Starting phenix.real_space_refine on Thu Jan 18 23:46:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejf_28180/01_2024/8ejf_28180.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejf_28180/01_2024/8ejf_28180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejf_28180/01_2024/8ejf_28180.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejf_28180/01_2024/8ejf_28180.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejf_28180/01_2024/8ejf_28180.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejf_28180/01_2024/8ejf_28180.pdb" } resolution = 3.72 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= 0.017 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 90 5.16 5 C 6081 2.51 5 N 1530 2.21 5 O 2100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 9801 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1560 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 4, 'TRANS': 192} Chain: "a" Number of atoms: 1321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1321 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 4, 'TRANS': 158} Chain: "B" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1560 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 4, 'TRANS': 192} Chain: "b" Number of atoms: 1321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1321 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 4, 'TRANS': 158} Chain: "C" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1560 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 4, 'TRANS': 192} Chain: "c" Number of atoms: 1321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1321 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 4, 'TRANS': 158} Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 5 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: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 5 Chain: "H" 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: "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: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 5 Chain: "K" 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: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 5 Chain: "M" 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: "N" 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: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 5 Chain: "P" 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 5 Chain: "S" 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: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 5 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 5 Chain: "X" 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 5 Chain: "d" 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: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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 Time building chain proxies: 5.83, per 1000 atoms: 0.59 Number of scatterers: 9801 At special positions: 0 Unit cell: (94.05, 91.96, 107.635, 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 90 16.00 O 2100 8.00 N 1530 7.00 C 6081 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=1.80 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.04 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.02 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 360 " distance=2.03 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 86 " - pdb=" SG CYS B 231 " distance=1.80 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.04 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.02 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 360 " 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 C 86 " - pdb=" SG CYS C 231 " distance=1.80 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.04 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.02 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=2.02 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA G 3 " - " MAN G 4 " " BMA J 3 " - " MAN J 4 " " BMA L 3 " - " MAN L 4 " " BMA O 3 " - " MAN O 4 " " BMA R 3 " - " MAN R 4 " " BMA T 3 " - " MAN T 4 " " BMA W 3 " - " MAN W 4 " " BMA Z 3 " - " MAN Z 4 " ALPHA1-6 " BMA D 3 " - " MAN D 5 " " BMA G 3 " - " MAN G 5 " " BMA J 3 " - " MAN J 5 " " BMA L 3 " - " MAN L 5 " " BMA O 3 " - " MAN O 5 " " BMA R 3 " - " MAN R 5 " " BMA T 3 " - " MAN T 5 " " BMA W 3 " - " MAN W 5 " " BMA Z 3 " - " MAN Z 5 " BETA1-4 " 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 G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 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 K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG 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 " BETA1-6 " NAG H 1 " - " FUC H 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG P 1 " - " FUC P 3 " " NAG X 1 " - " FUC X 3 " NAG-ASN " NAG A 501 " - " ASN A 99 " " NAG B 501 " - " ASN B 99 " " NAG C 501 " - " ASN C 99 " " NAG D 1 " - " ASN A 79 " " NAG E 1 " - " ASN A 89 " " NAG F 1 " - " ASN A 109 " " NAG G 1 " - " ASN A 119 " " NAG H 1 " - " ASN A 167 " " NAG I 1 " - " ASN A 224 " " NAG J 1 " - " ASN a 365 " " NAG K 1 " - " ASN a 373 " " NAG L 1 " - " ASN B 79 " " NAG M 1 " - " ASN B 89 " " NAG N 1 " - " ASN B 109 " " NAG O 1 " - " ASN B 119 " " NAG P 1 " - " ASN B 167 " " NAG Q 1 " - " ASN B 224 " " NAG R 1 " - " ASN b 365 " " NAG S 1 " - " ASN b 373 " " NAG T 1 " - " ASN C 79 " " NAG U 1 " - " ASN C 89 " " NAG V 1 " - " ASN C 109 " " NAG W 1 " - " ASN C 119 " " NAG X 1 " - " ASN C 167 " " NAG Y 1 " - " ASN C 224 " " NAG Z 1 " - " ASN c 365 " " NAG a 701 " - " ASN a 390 " " NAG a 702 " - " ASN a 395 " " NAG b 701 " - " ASN b 390 " " NAG b 702 " - " ASN b 395 " " NAG c 701 " - " ASN c 390 " " NAG c 702 " - " ASN c 395 " " NAG d 1 " - " ASN c 373 " Time building additional restraints: 5.78 Conformation dependent library (CDL) restraints added in 1.8 seconds 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2040 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 12 sheets defined 36.7% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 182 through 195 removed outlier: 3.647A pdb=" N GLY A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 202 removed outlier: 4.184A pdb=" N ILE A 201 " --> pdb=" O GLY A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'a' and resid 295 through 299 Processing helix chain 'a' and resid 300 through 303 Processing helix chain 'a' and resid 307 through 327 Processing helix chain 'a' and resid 333 through 345 removed outlier: 3.611A pdb=" N ASN a 342 " --> pdb=" O ASN a 338 " (cutoff:3.500A) Processing helix chain 'a' and resid 346 through 359 Processing helix chain 'a' and resid 395 through 400 Processing helix chain 'a' and resid 400 through 417 Processing helix chain 'B' and resid 74 through 79 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 132 through 142 Processing helix chain 'B' and resid 182 through 195 removed outlier: 3.647A pdb=" N GLY B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 202 removed outlier: 4.183A pdb=" N ILE B 201 " --> pdb=" O GLY B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 246 Processing helix chain 'b' and resid 295 through 299 Processing helix chain 'b' and resid 300 through 303 Processing helix chain 'b' and resid 307 through 327 Processing helix chain 'b' and resid 333 through 345 removed outlier: 3.611A pdb=" N ASN b 342 " --> pdb=" O ASN b 338 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 359 Processing helix chain 'b' and resid 395 through 400 Processing helix chain 'b' and resid 400 through 417 Processing helix chain 'C' and resid 74 through 79 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 132 through 142 Processing helix chain 'C' and resid 182 through 195 removed outlier: 3.647A pdb=" N GLY C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 202 removed outlier: 4.184A pdb=" N ILE C 201 " --> pdb=" O GLY C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 246 Processing helix chain 'c' and resid 295 through 299 Processing helix chain 'c' and resid 300 through 303 Processing helix chain 'c' and resid 307 through 327 Processing helix chain 'c' and resid 333 through 345 removed outlier: 3.611A pdb=" N ASN c 342 " --> pdb=" O ASN c 338 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 359 Processing helix chain 'c' and resid 395 through 400 Processing helix chain 'c' and resid 400 through 417 Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 89 removed outlier: 6.758A pdb=" N HIS A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A 154 " --> pdb=" O GLN A 165 