 0.8613 (tm130) cc_final: 0.8051 (tm-30) REVERT: c 420 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.6716 (mpt) REVERT: a 286 ILE cc_start: 0.8808 (mm) cc_final: 0.8575 (mm) REVERT: a 303 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8433 (mm-30) REVERT: a 308 GLU cc_start: 0.8863 (mp0) cc_final: 0.8021 (mt-10) REVERT: a 396 GLU cc_start: 0.8695 (tt0) cc_final: 0.8166 (tm-30) REVERT: b 306 ASP cc_start: 0.9184 (p0) cc_final: 0.8950 (p0) REVERT: b 317 ASP cc_start: 0.8910 (t70) cc_final: 0.8695 (t0) REVERT: H 75 LYS cc_start: 0.9163 (mtmm) cc_final: 0.8643 (mtmm) REVERT: H 100 ASP cc_start: 0.8355 (m-30) cc_final: 0.8046 (t0) REVERT: L 17 GLN cc_start: 0.8527 (pt0) cc_final: 0.8025 (pt0) REVERT: L 79 GLN cc_start: 0.7584 (mp10) cc_final: 0.6975 (mp10) outliers start: 29 outliers final: 11 residues processed: 194 average time/residue: 1.6413 time to fit residues: 339.2681 Evaluate side-chains 190 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain c residue 420 MET Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 401 ASP Chi-restraints excluded: chain b residue 411 ILE 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 85 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 76 optimal weight: 0.1980 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: 5.9990 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 50 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.075211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.058938 restraints weight = 27688.010| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.67 r_work: 0.2814 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11729 Z= 0.180 Angle : 0.596 10.115 15893 Z= 0.289 Chirality : 0.042 0.285 2015 Planarity : 0.004 0.053 1874 Dihedral : 8.276 74.749 3209 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.52 % Allowed : 13.10 % 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: 0.62 (0.23), residues: 1269 helix: 1.50 (0.29), residues: 355 sheet: 1.18 (0.37), residues: 198 loop : -0.35 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP b 283 HIS 0.003 0.001 HIS C 141 PHE 0.012 0.001 PHE H 78 TYR 0.020 0.001 TYR H 27 ARG 0.006 0.001 ARG c 379 *********************** 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 209 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8340 (mmtp) REVERT: C 125 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8120 (ttpt) REVERT: C 156 ASP cc_start: 0.8201 (t0) cc_final: 0.7749 (t0) REVERT: A 214 MET cc_start: 0.6745 (mmm) cc_final: 0.6420 (mmm) REVERT: B 192 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8442 (ttt) REVERT: c 331 GLN cc_start: 0.8065 (mp10) cc_final: 0.7711 (mp10) REVERT: c 405 GLN cc_start: 0.8584 (tm130) cc_final: 0.7999 (tm-30) REVERT: c 420 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.6716 (mpt) REVERT: a 286 ILE cc_start: 0.8806 (mm) cc_final: 0.8569 (mm) REVERT: a 303 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8422 (mm-30) REVERT: a 308 GLU cc_start: 0.8868 (mp0) cc_final: 0.8016 (mt-10) REVERT: b 317 ASP cc_start: 0.8898 (t70) cc_final: 0.8694 (t0) REVERT: b 404 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8406 (mm-30) REVERT: H 16 GLU cc_start: 0.7583 (mp0) cc_final: 0.7329 (mp0) REVERT: H 75 LYS cc_start: 0.9156 (mtmm) cc_final: 0.8573 (mtmm) REVERT: H 100 ASP cc_start: 0.8329 (m-30) cc_final: 0.8065 (t0) REVERT: L 17 GLN cc_start: 0.8534 (pt0) cc_final: 0.8050 (pt0) REVERT: L 79 GLN cc_start: 0.7625 (mp10) cc_final: 0.7001 (mp10) outliers start: 29 outliers final: 15 residues processed: 188 average time/residue: 1.6519 time to fit residues: 331.0887 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 : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain c residue 420 MET Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 401 ASP Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 33 TYR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 87 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 116 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 121 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.075713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.059061 restraints weight = 27794.698| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 3.77 r_work: 0.2818 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11729 Z= 0.187 Angle : 0.603 10.676 15893 