Starting phenix.real_space_refine on Wed Feb 14 17:15:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejf_28180/02_2024/8ejf_28180.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejf_28180/02_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_28180/02_2024/8ejf_28180.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejf_28180/02_2024/8ejf_28180.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejf_28180/02_2024/8ejf_28180.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejf_28180/02_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-dev-5238/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: 15 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: 15 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: 15 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: 15 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: 15 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: 15 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: 15 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: 15 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: 15 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: 5.53, per 1000 atoms: 0.56 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: 5.81 Conformation dependent library (CDL) restraints added in 1.5 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: 0.94 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: 2.48 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: 6735 21.24 - 42.49: 216 42.49 - 63.73: 42 63.73 - 84.97: 63 84.97 - 106.21: 66 Dihedral angle restraints: 7122 sinusoidal: 3951 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 7119 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: 0.010 Normalize map: mean=0, sd=1: 0.690 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: 4.100 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 29.680 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.130 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.030 ------------------------------------------------------------------------------- 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 : 17.178 106.214 5019 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 : 1.043 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: 0.3090 time to fit residues: 88.1173 Evaluate side-chains 116 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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: 0.7883 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.127 9993 Z= 0.379 Angle : 1.010 10.472 13536 Z= 0.503 Chirality : 0.052 0.313 1755 Planarity : 0.005 0.035 1587 Dihedral : 15.925 92.623 2988 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.49 % Favored : 89.14 % Rotamer: Outliers : 2.07 % Allowed : 7.76 % 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: -1.97 (0.23), residues: 1068 helix: -0.36 (0.26), residues: 381 sheet: -0.13 (0.57), residues: 87 loop : -2.21 (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 0.018 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 156 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 1.017 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: a 417 LYS cc_start: 0.9075 (tppp) cc_final: 0.8845 (mptt) REVERT: B 82 MET cc_start: 0.8641 (pmm) cc_final: 0.8301 (pmm) REVERT: C 75 MET cc_start: 0.8212 (mmm) cc_final: 0.7855 (mmm) REVERT: C 134 MET cc_start: 0.8090 (tpp) cc_final: 0.7887 (tpp) REVERT: c 414 MET cc_start: 0.8538 (tmm) cc_final: 0.8062 (tmm) REVERT: c 417 LYS cc_start: 0.8931 (tppp) cc_final: 0.8687 (mptt) outliers start: 20 outliers final: 10 residues processed: 151 average time/residue: 0.2469 time to fit residues: 50.6881 Evaluate side-chains 122 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 29 optimal weight: 0.6980 chunk 79 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 26 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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: 0.7893 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 9993 Z= 0.287 Angle : 0.870 12.049 13536 Z= 0.434 Chirality : 0.050 0.335 1755 Planarity : 0.004 0.035 1587 Dihedral : 13.422 84.945 2988 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.56 % Allowed : 11.89 % Favored : 87.55 % Rotamer: Outliers : 2.38 % Allowed : 9.11 % 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: -2.11 (0.23), residues: 1068 helix: -0.28 (0.27), residues: 384 sheet: -0.48 (0.58), residues: 87 loop : -2.41 (0.21), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 210 HIS 0.007 0.001 HIS A 124 PHE 0.011 0.001 PHE c 309 TYR 0.018 0.002 TYR c 419 ARG 0.007 0.001 ARG a 422 *********************** 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 148 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 125 time to evaluate : 0.938 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: C 82 MET cc_start: 0.8602 (pmm) cc_final: 0.7729 (pmm) REVERT: c 414 MET cc_start: 0.8653 (tmm) cc_final: 0.8159 (tmm) outliers start: 23 outliers final: 15 residues processed: 140 average time/residue: 0.2169 time to fit residues: 42.5823 Evaluate side-chains 126 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 PHE 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 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: 5.9990 chunk 71 optimal weight: 8.9990 chunk 49 optimal weight: 0.5980 chunk 10 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 overall best weight: 5.