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 277 through 280 Processing sheet with id=AA4, first strand: chain 'a' and resid 388 through 389 Processing sheet with id=AA5, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'B' and resid 84 through 89 removed outlier: 6.758A pdb=" N HIS B 92 " --> pdb=" O LYS B 88 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER B 154 " --> pdb=" O GLN B 165 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 277 through 280 Processing sheet with id=AA8, first strand: chain 'b' and resid 388 through 389 Processing sheet with id=AA9, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'C' and resid 84 through 89 removed outlier: 6.758A pdb=" N HIS C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER C 154 " --> pdb=" O GLN C 165 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'c' and resid 277 through 280 Processing sheet with id=AB3, first strand: chain 'c' and resid 388 through 389 333 hydrogen bonds defined for protein. 891 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: 2.59 Time building geometry restraints manager: 6.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1848 1.32 - 1.46: 3260 1.46 - 1.59: 4724 1.59 - 1.73: 32 1.73 - 1.87: 129 Bond restraints: 9993 Sorted by residual: bond pdb=" NE ARG b 422 " pdb=" CZ ARG b 422 " ideal model delta sigma weight residual 1.326 1.407 -0.081 1.10e-02 8.26e+03 5.41e+01 bond pdb=" NE ARG c 422 " pdb=" CZ ARG c 422 " ideal model delta sigma weight residual 1.326 1.407 -0.081 1.10e-02 8.26e+03 5.40e+01 bond pdb=" NE ARG a 422 " pdb=" CZ ARG a 422 " ideal model delta sigma weight residual 1.326 1.407 -0.081 1.10e-02 8.26e+03 5.39e+01 bond pdb=" CB PHE a 399 " pdb=" CG PHE a 399 " ideal model delta sigma weight residual 1.502 1.373 0.129 2.30e-02 1.89e+03 3.17e+01 bond pdb=" CB PHE c 399 " pdb=" CG PHE c 399 " ideal model delta sigma weight residual 1.502 1.373 0.129 2.30e-02 1.89e+03 3.16e+01 ... (remaining 9988 not shown) Histogram of bond angle deviations from ideal: 99.12 - 106.16: 305 106.16 - 113.20: 5456 113.20 - 120.24: 4057 120.24 - 127.28: 3566 127.28 - 134.31: 152 Bond angle restraints: 13536 Sorted by residual: angle pdb=" N ILE b 345 " pdb=" CA ILE b 345 " pdb=" C ILE b 345 " ideal model delta sigma weight residual 112.29 123.82 -11.53 9.40e-01 1.13e+00 1.50e+02 angle pdb=" N ILE c 345 " pdb=" CA ILE c 345 " pdb=" C ILE c 345 " ideal model delta sigma weight residual 112.29 123.80 -11.51 9.40e-01 1.13e+00 1.50e+02 angle pdb=" N ILE a 345 " pdb=" CA ILE a 345 " pdb=" C ILE a 345 " ideal model delta sigma weight residual 112.29 123.80 -11.51 9.40e-01 1.13e+00 1.50e+02 angle pdb=" N SER A 171 " pdb=" CA SER A 171 " pdb=" C SER A 171 " ideal model delta sigma weight residual 114.31 99.79 14.52 1.29e+00 6.01e-01 1.27e+02 angle pdb=" N SER B 171 " pdb=" CA SER B 171 " pdb=" C SER B 171 " ideal model delta sigma weight residual 114.31 99.79 14.52 1.29e+00 6.01e-01 1.27e+02 ... (remaining 13531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.24: 6393 21.24 - 42.49: 216 42.49 - 63.73: 42 63.73 - 84.97: 63 84.97 - 106.21: 66 Dihedral angle restraints: 6780 sinusoidal: 3609 harmonic: 3171 Sorted by residual: dihedral pdb=" CA CYS C 118 " pdb=" CB CYS C 118 " pdb=" SG CYS C 118 " pdb=" SG CYS C 155 " ideal model delta sinusoidal sigma weight residual 79.00 5.99 73.01 1 2.00e+01 2.50e-03 1.70e+01 dihedral pdb=" CA CYS A 118 " pdb=" CB CYS A 118 " pdb=" SG CYS A 118 " pdb=" SG CYS A 155 " ideal model delta sinusoidal sigma weight residual 79.00 6.01 72.99 1 2.00e+01 2.50e-03 1.70e+01 dihedral pdb=" CA CYS B 118 " pdb=" CB CYS B 118 " pdb=" SG CYS B 118 " pdb=" SG CYS B 155 " ideal model delta sinusoidal sigma weight residual 79.00 6.03 72.97 1 2.00e+01 2.50e-03 1.70e+01 ... (remaining 6777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 988 0.106 - 0.212: 421 0.212 - 0.318: 215 0.318 - 0.423: 106 0.423 - 0.529: 25 Chirality restraints: 1755 Sorted by residual: chirality pdb=" C1 MAN G 4 " pdb=" O3 BMA G 3 " pdb=" C2 MAN G 4 " pdb=" O5 MAN G 4 " both_signs ideal model delta sigma weight residual False 2.40 2.62 -0.22 2.00e-02 2.50e+03 1.16e+02 chirality pdb=" C1 MAN W 4 " pdb=" O3 BMA W 3 " pdb=" C2 MAN W 4 " pdb=" O5 MAN W 4 " both_signs ideal model delta sigma weight residual