Starting phenix.real_space_refine on Sat Oct 12 04:02:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cj7_45624/10_2024/9cj7_45624.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cj7_45624/10_2024/9cj7_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cj7_45624/10_2024/9cj7_45624.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cj7_45624/10_2024/9cj7_45624.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cj7_45624/10_2024/9cj7_45624.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cj7_45624/10_2024/9cj7_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 7.71, per 1000 atoms: 0.67 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 1.5 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: 1.33 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: 3.73 Time building geometry restraints manager: 4.50 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: 1.700 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.010 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.080 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:11.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.790 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 1.320 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: 1.6509 time to fit residues: 447.1615 Evaluate side-chains 178 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.494 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 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 fitting. rotamer outliers: 29 poor density : 189 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 125 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8594 (ttpt) REVERT: B 192 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7433 (ttt) REVERT: c 405 GLN cc_start: 0.8227 (tm130) cc_final: 0.7716 (tm-30) REVERT: c 420 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.6850 (mpt) REVERT: a 307 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7793 (mm-30) REVERT: a 323 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8292 (mp) REVERT: a 416 GLN cc_start: 0.8396 (tp40) cc_final: 0.8116 (tp-100) REVERT: b 408 ASP cc_start: 0.8228 (m-30) cc_final: 0.7974 (m-30) outliers start: 29 outliers final: 6 residues processed: 196 average time/residue: 1.5610 time to fit residues: 326.7599 Evaluate side-chains 182 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 172 time to evaluate : 1.357 ------------------------------------------------------------------------------- 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 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 63 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 113 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2193 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 : 0.668 9.890 15893 Z= 0.327 Chirality : 0.045 0.355 2015 Planarity : 0.004 0.042 1874 Dihedral : 10.212 77.216 3209 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.95 % Allowed : 10.58 % Favored : 86.47 % 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: 0.25 (0.23), residues: 1269 helix: 1.07 (0.28), residues: 356 sheet: 0.44 (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 b 283 HIS 0.006 0.001 HIS B 141 PHE 0.013 0.001 PHE c 399 TYR 0.023 0.001 TYR b 419 ARG 0.003 0.000 ARG b 379 *********************** 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 fitting. rotamer outliers: 34 poor density : 188 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8473 (mmtp) REVERT: C 125 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8615 (ttpt) REVERT: B 192 MET cc_start: 0.7878 (ttt) cc_final: 0.7557 (ttt) REVERT: c 268 ASP cc_start: 0.6742 (p0) cc_final: 0.6492 (p0) REVERT: c 405 GLN cc_start: 0.8255 (tm130) cc_final: 0.7779 (tm-30) REVERT: c 414 MET cc_start: 0.8109 (ptm) cc_final: 0.7842 (ptt) REVERT: c 420 MET cc_start: 0.7537 (mpp) cc_final: 0.6709 (mpt) REVERT: b 306 ASP cc_start: 0.8859 (p0) cc_final: 0.8649 (p0) REVERT: b 408 ASP cc_start: 0.8339 (m-30) cc_final: 0.8068 (m-30) REVERT: L 45 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.8975 (ttpp) outliers start: 34 outliers final: 14 residues processed: 199 average time/residue: 1.6395 time to fit residues: 348.6591 Evaluate side-chains 189 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 172 time to evaluate : 1.320 ------------------------------------------------------------------------------- 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 414 MET 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 113 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 115 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 L 17 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 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 0.064 11729 Z= 0.205 Angle : 0.617 9.681 15893 Z= 0.302 Chirality : 0.043 0.283 2015 Planarity : 0.004 0.055 1874 Dihedral : 9.139 75.081 3209 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.86 % Allowed : 12.23 % Favored : 84.91 % 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: 1.27 (0.28), residues: 357 sheet: 0.69 (0.36), residues: 214 loop : -0.40 (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 213 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 180 time to evaluate : 2.