Z= 0.292 Chirality : 0.042 0.286 2015 Planarity : 0.003 0.039 1874 Dihedral : 8.086 83.493 3209 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.69 % Allowed : 13.36 % Favored : 83.95 % 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: 0.63 (0.23), residues: 1269 helix: 1.52 (0.29), residues: 355 sheet: 1.10 (0.37), residues: 198 loop : -0.32 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP b 283 HIS 0.003 0.001 HIS C 141 PHE 0.012 0.001 PHE H 78 TYR 0.015 0.001 TYR a 366 ARG 0.009 0.001 ARG c 379 *********************** 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: 31 poor density : 177 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8337 (mmtp) REVERT: C 125 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8130 (ttpt) REVERT: C 156 ASP cc_start: 0.8297 (t0) cc_final: 0.7803 (t0) REVERT: C 229 ASP cc_start: 0.8644 (p0) cc_final: 0.8432 (p0) REVERT: A 214 MET cc_start: 0.6856 (mmm) cc_final: 0.6599 (mmm) REVERT: B 192 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8436 (ttt) REVERT: c 331 GLN cc_start: 0.8030 (mp10) cc_final: 0.7639 (mp10) REVERT: c 405 GLN cc_start: 0.8598 (tm130) cc_final: 0.7966 (tm-30) REVERT: c 420 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.6734 (mpt) REVERT: a 286 ILE cc_start: 0.8852 (mm) cc_final: 0.8620 (mm) REVERT: a 303 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8401 (mm-30) REVERT: a 308 GLU cc_start: 0.8877 (mp0) cc_final: 0.8100 (mt-10) REVERT: a 396 GLU cc_start: 0.8603 (tt0) cc_final: 0.8103 (tm-30) REVERT: b 317 ASP cc_start: 0.8916 (t70) cc_final: 0.8706 (t0) REVERT: b 404 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8622 (mm-30) REVERT: H 6 GLU cc_start: 0.7884 (mp0) cc_final: 0.7684 (mp0) REVERT: H 16 GLU cc_start: 0.7634 (mp0) cc_final: 0.7350 (mp0) REVERT: H 75 LYS cc_start: 0.9154 (mtmm) cc_final: 0.8601 (mtmm) REVERT: H 100 ASP cc_start: 0.8309 (m-30) cc_final: 0.8075 (t0) REVERT: L 17 GLN cc_start: 0.8555 (pt0) cc_final: 0.8071 (pt0) REVERT: L 79 GLN cc_start: 0.7647 (mp10) cc_final: 0.7060 (mp10) REVERT: L 81 GLU cc_start: 0.7921 (pm20) cc_final: 0.7622 (pm20) outliers start: 31 outliers final: 15 residues processed: 187 average time/residue: 1.5943 time to fit residues: 317.9236 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 : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain c residue 420 MET Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain b residue 298 VAL Chi-restraints excluded: chain b residue 332 MET Chi-restraints excluded: chain b residue 401 ASP Chi-restraints excluded: chain b residue 411 ILE 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: 7.9990 chunk 46 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN c 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 = 0.3330 r_free = 0.3330 target = 0.076082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.059244 restraints weight = 27552.214| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.77 r_work: 0.2817 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11729 Z= 0.182 Angle : 0.591 11.652 15893 Z= 0.287 Chirality : 0.042 0.287 2015 Planarity : 0.003 0.039 1874 Dihedral : 7.781 88.913 3209 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.86 % Allowed : 13.70 % 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: 0.70 (0.23), residues: 1269 helix: 1.56 (0.29), residues: 354 sheet: 1.17 (0.37), residues: 198 loop : -0.27 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP b 283 HIS 0.003 0.001 HIS c 305 PHE 0.011 0.001 PHE H 78 TYR 0.024 0.001 TYR c 419 ARG 0.009 0.001 ARG c 379 *********************** 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 212 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8329 (mmtp) REVERT: C 156 ASP cc_start: 0.8327 (t0) cc_final: 0.7821 (t0) REVERT: A 214 MET cc_start: 0.6952 (mmm) cc_final: 0.6701 (mmm) REVERT: B 192 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8425 (ttt) REVERT: c 317 ASP cc_start: 0.8428 (t70) cc_final: 0.8227 (t70) REVERT: c 331 GLN cc_start: 0.8041 (mp10) cc_final: 0.7437 (pm20) REVERT: c 405 GLN cc_start: 0.8568 (tm130) cc_final: 0.7951 (tm-30) REVERT: c 420 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.6752 (mpt) REVERT: a 286 ILE cc_start: 0.8850 (mm) cc_final: 0.8586 (mm) REVERT: a 303 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8383 (mm-30) REVERT: a 308 GLU