Starting phenix.real_space_refine (version: 1.21rc1) on Wed Jul 5 12:24:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejf_28180/07_2023/8ejf_28180.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejf_28180/07_2023/8ejf_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_28180/07_2023/8ejf_28180.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejf_28180/07_2023/8ejf_28180.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejf_28180/07_2023/8ejf_28180.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejf_28180/07_2023/8ejf_28180.pdb" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-5013/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 2 Time building chain proxies: 5.18, per 1000 atoms: 0.53 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: 5.85 Conformation dependent library (CDL) restraints added in 1.3 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: 0.45 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: 6.13 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 - 14.60: 4978 14.60 - 29.21: 245 29.21 - 43.81: 39 43.81 - 58.41: 18 58.41 - 73.01: 24 Dihedral angle restraints: 5304 sinusoidal: 2133 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 5301 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: 1.260 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: 4.460 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 29.150 Find NCS groups from input model: 0.610 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.460 ------------------------------------------------------------------------------- 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 : 10.607 69.359 3201 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 % 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 *********************** 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 : 1.008 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 outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.3048 time to fit residues: 87.0465 Evaluate side-chains 117 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.093 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3978 ------------------------------------------------------------------------------- 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: 3.9990 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: 1.9990 chunk 95 optimal weight: 0.0370 overall best weight: 1.0064 ------------------------------------------------------------------------------- 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 124 HIS 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 319 ASN c 406 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.113 9993 Z= 0.342 Angle : 0.994 10.983 13536 Z= 0.499 Chirality : 0.048 0.230 1755 Planarity : 0.005 0.035 1587 Dihedral : 6.744 38.592 1170 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.58 % Favored : 89.14 % Rotamer Outliers : 2.28 % 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: -1.81 (0.23), residues: 1068 helix: -0.07 (0.26), residues: 357 sheet: -0.10 (0.57), residues: 87 loop : -2.15 (0.20), residues: 624 *********************** 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 158 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 136 time to evaluate : 1.638 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 outliers start: 22 outliers final: 10 residues processed: 151 average time/residue: 0.2525 time to fit residues: 52.4621 Evaluate side-chains 123 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 1.101 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1897 time to fit residues: 4.0381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 79 optimal weight: 8.9990 chunk 64 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS a 319 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 9993 Z= 0.275 Angle : 0.865 11.466 13536 Z= 0.434 Chirality : 0.045 0.217 1755 Planarity : 0.004 0.029 1587 Dihedral : 6.570 39.990 1170 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.56 % Allowed : 11.14 % Favored : 88.30 % Rotamer Outliers : 1.45 % 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: -0.30 (0.27), residues: 384 sheet: -0.38 (0.59), residues: 87 loop : -2.42 (0.21), residues: 597 *********************** 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 141 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 134 average time/residue: 0.2300 time to fit residues: 43.1593 Evaluate side-chains 123 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 112 time to evaluate : 1.117 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1035 time to fit residues: 3.4380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 64 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 30.0000 chunk 27 optimal weight: 3.9990 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 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 9993 Z= 0.308 Angle : 0.832 10.179 13536 Z= 0.409 Chirality : 0.045 0.217 1755 Planarity : 0.004 0.034 1587 Dihedral : 6.206 37.932 1170 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.70 % Favored : 88.01 % Rotamer Outliers : 1.86 % 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: -2.01 (0.24), residues: 1068 helix: -0.09 (0.28), residues: 378 sheet: -0.51 (0.58), residues: 87 loop : -2.41 (0.21), residues: 603 *********************** 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 133 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 1.074 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 outliers start: 18 outliers final: 8 residues processed: 129 average time/residue: 0.2199 time to fit residues: 40.3169 Evaluate side-chains 108 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 1.084 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0912 time to fit residues: 2.7108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 20.0000 chunk 57 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 overall best weight: 2.2984 ------------------------------------------------------------------------------- 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: 0.7967 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 9993 Z= 0.275 Angle : 0.840 10.901 13536 Z= 0.411 Chirality : 0.045 0.207 1755 Planarity : 0.004 0.046 1587 Dihedral : 6.355 38.299 1170 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.56 % Allowed : 12.73 % Favored : 86.70 % Rotamer Outliers : 1.55 % 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: -2.23 (0.24), residues: 1068 helix: -0.40 (0.27), residues: 399 sheet: -0.39 (0.54), residues: 105 loop : -2.60 (0.22), residues: 564 *********************** 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 125 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 124 average time/residue: 0.2231 time to fit residues: 39.3765 Evaluate side-chains 108 