False 2.40 2.61 -0.21 2.00e-02 2.50e+03 1.15e+02 chirality pdb=" C1 MAN O 4 " pdb=" O3 BMA O 3 " pdb=" C2 MAN O 4 " pdb=" O5 MAN O 4 " both_signs ideal model delta sigma weight residual False 2.40 2.61 -0.21 2.00e-02 2.50e+03 1.13e+02 ... (remaining 1752 not shown) Planarity restraints: 1620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN a 395 " -0.069 2.00e-02 2.50e+03 7.02e-02 6.17e+01 pdb=" CG ASN a 395 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN a 395 " 0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN a 395 " 0.108 2.00e-02 2.50e+03 pdb=" C1 NAG a 702 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN b 395 " 0.068 2.00e-02 2.50e+03 7.02e-02 6.16e+01 pdb=" CG ASN b 395 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN b 395 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN b 395 " -0.108 2.00e-02 2.50e+03 pdb=" C1 NAG b 702 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN c 395 " -0.068 2.00e-02 2.50e+03 7.01e-02 6.14e+01 pdb=" CG ASN c 395 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN c 395 " 0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN c 395 " 0.107 2.00e-02 2.50e+03 pdb=" C1 NAG c 702 " -0.085 2.00e-02 2.50e+03 ... (remaining 1617 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2691 2.82 - 3.34: 9986 3.34 - 3.86: 16323 3.86 - 4.38: 20471 4.38 - 4.90: 30916 Nonbonded interactions: 80387 Sorted by model distance: nonbonded pdb=" N SER B 171 " pdb=" N TYR B 172 " model vdw 2.299 2.560 nonbonded pdb=" N SER A 171 " pdb=" N TYR A 172 " model vdw 2.299 2.560 nonbonded pdb=" N SER C 171 " pdb=" N TYR C 172 " model vdw 2.300 2.560 nonbonded pdb=" N ASP b 347 " pdb=" OD1 ASP b 347 " model vdw 2.378 2.520 nonbonded pdb=" N ASP c 347 " pdb=" OD1 ASP c 347 " model vdw 2.379 2.520 ... (remaining 80382 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'L' selection = chain 'O' selection = chain 'R' selection = chain 'T' selection = chain 'W' selection = chain 'Z' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'U' selection = chain 'V' selection = chain 'Y' } ncs_group { reference = (chain 'H' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } 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 group one per residue 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: 0.980 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: 4.010 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 31.100 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.120 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 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 : 0.024 0.129 9993 Z= 1.502 Angle : 1.995 14.517 13536 Z= 1.262 Chirality : 0.164 0.529 1755 Planarity : 0.011 0.049 1587 Dihedral : 17.780 106.214 4677 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: -1.87 (0.23), residues: 1068 helix: -1.24 (0.24), residues: 384 sheet: -0.18 (0.57), residues: 87 loop : -1.38 (0.23), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.008 TRP B 210 HIS 0.011 0.003 HIS B 93 PHE 0.018 0.006 PHE c 309 TYR 0.088 0.011 TYR C 166 ARG 0.007 0.001 ARG c 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 312 MET cc_start: 0.8327 (mmm) cc_final: 0.8093 (tpp) REVERT: b 359 MET cc_start: 0.8390 (mmm) cc_final: 0.8004 (mmm) REVERT: C 82 MET cc_start: 0.8895 (pmm) cc_final: 0.8468 (pmm) REVERT: c 359 MET cc_start: 0.8275 (mmm) cc_final: 0.7709 (tpp) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.3180 time to fit residues: 90.9585 Evaluate side-chains 116 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 ASN a 406 GLN B 92 HIS ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 ASN b 406 GLN C 92 HIS ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 406 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.142 9993 Z= 0.385 Angle : 1.010 10.688 13536 Z= 0.506 Chirality : 0.052 0.304 1755 Planarity : 0.005 0.035 1587 Dihedral : 16.905 92.746 2646 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.67 % Favored : 89.04 % Rotamer: Outliers : 2.17 % Allowed : 7.66 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -1.96 (0.23), residues: 1068 helix: -0.36 (0.26), residues: 381 sheet: -0.12 (0.57), residues: 87 loop : -2.20 (0.20), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP a 370 HIS 0.008 