cc_start: 0.8877 (mp0) cc_final: 0.8008 (mt-10) REVERT: a 379 ARG cc_start: 0.8010 (mmm-85) cc_final: 0.7778 (mmm160) REVERT: a 396 GLU cc_start: 0.8640 (tt0) cc_final: 0.8134 (tm-30) REVERT: b 317 ASP cc_start: 0.8918 (t70) cc_final: 0.8705 (t0) REVERT: b 404 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8482 (mm-30) REVERT: H 16 GLU cc_start: 0.7594 (mp0) cc_final: 0.7236 (mp0) REVERT: L 17 GLN cc_start: 0.8649 (pt0) cc_final: 0.8212 (pt0) REVERT: L 79 GLN cc_start: 0.7641 (mp10) cc_final: 0.7305 (mt0) REVERT: L 81 GLU cc_start: 0.7939 (pm20) cc_final: 0.7576 (pm20) outliers start: 33 outliers final: 13 residues processed: 193 average time/residue: 1.5906 time to fit residues: 327.5981 Evaluate side-chains 190 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 415 LEU Chi-restraints excluded: chain c residue 420 MET Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain b residue 298 VAL Chi-restraints excluded: chain b residue 401 ASP Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain H residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 121 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 119 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 120 optimal weight: 0.0980 chunk 24 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN c 354 HIS ** c 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 335 GLN a 405 GLN 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 = 0.075852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.059250 restraints weight = 27646.217| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.72 r_work: 0.2820 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11729 Z= 0.181 Angle : 0.616 11.958 15893 Z= 0.297 Chirality : 0.042 0.288 2015 Planarity : 0.003 0.040 1874 Dihedral : 7.525 76.177 3209 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.99 % Allowed : 15.00 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.74 (0.24), residues: 1269 helix: 1.59 (0.29), residues: 355 sheet: 1.22 (0.36), residues: 210 loop : -0.29 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 283 HIS 0.004 0.001 HIS C 230 PHE 0.012 0.001 PHE H 78 TYR 0.016 0.001 TYR a 366 ARG 0.009 0.001 ARG c 379 *********************** 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 201 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8308 (mmtp) REVERT: C 156 ASP cc_start: 0.8311 (t0) cc_final: 0.7841 (t0) REVERT: A 214 MET cc_start: 0.6982 (mmm) cc_final: 0.6690 (mmm) REVERT: B 76 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8477 (tt0) REVERT: B 192 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8412 (ttt) REVERT: c 317 ASP cc_start: 0.8414 (t70) cc_final: 0.8208 (t70) REVERT: c 331 GLN cc_start: 0.7984 (mp10) cc_final: 0.7441 (pm20) REVERT: c 405 GLN cc_start: 0.8571 (tm130) cc_final: 0.7994 (tm-30) REVERT: c 420 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.6823 (mpt) REVERT: a 286 ILE cc_start: 0.8793 (mm) cc_final: 0.8557 (mm) REVERT: a 303 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8389 (mm-30) REVERT: a 308 GLU cc_start: 0.8871 (mp0) cc_final: 0.8024 (mt-10) REVERT: a 379 ARG cc_start: 0.7975 (mmm-85) cc_final: 0.7651 (mtp-110) REVERT: a 396 GLU cc_start: 0.8640 (tt0) cc_final: 0.8128 (tm-30) REVERT: b 317 ASP cc_start: 0.8934 (t70) cc_final: 0.8718 (t0) REVERT: b 404 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8451 (mm-30) REVERT: b 413 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8399 (pt0) REVERT: H 16 GLU cc_start: 0.7669 (mp0) cc_final: 0.7301 (mp0) REVERT: H 75 LYS cc_start: 0.9056 (mtmm) cc_final: 0.8532 (mtmm) REVERT: L 17 GLN cc_start: 0.8641 (pt0) cc_final: 0.8199 (pt0) REVERT: L 79 GLN cc_start: 0.7667 (mp10) cc_final: 0.7286 (mt0) REVERT: L 81 GLU cc_start: 0.8001 (pm20) cc_final: 0.7667 (pm20) outliers start: 23 outliers final: 13 residues processed: 188 average time/residue: 1.6107 time to fit residues: 322.9623 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 : 1.331 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 70 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN c 354 HIS c 409 ASN a 335 GLN a 405 GLN 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 = 0.075783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.059207 restraints weight = 27507.906| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.75 r_work: 0.2824 