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN b 319 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 9993 Z= 0.503 Angle : 0.997 9.331 13536 Z= 0.485 Chirality : 0.053 0.307 1755 Planarity : 0.005 0.034 1587 Dihedral : 12.677 83.137 2988 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 21.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 12.64 % Favored : 87.17 % Rotamer: Outliers : 3.73 % Allowed : 11.18 % Favored : 85.09 % 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: -2.36 (0.24), residues: 1068 helix: -0.78 (0.26), residues: 402 sheet: 0.89 (0.59), residues: 75 loop : -2.59 (0.22), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 210 HIS 0.007 0.002 HIS B 124 PHE 0.016 0.002 PHE b 309 TYR 0.022 0.003 TYR C 129 ARG 0.011 0.001 ARG b 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 146 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 110 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8491 (pmm) cc_final: 0.8241 (pmm) REVERT: a 414 MET cc_start: 0.8645 (tmm) cc_final: 0.7965 (tmm) REVERT: c 414 MET cc_start: 0.8752 (tmm) cc_final: 0.8232 (tmm) outliers start: 36 outliers final: 22 residues processed: 136 average time/residue: 0.2153 time to fit residues: 41.4452 Evaluate side-chains 114 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 92 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 254 ILE 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 a residue 413 GLU 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 397 THR 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 266 LEU Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 304 LYS Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 355 LEU Chi-restraints excluded: chain c residue 397 THR Chi-restraints excluded: chain c residue 398 HIS Chi-restraints excluded: chain c residue 413 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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: 0.8011 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 9993 Z= 0.264 Angle : 0.826 11.475 13536 Z= 0.407 Chirality : 0.051 0.359 1755 Planarity : 0.004 0.040 1587 Dihedral : 11.359 78.027 2988 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.56 % Allowed : 13.95 % Favored : 85.49 % Rotamer: Outliers : 2.59 % Allowed : 13.25 % Favored : 84.16 % 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: -2.44 (0.24), residues: 1068 helix: -0.74 (0.26), residues: 402 sheet: 0.83 (0.58), residues: 75 loop : -2.71 (0.21), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 210 HIS 0.009 0.001 HIS C 124 PHE 0.012 0.001 PHE c 399 TYR 0.016 0.001 TYR c 419 ARG 0.005 0.001 ARG b 422 *********************** 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 129 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 104 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.8186 (tpp) cc_final: 0.7939 (tpt) REVERT: a 414 MET cc_start: 0.8604 (tmm) cc_final: 0.8038 (tmm) REVERT: b 410 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7392 (ttm) REVERT: b 417 LYS cc_start: 0.9095 (tppp) cc_final: 0.8859 (tppp) REVERT: C 134 MET cc_start: 0.7994 (ttm) cc_final: 0.7735 (tmm) REVERT: c 414 MET cc_start: 0.8710 (tmm) cc_final: 0.8219 (tmm) outliers start: 25 outliers final: 17 residues processed: 123 average time/residue: 0.2169 time to fit residues: 38.0372 Evaluate side-chains 112 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 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 347 ASP Chi-restraints excluded: chain b residue 397 THR 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 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 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: 4.9990 chunk 91 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 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 354 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.5434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9993 Z= 0.261 Angle : 0.807 9.149 13536 Z= 0.391 Chirality : 0.049 0.349 1755 Planarity : 0.004 0.047 1587 Dihedral : 10.739 75.330 2988 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.56 % Allowed : 13.01 % Favored : 86.42 % Rotamer: Outliers : 2.48 % Allowed : 14.70 % Favored : 82.82 % 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: -2.39 (0.24), residues: 1068 helix: -0.67 (0.26), residues: 402 sheet: 0.81 (0.58), residues: 75 loop : -2.72 (0.22), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 210 HIS 0.004 0.001 HIS C 124 PHE 0.011 0.001 PHE c 309 TYR 0.015 0.001 TYR b 419 ARG 0.004 0.001 ARG b 422 *********************** 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 