0.001 HIS a 305 PHE 0.017 0.002 PHE a 309 TYR 0.019 0.002 TYR B 253 ARG 0.005 0.001 ARG a 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 136 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 417 LYS cc_start: 0.9078 (tppp) cc_final: 0.8844 (mptt) REVERT: B 82 MET cc_start: 0.8620 (pmm) cc_final: 0.8268 (pmm) REVERT: C 75 MET cc_start: 0.8198 (mmm) cc_final: 0.7856 (mmm) REVERT: C 82 MET cc_start: 0.8801 (pmm) cc_final: 0.8154 (pmm) REVERT: C 134 MET cc_start: 0.8097 (tpp) cc_final: 0.7886 (tpp) REVERT: c 410 MET cc_start: 0.7497 (ttm) cc_final: 0.7167 (ttp) REVERT: c 414 MET cc_start: 0.8537 (tmm) cc_final: 0.7970 (tmm) outliers start: 21 outliers final: 11 residues processed: 151 average time/residue: 0.2467 time to fit residues: 50.6359 Evaluate side-chains 122 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 111 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 253 TYR Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 253 TYR Chi-restraints excluded: chain c residue 284 MET Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 355 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 85 optimal weight: 0.3980 chunk 94 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 319 ASN c 319 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 9993 Z= 0.304 Angle : 0.874 11.649 13536 Z= 0.437 Chirality : 0.049 0.325 1755 Planarity : 0.004 0.032 1587 Dihedral : 14.326 85.598 2646 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.56 % Allowed : 11.61 % Favored : 87.83 % Rotamer: Outliers : 2.28 % Allowed : 9.21 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -2.10 (0.24), residues: 1068 helix: -0.25 (0.27), residues: 384 sheet: -0.51 (0.58), residues: 87 loop : -2.42 (0.21), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 210 HIS 0.006 0.001 HIS A 124 PHE 0.012 0.001 PHE c 309 TYR 0.017 0.002 TYR c 419 ARG 0.004 0.001 ARG a 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 123 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8297 (pmm) cc_final: 0.8003 (pmm) REVERT: A 125 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8444 (ptmm) REVERT: C 75 MET cc_start: 0.8343 (mmm) cc_final: 0.8129 (mmm) REVERT: C 82 MET cc_start: 0.8669 (pmm) cc_final: 0.7989 (pmm) REVERT: C 125 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8561 (ptmm) REVERT: c 414 MET cc_start: 0.8584 (tmm) cc_final: 0.7980 (tmm) outliers start: 22 outliers final: 15 residues processed: 138 average time/residue: 0.2269 time to fit residues: 43.4305 Evaluate side-chains 127 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain a residue 266 LEU Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 410 MET Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 253 TYR Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 355 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 0.7980 chunk 71 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9993 Z= 0.288 Angle : 0.819 8.211 13536 Z= 0.404 Chirality : 0.049 0.331 1755 Planarity : 0.004 0.033 1587 Dihedral : 12.896 81.636 2646 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.33 % Favored : 88.39 % Rotamer: Outliers : 3.11 % Allowed : 10.14 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -2.11 (0.24), residues: 1068 helix: -0.25 (0.28), residues: 378 sheet: -0.64 (0.57), residues: 87 loop : -2.39 (0.22), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 210 HIS 0.006 0.001 HIS A 179 PHE 0.011 0.001 PHE b 309 TYR 0.017 0.002 TYR c 419 ARG 0.003 0.000 ARG c 422 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 112 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8380 (pmm) cc_final: 0.8161 (pmm) REVERT: a 359 MET cc_start: 0.8661 (tpp) cc_final: 0.8235 (mtp) REVERT: a 381 SER cc_start: 0.7619 (p) cc_final: 0.7307 (p) REVERT: b 410 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7381 (ttm) REVERT: c 414 MET cc_start: 0.8583 (tmm) cc_final: 0.8126 (tmm) outliers start: 30 outliers final: 13 residues processed: 135 average time/residue: 0.2231 time to fit residues: 42.3449 Evaluate side-chains 110 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 266 LEU Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain a residue 397 THR Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 410 