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11729 Z= 0.191 Angle : 0.620 12.292 15893 Z= 0.300 Chirality : 0.042 0.286 2015 Planarity : 0.004 0.040 1874 Dihedral : 7.301 76.246 3209 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.73 % Allowed : 15.61 % Favored : 82.65 % 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: 0.76 (0.24), residues: 1269 helix: 1.63 (0.29), residues: 354 sheet: 1.28 (0.37), residues: 210 loop : -0.31 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.003 0.001 HIS A 115 PHE 0.012 0.001 PHE H 78 TYR 0.026 0.001 TYR c 419 ARG 0.009 0.001 ARG c 379 ********************** 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 197 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8320 (mmtp) REVERT: C 156 ASP cc_start: 0.8329 (t0) cc_final: 0.7833 (t0) REVERT: A 211 ASP cc_start: 0.8689 (m-30) cc_final: 0.8444 (m-30) REVERT: B 76 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8499 (tt0) REVERT: B 192 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8409 (ttt) REVERT: c 317 ASP cc_start: 0.8436 (t70) cc_final: 0.8227 (t70) REVERT: c 331 GLN cc_start: 0.8007 (mp10) cc_final: 0.7465 (pm20) REVERT: c 420 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.6829 (mpt) REVERT: a 286 ILE cc_start: 0.8797 (mm) cc_final: 0.8543 (mm) REVERT: a 303 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8375 (mm-30) REVERT: a 308 GLU cc_start: 0.8831 (mp0) cc_final: 0.7999 (mt-10) REVERT: a 379 ARG cc_start: 0.8027 (mmm-85) cc_final: 0.7624 (mtp-110) REVERT: a 396 GLU cc_start: 0.8639 (tt0) cc_final: 0.8125 (tm-30) REVERT: b 317 ASP cc_start: 0.8944 (t70) cc_final: 0.8730 (t0) REVERT: b 404 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8488 (mm-30) REVERT: H 11 LEU cc_start: 0.9209 (tp) cc_final: 0.8931 (tp) REVERT: H 16 GLU cc_start: 0.7686 (mp0) cc_final: 0.7308 (mp0) REVERT: H 64 LYS cc_start: 0.8898 (tptp) cc_final: 0.8677 (tptm) REVERT: H 75 LYS cc_start: 0.9044 (mtmm) cc_final: 0.8514 (mtmm) REVERT: L 17 GLN cc_start: 0.8647 (pt0) cc_final: 0.8271 (pt0) REVERT: L 79 GLN cc_start: 0.7742 (mp10) cc_final: 0.7332 (mt0) REVERT: L 81 GLU cc_start: 0.8089 (pm20) cc_final: 0.7745 (pm20) outliers start: 20 outliers final: 13 residues processed: 185 average time/residue: 1.6443 time to fit residues: 324.6546 Evaluate side-chains 188 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 1.168 ------------------------------------------------------------------------------- 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 H residue 5 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.2374 > 50: distance: 13 - 18: 4.969 distance: 18 - 19: 11.700 distance: 19 - 20: 3.407 distance: 19 - 22: 29.461 distance: 20 - 21: 14.328 distance: 20 - 24: 8.845 distance: 22 - 23: 8.895 distance: 24 - 25: 10.963 distance: 25 - 26: 6.550 distance: 25 - 28: 10.895 distance: 26 - 27: 15.219 distance: 26 - 33: 15.851 distance: 28 - 29: 12.124 distance: 30 - 31: 9.178 distance: 30 - 32: 7.253 distance: 33 - 34: 6.148 distance: 34 - 35: 15.189 distance: 35 - 36: 28.639 distance: 35 - 37: 26.375 distance: 37 - 38: 10.037 distance: 38 - 39: 4.391 distance: 38 - 41: 9.828 distance: 39 - 40: 3.808 distance: 39 - 46: 8.968 distance: 41 - 42: 6.200 distance: 42 - 43: 5.682 distance: 43 - 44: 10.871 distance: 44 - 45: 9.013 distance: 46 - 47: 4.325 distance: 47 - 48: 13.455 distance: 47 - 50: 6.198 distance: 48 - 49: 14.081 distance: 48 - 54: 17.249 distance: 50 - 51: 13.891 distance: 51 - 52: 15.900 distance: 51 - 53: 10.333 distance: 54 - 55: 5.481 distance: 55 - 56: 11.753 distance: 55 - 58: 21.719 distance: 56 - 57: 14.749 distance: 56 - 61: 21.921 distance: 58 - 59: 9.174 distance: 58 - 60: 16.585 distance: 61 - 62: 8.254 distance: 61 - 67: 13.242 distance: 62 - 63: 13.923 distance: 62 - 65: 6.894 distance: 63 - 64: 21.084 distance: 63 - 68: 11.537 distance: 65 - 66: 7.745 distance: 66 - 67: 11.434 distance: 68 - 69: 10.672 distance: 69 - 70: 13.644 distance: 70 - 71: 29.660 distance: 70 - 72: 8.992 distance: 72 - 73: 28.185 distance: 73 - 74: 24.025 distance: 74 - 75: 23.222 distance: 74 - 76: 19.618 distance: 76 - 77: 9.768 distance: 76 - 110: 13.926 distance: 77 - 78: 7.461 distance: 77 - 80: 3.560 distance: 78 - 79: 8.139 distance: 78 - 88: 7.679 distance: 79 - 107: 5.710 distance: 80 - 81: 7.196 distance: 81 - 83: 5.711 distance: 82 - 84: 3.101 distance: 85 - 86: 4.483