127 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 414 MET cc_start: 0.8597 (tmm) cc_final: 0.8097 (tmm) REVERT: B 82 MET cc_start: 0.7697 (pmm) cc_final: 0.7497 (pmm) REVERT: b 410 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7388 (ttm) REVERT: C 134 MET cc_start: 0.7935 (ttm) cc_final: 0.7647 (tmm) REVERT: c 414 MET cc_start: 0.8683 (tmm) cc_final: 0.8347 (tmm) outliers start: 24 outliers final: 15 residues processed: 123 average time/residue: 0.2389 time to fit residues: 42.0867 Evaluate side-chains 107 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 PHE 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 347 ASP Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain b residue 397 THR 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 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: 1.9990 chunk 11 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 61 optimal weight: 0.1980 chunk 46 optimal weight: 0.2980 chunk 62 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 319 ASN b 398 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9993 Z= 0.217 Angle : 0.799 13.035 13536 Z= 0.385 Chirality : 0.049 0.363 1755 Planarity : 0.004 0.057 1587 Dihedral : 10.046 71.429 2988 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.56 % Allowed : 13.67 % Favored : 85.77 % Rotamer: Outliers : 2.48 % Allowed : 15.32 % Favored : 82.19 % 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: -2.38 (0.24), residues: 1068 helix: -0.72 (0.26), residues: 402 sheet: 0.85 (0.57), residues: 75 loop : -2.66 (0.23), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 210 HIS 0.006 0.001 HIS A 124 PHE 0.011 0.001 PHE a 399 TYR 0.014 0.001 TYR c 419 ARG 0.017 0.001 ARG b 314 *********************** 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 129 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 105 time to evaluate : 1.139 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: a 414 MET cc_start: 0.8551 (tmm) cc_final: 0.8084 (tmm) REVERT: b 402 ASP cc_start: 0.7736 (m-30) cc_final: 0.6907 (m-30) REVERT: b 410 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7384 (ttm) REVERT: C 134 MET cc_start: 0.7849 (ttm) cc_final: 0.7647 (tmm) REVERT: c 311 ASP cc_start: 0.8112 (m-30) cc_final: 0.7593 (m-30) REVERT: c 414 MET cc_start: 0.8750 (tmm) cc_final: 0.8444 (tmm) outliers start: 24 outliers final: 13 residues processed: 126 average time/residue: 0.2211 time to fit residues: 39.1651 Evaluate side-chains 111 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 254 ILE 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 347 ASP Chi-restraints excluded: chain b residue 397 THR 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 274 THR Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 355 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 64 optimal weight: 0.4980 chunk 68 optimal weight: 0.9980 chunk 50 optimal weight: 0.0770 chunk 9 optimal weight: 8.9990 chunk 79 optimal weight: 9.9990 chunk 92 optimal weight: 0.2980 chunk 96 optimal weight: 1.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- 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: 0.7953 moved from start: 0.5813 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= 0.212 Angle : 0.776 9.532 13536 Z= 0.376 Chirality : 0.048 0.356 1755 Planarity : 0.004 0.062 1587 Dihedral : 9.605 68.360 2988 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.66 % Allowed : 13.30 % Favored : 86.05 % Rotamer: Outliers : 1.86 % Allowed : 15.63 % Favored : 82.51 % 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: -2.21 (0.24), residues: 1068 helix: -0.31 (0.27), residues: 378 sheet: 0.82 (0.57), residues: 75 loop : -2.67 (0.22), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 210 HIS 0.005 0.001 HIS A 124 PHE 0.021 0.001 PHE c 399 TYR 0.012 0.001 TYR b 419 ARG 0.012 0.001 ARG B 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 123 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 1.141 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: a 311 ASP cc_start: 0.8052 (m-30) cc_final: 0.7644 (m-30) REVERT: a 414 MET cc_start: 0.8563 (tmm) cc_final: 0.8096 (tmm) REVERT: b 332 MET cc_start: 0.8968 (tpp) cc_final: 0.8357 (tpp) REVERT: b 410 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.7374 (ttm) REVERT: C 134 MET cc_start: 0.7892 (ttm) cc_final: 0.7417 (tmm) REVERT: c 311 ASP cc_start: 0.8100 (m-30) cc_final: 0.7566 (m-30) REVERT: c 334 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8666 (pt) REVERT: c 414 MET cc_start: 0.8728 (tmm) cc_final: 0.8261 (tmm) outliers start: 18 outliers final: 14 residues processed: 120 average time/residue: 0.2319 time to fit residues: 39.8871 Evaluate side-chains 115 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 99 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 254 ILE 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 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 274 THR Chi-restraints excluded: chain c residue 334 