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8445 (mmtp) REVERT: B 192 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7491 (ttt) REVERT: c 268 ASP cc_start: 0.6735 (p0) cc_final: 0.6482 (p0) REVERT: c 405 GLN cc_start: 0.8204 (tm130) cc_final: 0.7660 (tm-30) REVERT: c 414 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7861 (ptt) REVERT: c 420 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.6738 (mpt) outliers start: 33 outliers final: 10 residues processed: 190 average time/residue: 1.6809 time to fit residues: 340.8600 Evaluate side-chains 186 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 172 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain c residue 414 MET 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 H residue 29 ILE Chi-restraints excluded: chain H residue 50 ASN Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 84 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 109 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11729 Z= 0.189 Angle : 0.599 9.574 15893 Z= 0.293 Chirality : 0.042 0.279 2015 Planarity : 0.003 0.033 1874 Dihedral : 8.681 75.479 3209 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.69 % Allowed : 12.84 % Favored : 84.48 % 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: 0.44 (0.23), residues: 1269 helix: 1.34 (0.29), residues: 357 sheet: 0.81 (0.36), residues: 210 loop : -0.40 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 283 HIS 0.003 0.001 HIS C 141 PHE 0.012 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 fitting. rotamer outliers: 31 poor density : 184 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8423 (mmtp) REVERT: B 192 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7454 (ttt) REVERT: c 405 GLN cc_start: 0.8245 (tm130) cc_final: 0.7689 (tm-30) REVERT: c 420 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.6653 (mpt) outliers start: 31 outliers final: 14 residues processed: 195 average time/residue: 1.5951 time to fit residues: 331.7862 Evaluate side-chains 188 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 171 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain A residue 61 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 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 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 Chi-restraints excluded: chain L residue 89 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 117 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 354 HIS ** c 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 335 GLN a 405 GLN H 1 GLN ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2789 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= 0.182 Angle : 0.602 10.293 15893 Z= 0.293 Chirality : 0.042 0.284 2015 Planarity : 0.003 0.031 1874 Dihedral : 8.374 78.760 3209 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.78 % Allowed : 13.53 % Favored : 83.69 % 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: 0.53 (0.23), residues: 1269 helix: 1.37 (0.29), residues: 356 sheet: 1.00 (0.37), residues: 204 loop : -0.35 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 283 HIS 0.003 0.001 HIS C 141 PHE 0.012 0.001 PHE H 78 TYR 0.016 0.001 TYR b 419 ARG 0.005 0.000 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 205 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 173 time to evaluate : 1.402 Fit side-chains revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8449 (mmtp) REVERT: B 192 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7472 (ttt) REVERT: c 405 GLN cc_start: 0.8215 (tm130) cc_final: 0.7615 (tm-30) REVERT: c 414 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7798 (ptt) REVERT: c 420 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.6689 (mpt) REVERT: b 404 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8021 (mm-30) REVERT: b 408 ASP cc_start: 0.8398 (m-30) cc_final: 0.8092 (m-30) REVERT: b 413 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7410 (pt0) outliers start: 32 outliers final: 14 residues processed: 184 average time/residue: 1.5293 time to fit residues: 300.6243 Evaluate side-chains 185 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 166 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain c residue 414 MET Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain c residue 420 MET Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain b residue 298 VAL Chi-restraints excluded: chain b residue 401 ASP Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain b residue 413 GLU Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 85 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN B 146 ASN c 305 HIS c 342 ASN c 354 HIS c 409 ASN a 335 GLN a 405 GLN H 1 GLN L 17 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 11729 Z= 0.463 Angle : 0.740 10.902 15893 Z= 0.357 Chirality : 0.046 0.371 2015 Planarity : 0.004 0.037 1874 Dihedral : 8.601 72.581 3209 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.73 % Allowed : 13.10 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.23), residues: 1269 helix: 1.09 (0.28), residues: 356 sheet: 0.57 (0.35), residues: 228 loop : -0.35 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP b 283 HIS 0.008 0.001 HIS C 141 PHE 0.014 0.002 PHE H 78 TYR 0.022 0.002 TYR c 419 ARG 0.004 0.001 ARG A 248 *********************** 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 216 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 173 time to evaluate : 1.336 Fit side-chains revert: symmetry clash REVERT: C 116 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8504 (mmtp) REVERT: B 192 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7555 (ttt) REVERT: c 405 GLN cc_start: 0.8272 (tm130) cc_final: 0.7701 (tm-30) REVERT: c 420 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7525 (mpt) REVERT: a 323 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8452 (mp) REVERT: a 396 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7596 (tt0) REVERT: b 306 ASP cc_start: 0.8821 (p0) cc_final: 0.8600 (p0) REVERT: L 45 LYS cc_start: 0.9376 (OUTLIER) cc_final: 0.9035 (ttpp) outliers start: 43 outliers final: 14 residues processed: 190 average time/residue: 1.5873 time to fit residues: 321.2884 Evaluate side-chains 181 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 161 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 116 LYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain c residue 414 MET Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain c residue 420 MET Chi-restraints excluded: chain a residue 323 ILE Chi-restraints excluded: chain a residue 396 GLU Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain b residue 298 VAL Chi-restraints excluded: chain b residue 396 GLU 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 45 LYS Chi-restraints excluded: chain L residue 51 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 95 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 a 335 GLN a 405 GLN H 1 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11729 Z= 0.189 