MET Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 253 TYR Chi-restraints excluded: chain c residue 266 LEU Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 355 LEU Chi-restraints excluded: chain c residue 397 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 25 optimal weight: 0.0170 overall best weight: 2.3024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 9993 Z= 0.287 Angle : 0.846 11.267 13536 Z= 0.413 Chirality : 0.050 0.337 1755 Planarity : 0.004 0.045 1587 Dihedral : 12.091 78.324 2646 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.56 % Allowed : 13.01 % Favored : 86.42 % Rotamer: Outliers : 2.48 % Allowed : 12.42 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % 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: -2.36 (0.24), residues: 1068 helix: -0.61 (0.26), residues: 396 sheet: -0.43 (0.54), residues: 105 loop : -2.60 (0.22), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 210 HIS 0.011 0.001 HIS B 124 PHE 0.014 0.001 PHE b 309 TYR 0.015 0.002 TYR c 419 ARG 0.003 0.000 ARG a 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 414 MET cc_start: 0.8508 (tmm) cc_final: 0.7859 (tmm) REVERT: b 410 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7261 (ttm) REVERT: C 134 MET cc_start: 0.7785 (ttm) cc_final: 0.7420 (tmm) REVERT: c 414 MET cc_start: 0.8636 (tmm) cc_final: 0.8252 (tmm) outliers start: 24 outliers final: 17 residues processed: 121 average time/residue: 0.2115 time to fit residues: 36.6168 Evaluate side-chains 110 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 92 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain a residue 397 THR Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 410 MET Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain c residue 266 LEU Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 355 LEU Chi-restraints excluded: chain c residue 397 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 0.0980 chunk 91 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 47 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 354 HIS ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.5289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9993 Z= 0.313 Angle : 0.854 10.957 13536 Z= 0.409 Chirality : 0.050 0.335 1755 Planarity : 0.004 0.042 1587 Dihedral : 11.515 75.847 2646 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.56 % Allowed : 13.76 % Favored : 85.67 % Rotamer: Outliers : 2.69 % Allowed : 13.56 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % 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: -2.32 (0.24), residues: 1068 helix: -0.64 (0.26), residues: 396 sheet: 1.00 (0.59), residues: 75 loop : -2.66 (0.22), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 210 HIS 0.005 0.001 HIS A 124 PHE 0.011 0.001 PHE c 309 TYR 0.015 0.002 TYR C 217 ARG 0.004 0.001 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 414 MET cc_start: 0.8607 (tmm) cc_final: 0.8055 (tmm) REVERT: b 410 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7402 (ttm) REVERT: b 417 LYS cc_start: 0.9100 (tppp) cc_final: 0.8870 (tppp) REVERT: C 134 MET cc_start: 0.7877 (ttm) cc_final: 0.7564 (tmm) REVERT: c 414 MET cc_start: 0.8695 (tmm) cc_final: 0.8331 (tmm) outliers start: 26 outliers final: 18 residues processed: 119 average time/residue: 0.1996 time to fit residues: 34.3763 Evaluate side-chains 110 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain a residue 397 THR Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain b residue 410 MET Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain c residue 266 LEU Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 355 LEU Chi-restraints excluded: chain c residue 397 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 354 HIS ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 398 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.5512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 9993 Z= 0.295 Angle : 0.840 9.375 13536 Z= 0.402 Chirality : 0.049 0.340 1755 Planarity : 0.004 0.042 1587 Dihedral : 11.073 73.397 2646 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.56 % Allowed : 13.86 % Favored : 85.58 % Rotamer: Outliers : 2.28 % Allowed : 14.80 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % 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: -2.45 (0.24), residues: 1068 helix: -0.77 (0.26), residues: 405 sheet: 0.83 (0.58), residues: 75 loop : -2.72 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP C 210 HIS 0.004 0.001 HIS B 124 PHE 0.014 0.001 PHE c 309 TYR 0.014 0.002 TYR A 217 ARG 0.003 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 414 MET cc_start: 0.8603 (tmm) cc_final: 0.8070 (tmm) REVERT: b 332 MET cc_start: 0.9105 (tpp) cc_final: 0.8678 (tpp) REVERT: b 410 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7279 (ttm) REVERT: b 417 LYS cc_start: 0.9125 (tppp) cc_final: 0.8888 (tppp) REVERT: C 134 MET cc_start: 0.7942 (ttm) cc_final: 0.7669 (tmm) REVERT: c 311 ASP cc_start: 0.8288 (m-30) cc_final: 0.7786 (m-30) REVERT: c 414 MET cc_start: 0.8731 (tmm) cc_final: 0.8095 (tmm) outliers start: 22 outliers final: 18 residues processed: 113 average time/residue: 0.2238 time to fit residues: 35.6152 Evaluate side-chains 110 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain a residue 397 THR Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain b residue 410 MET Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain c residue 266 LEU Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 355 LEU Chi-restraints excluded: chain c residue 397 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 92 optimal weight: 0.0040 chunk 96 optimal weight: 0.5980 overall best weight: 1.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.5694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9993 Z= 0.228 Angle : 0.811 10.767 13536 Z= 0.388 Chirality : 0.049 0.348 1755 Planarity : 0.004 0.054 1587 Dihedral : 10.425 69.774 2646 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.56 % Allowed : 13.20 % Favored : 86.24 % Rotamer: Outliers : 1.97 % Allowed : 14.91 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % 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: -2.35 (0.24), residues: 1068 helix: -0.67 (0.26), residues: 408 sheet: 0.84 (0.58), residues: 75 loop : -2.67 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 210 HIS 0.004 0.001 HIS A 124 PHE 0.025 0.001 PHE b 399 TYR 0.013 0.001 TYR b 419 ARG 0.014 0.001 ARG C 178 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 311 ASP cc_start: 0.7990 (m-30) cc_final: 0.7570 (m-30) REVERT: a 414 MET cc_start: 0.8518 (tmm) cc_final: 0.8133 (tmm) REVERT: b 332 MET cc_start: 0.8951 (tpp) cc_final: 0.8300 (tpp) REVERT: b 410 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7324 (ttm) REVERT: b 417 LYS cc_start: 0.9103 (tppp) cc_final: 0.8864 (tppp) REVERT: C 134 MET cc_start: 0.7880 (ttm) cc_final: 0.7654 (tmm) REVERT: c 311 ASP cc_start: 0.8189 (m-30) cc_final: 0.7641 (m-30) REVERT: c 414 MET cc_start: 0.8735 (tmm) cc_final: 0.8137 (tmm) REVERT: c 417 LYS cc_start: 0.8752 (mptt) cc_final: 0.8534 (mtmt) outliers start: 19 outliers final: 14 residues processed: 119 average time/residue: 0.2318 time to fit residues: 38.6350 Evaluate side-chains 112 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain a residue 397 THR Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 410 MET Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain c residue 266 LEU Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 355 LEU Chi-restraints excluded: chain c residue 397 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.5869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 9993 Z= 0.223 Angle : 0.813 12.327 13536 Z= 0.389 Chirality : 0.048 0.343 1755 Planarity : 0.004 0.064 1587 Dihedral : 10.037 67.101 2646 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.66 % Allowed : 13.95 % Favored : 85.39 % Rotamer: Outliers : 1.86 % Allowed : 16.05 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.32 (0.24), residues: 1068 helix: -0.53 (0.26), residues: 402 sheet: 0.53 (0.65), residues: 57 loop : -2.59 (0.23), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP C 210 HIS 0.004 0.001 HIS A 124 PHE 0.011 0.001 PHE b 399 TYR 0.018 0.001 TYR b 371 ARG 0.015 0.001 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 414 MET cc_start: 0.8519 (tmm) cc_final: 0.8136 (tmm) REVERT: b 332 MET cc_start: 0.9000 (tpp) cc_final: 0.8608 (tpp) REVERT: b 410 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7283 (ttm) REVERT: b 417 LYS cc_start: 0.9070 (tppp) cc_final: 0.8826 (tppp) REVERT: C 134 MET cc_start: 0.7907 (ttm) cc_final: 0.7597 (tmm) REVERT: c 311 ASP cc_start: 0.8159 (m-30) cc_final: 0.7607 (m-30) REVERT: c 414 MET cc_start: 0.8754 (tmm) cc_final: 0.8185 (tmm) REVERT: c 417 LYS cc_start: 0.8739 (mptt) cc_final: 0.8525 (mtmt) outliers start: 18 outliers final: 15 residues processed: 120 average time/residue: 0.2221 time to fit residues: 37.6708 Evaluate side-chains 113 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 97 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain b residue 410 MET Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain c residue 266 LEU Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 355 LEU Chi-restraints excluded: chain c residue 397 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 0.7980 chunk 60 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 8 optimal weight: 0.0970 chunk 64 optimal weight: 0.3980 chunk 51 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN B 124 HIS B 179 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.6054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9993 Z= 0.215 Angle : 0.809 14.186 13536 Z= 0.385 Chirality : 0.048 0.343 1755 Planarity : 0.004 0.050 1587 Dihedral : 9.655 63.917 2646 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.56 % Allowed : 13.76 % Favored : 85.67 % Rotamer: Outliers : 1.55 % Allowed : 16.67 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.08 (0.25), residues: 1068 helix: -0.18 (0.27), residues: 384 sheet: 0.85 (0.59), residues: 75 loop : -2.64 (0.23), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP C 210 HIS 0.004 0.001 HIS A 124 PHE 0.012 0.001 PHE c 399 TYR 0.022 0.001 TYR c 371 ARG 0.012 0.001 ARG A 178 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 332 MET cc_start: 0.8437 (tpt) cc_final: 0.8230 (tpt) REVERT: a 414 MET cc_start: 0.8502 (tmm) cc_final: 0.8132 (tmm) REVERT: b 332 MET cc_start: 0.8959 (tpp) cc_final: 0.8591 (tpp) REVERT: C 82 MET cc_start: 0.8464 (pmm) cc_final: 0.8217 (pmm) REVERT: C 134 MET cc_start: 0.7919 (ttm) cc_final: 0.7595 (tmm) REVERT: c 311 ASP cc_start: 0.8130 (m-30) cc_final: 0.7620 (m-30) REVERT: c 414 MET cc_start: 0.8729 (tmm) cc_final: 0.8177 (tmm) REVERT: c 417 LYS cc_start: 0.8731 (mptt) cc_final: 0.8525 (mtmt) outliers start: 15 outliers final: 10 residues processed: 120 average time/residue: 0.2247 time to fit residues: 38.4350 Evaluate side-chains 108 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 397 THR Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain c residue 266 LEU Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 355 LEU Chi-restraints excluded: chain c residue 397 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.7980 chunk 25 optimal weight: 0.0870 chunk 76 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 85 optimal weight: 0.0070 chunk 10 optimal weight: 0.0050 chunk 15 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 overall best weight: 0.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 319 ASN ** b 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.054002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.042933 restraints weight = 56043.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.044318 restraints weight = 32315.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.045281 restraints weight = 23044.479| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.6216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9993 Z= 0.211 Angle : 0.802 11.277 13536 Z= 0.387 Chirality : 0.048 0.342 1755 Planarity : 0.004 0.047 1587 Dihedral : 9.553 60.905 2646 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.56 % Allowed : 13.39 % Favored : 86.05 % Rotamer: Outliers : 1.24 % Allowed : 17.08 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.08 (0.25), residues: 1068 helix: -0.21 (0.27), residues: 384 sheet: 0.97 (0.59), residues: 75 loop : -2.63 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP C 210 HIS 0.005 0.001 HIS c 305 PHE 0.028 0.001 PHE A 117 TYR 0.013 0.001 TYR b 419 ARG 0.012 0.001 ARG b 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1883.02 seconds wall clock time: 35 minutes 44.83 seconds (2144.83 seconds total)