ILE Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 355 LEU Chi-restraints excluded: chain c residue 397 THR Chi-restraints excluded: chain c residue 398 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 28 optimal weight: 0.6980 chunk 85 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 HIS C 209 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.5988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 9993 Z= 0.402 Angle : 0.904 10.280 13536 Z= 0.433 Chirality : 0.050 0.331 1755 Planarity : 0.005 0.047 1587 Dihedral : 10.130 68.085 2988 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 0.56 % Allowed : 13.30 % Favored : 86.14 % Rotamer: Outliers : 2.28 % Allowed : 16.77 % Favored : 80.95 % 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: -2.56 (0.24), residues: 1068 helix: -0.77 (0.26), residues: 399 sheet: 0.29 (0.57), residues: 75 loop : -2.76 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP C 210 HIS 0.003 0.001 HIS C 131 PHE 0.014 0.002 PHE c 399 TYR 0.018 0.002 TYR B 217 ARG 0.012 0.001 ARG C 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 115 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 311 ASP cc_start: 0.8264 (m-30) cc_final: 0.7685 (m-30) REVERT: a 414 MET cc_start: 0.8617 (tmm) cc_final: 0.8245 (tmm) REVERT: b 410 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7265 (ttm) REVERT: c 311 ASP cc_start: 0.8250 (m-30) cc_final: 0.7679 (m-30) REVERT: c 414 MET cc_start: 0.8833 (tmm) cc_final: 0.8296 (tmm) outliers start: 22 outliers final: 15 residues processed: 110 average time/residue: 0.2167 time to fit residues: 34.0419 Evaluate side-chains 107 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain b residue 345 ILE Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 397 THR 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 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 Chi-restraints excluded: chain c residue 398 HIS Chi-restraints excluded: chain c residue 413 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 0.6980 chunk 60 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN C 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.6119 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= 0.222 Angle : 0.820 12.182 13536 Z= 0.394 Chirality : 0.049 0.370 1755 Planarity : 0.004 0.063 1587 Dihedral : 9.388 63.354 2988 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.56 % Allowed : 12.73 % Favored : 86.70 % Rotamer: Outliers : 1.35 % Allowed : 18.01 % Favored : 80.64 % 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: -2.47 (0.24), residues: 1068 helix: -0.63 (0.26), residues: 399 sheet: 0.22 (0.56), residues: 75 loop : -2.75 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 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 0.015 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 112 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 311 ASP cc_start: 0.7942 (m-30) cc_final: 0.7529 (m-30) REVERT: a 414 MET cc_start: 0.8487 (tmm) cc_final: 0.8128 (tmm) REVERT: b 332 MET cc_start: 0.8893 (tpp) cc_final: 0.8458 (tpp) REVERT: b 410 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.7367 (ttm) REVERT: b 417 LYS cc_start: 0.9101 (tppp) cc_final: 0.8820 (tppp) REVERT: C 134 MET cc_start: 0.7960 (ttm) cc_final: 0.7443 (tmm) REVERT: c 311 ASP cc_start: 0.8000 (m-30) cc_final: 0.7529 (m-30) REVERT: c 414 MET cc_start: 0.8720 (tmm) cc_final: 0.8304 (tmm) outliers start: 13 outliers final: 11 residues processed: 110 average time/residue: 0.2089 time to fit residues: 33.3622 Evaluate side-chains 106 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain B residue 117 PHE 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 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 88 optimal weight: 6.9990 chunk 25 optimal weight: 0.3980 chunk 76 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.052720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.041517 restraints weight = 57306.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.042849 restraints weight = 33974.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.043780 restraints weight = 24736.148| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.6235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9993 Z= 0.235 Angle : 0.802 10.251 13536 Z= 0.386 Chirality : 0.048 0.347 1755 Planarity : 0.004 0.055 1587 Dihedral : 9.208 61.442 2988 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.47 % Allowed : 13.11 % Favored : 86.42 % Rotamer: Outliers : 1.45 % Allowed : 18.01 % Favored : 80.54 % 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: -2.43 (0.24), residues: 1068 helix: -0.58 (0.26), residues: 402 sheet: 0.34 (0.57), residues: 75 loop : -2.76 (0.23), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 210 HIS 0.003 0.001 HIS a 305 PHE 0.011 0.001 PHE c 399 TYR 0.022 0.001 TYR b 419 ARG 0.013 0.001 ARG A 178 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1882.78 seconds wall clock time: 35 minutes 46.22 seconds (2146.22 seconds total)