Angle : 0.635 11.728 15893 Z= 0.309 Chirality : 0.042 0.286 2015 Planarity : 0.004 0.041 1874 Dihedral : 8.145 82.687 3209 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.60 % Allowed : 14.22 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.23), residues: 1269 helix: 1.27 (0.29), residues: 356 sheet: 0.93 (0.36), residues: 210 loop : -0.36 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 283 HIS 0.007 0.001 HIS C 230 PHE 0.013 0.001 PHE H 78 TYR 0.014 0.001 TYR b 419 ARG 0.010 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 200 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 170 time to evaluate : 1.415 Fit side-chains revert: symmetry clash REVERT: B 192 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7474 (ttt) REVERT: c 405 GLN cc_start: 0.8174 (tm130) cc_final: 0.7535 (tm-30) REVERT: c 414 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7823 (ptt) REVERT: c 420 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7598 (mpt) REVERT: a 395 ASN cc_start: 0.8465 (OUTLIER) cc_final: 0.8219 (m-40) outliers start: 30 outliers final: 11 residues processed: 182 average time/residue: 1.5709 time to fit residues: 305.3574 Evaluate side-chains 178 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 163 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain c residue 414 MET Chi-restraints excluded: chain c residue 415 LEU Chi-restraints excluded: chain c residue 420 MET Chi-restraints excluded: chain a residue 395 ASN Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain b residue 401 ASP Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 51 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 107 optimal weight: 0.3980 chunk 112 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 a 335 GLN a 405 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3045 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= 0.196 Angle : 0.644 11.742 15893 Z= 0.312 Chirality : 0.042 0.285 2015 Planarity : 0.004 0.041 1874 Dihedral : 7.922 87.180 3209 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.73 % Allowed : 15.09 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.24), residues: 1269 helix: 1.52 (0.29), residues: 347 sheet: 0.99 (0.37), residues: 210 loop : -0.30 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 283 HIS 0.003 0.001 HIS B 141 PHE 0.013 0.001 PHE H 78 TYR 0.025 0.001 TYR c 419 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 184 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 164 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 192 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7460 (ttt) REVERT: c 405 GLN cc_start: 0.8171 (tm130) cc_final: 0.7532 (tm-30) REVERT: c 420 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.6867 (mpt) outliers start: 20 outliers final: 9 residues processed: 172 average time/residue: 1.5490 time to fit residues: 285.1053 Evaluate side-chains 173 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 162 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 411 ILE Chi-restraints excluded: chain b residue 401 ASP Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain b residue 413 GLU Chi-restraints excluded: chain H residue 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 a 335 GLN a 405 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11729 Z= 0.305 Angle : 0.692 12.677 15893 Z= 0.332 Chirality : 0.044 0.314 2015 Planarity : 0.004 0.043 1874 Dihedral : 7.851 75.206 3209 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % 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: 0.55 (0.24), residues: 1269 helix: 1.47 (0.29), residues: 347 sheet: 0.73 (0.36), residues: 222 loop : -0.28 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP b 283 HIS 0.005 0.001 HIS C 141 PHE 0.014 0.001 PHE H 78 TYR 0.014 0.001 TYR b 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 187 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 164 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 192 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7528 (ttt) REVERT: c 405 GLN cc_start: 0.8211 (tm130) cc_final: 0.7578 (tm-30) REVERT: c 420 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.6885 (mpt) REVERT: a 395 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.8267 (m-40) REVERT: b 404 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8210 (mm-30) REVERT: H 105 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.7439 (pt0) outliers start: 23 outliers final: 9 residues processed: 176 average time/residue: 1.4931 time to fit residues: 281.0407 Evaluate side-chains 173 residues out of total 1153 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 160 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 395 ASN Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain b residue 401 ASP Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain b residue 413 GLU Chi-restraints excluded: chain H residue 5 ARG Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 51 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.0060 chunk 92 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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 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 = 0.3314 r_free = 0.3314 target = 0.075180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.058543 restraints weight = 27238.668| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.73 r_work: 0.2804 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11729 Z= 0.192 Angle : 0.643 12.282 15893 Z= 0.311 Chirality : 0.042 0.289 2015 Planarity : 0.004 0.040 1874 Dihedral : 7.537 77.320 3209 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.56 % Allowed : 15.78 % 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: 0.68 (0.24), residues: 1269 helix: 1.59 (0.29), residues: 346 sheet: 1.09 (0.37), residues: 204 loop : -0.28 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 283 HIS 0.003 0.001 HIS A 230 PHE 0.013 0.001 PHE H 78 TYR 0.027 0.001 TYR c 419 ARG 0.009 0.001 ARG c 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5038.35 seconds wall clock time: 91 minutes 51.18 seconds (5511.18 seconds total)