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 1.094 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0960 time to fit residues: 3.1476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 84 optimal weight: 20.0000 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 9993 Z= 0.254 Angle : 0.803 10.633 13536 Z= 0.392 Chirality : 0.044 0.206 1755 Planarity : 0.004 0.041 1587 Dihedral : 6.288 39.104 1170 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.56 % Allowed : 13.58 % Favored : 85.86 % Rotamer Outliers : 0.62 % 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: -2.25 (0.24), residues: 1068 helix: -0.57 (0.26), residues: 399 sheet: 1.15 (0.59), residues: 75 loop : -2.64 (0.22), residues: 594 *********************** 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 111 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 109 average time/residue: 0.2293 time to fit residues: 35.5806 Evaluate side-chains 98 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 1.156 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0921 time to fit residues: 1.7700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 61 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 398 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.5438 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= 0.222 Angle : 0.770 10.443 13536 Z= 0.377 Chirality : 0.043 0.212 1755 Planarity : 0.004 0.038 1587 Dihedral : 6.073 39.730 1170 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.56 % Allowed : 13.11 % Favored : 86.33 % Rotamer Outliers : 0.31 % 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: -2.29 (0.24), residues: 1068 helix: -0.64 (0.26), residues: 402 sheet: 1.15 (0.59), residues: 75 loop : -2.64 (0.23), residues: 591 *********************** 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 109 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 106 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 outliers start: 3 outliers final: 1 residues processed: 108 average time/residue: 0.2355 time to fit residues: 36.1107 Evaluate side-chains 95 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 1.165 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0883 time to fit residues: 1.7051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 30 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 50 optimal weight: 0.0970 chunk 9 optimal weight: 0.0770 chunk 79 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.0342 ------------------------------------------------------------------------------- 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: 0.7934 moved from start: 0.5641 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= 0.208 Angle : 0.779 11.050 13536 Z= 0.379 Chirality : 0.043 0.222 1755 Planarity : 0.004 0.047 1587 Dihedral : 5.939 37.197 1170 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.66 % Allowed : 13.20 % Favored : 86.14 % Rotamer Outliers : 0.21 % 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 (0.25), residues: 1068 helix: -0.32 (0.27), residues: 384 sheet: 1.03 (0.58), residues: 75 loop : -2.59 (0.23), residues: 609 *********************** 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 107 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 106 average time/residue: 0.2418 time to fit residues: 36.3995 Evaluate side-chains 90 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 1.128 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1130 time to fit residues: 1.5338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 61 optimal weight: 0.3980 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS B 69 GLN c 319 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.5780 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= 0.230 Angle : 0.794 10.174 13536 Z= 0.388 Chirality : 0.044 0.255 1755 Planarity : 0.004 0.042 1587 Dihedral : 5.866 36.348 1170 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.84 % Allowed : 13.20 % Favored : 85.96 % Rotamer Outliers : 0.10 % 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: -2.12 (0.25), residues: 1068 helix: -0.31 (0.27), residues: 387 sheet: 1.02 (0.59), residues: 75 loop : -2.61 (0.23), residues: 606 *********************** 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 95 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 94 average time/residue: 0.2356 time to fit residues: 32.3442 Evaluate side-chains 91 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 1.200 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1307 time to fit residues: 1.7645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 0.2980 chunk 60 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 8 optimal weight: 0.3980 chunk 64 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 HIS b 319 ASN C 141 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.5938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 9993 Z= 0.313 Angle : 0.857 13.197 13536 Z= 0.413 Chirality : 0.045 0.247 1755 Planarity : 0.004 0.039 1587 Dihedral : 5.985 36.194 1170 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.66 % Allowed : 13.20 % Favored : 86.14 % Rotamer Outliers : 0.21 % 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: -2.39 (0.24), residues: 1068 helix: -0.61 (0.26), residues: 405 sheet: 0.75 (0.59), residues: 75 loop : -2.76 (0.23), residues: 588 ********************** 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 94 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 1.213 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 92 average time/residue: 0.2321 time to fit residues: 30.7533 Evaluate side-chains 85 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 1.112 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1095 time to fit residues: 1.7106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 3.9990 chunk 25 optimal weight: 0.0020 chunk 76 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 overall best weight: 2.3996 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.052364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.040736 restraints weight = 58365.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.042041 restraints weight = 35600.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.042940 restraints weight = 26208.463| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.6085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 9993 Z= 0.273 Angle : 0.834 10.781 13536 Z= 0.403 Chirality : 0.045 0.308 1755 Planarity : 0.004 0.045 1587 Dihedral : 5.880 31.698 1170 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.66 % Allowed : 13.76 % Favored : 85.58 % Rotamer Outliers : 0.21 % 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: -2.41 (0.24), residues: 1068 helix: -0.64 (0.26), residues: 405 sheet: 0.64 (0.59), residues: 75 loop : -2.73 (0.23), residues: 588 =============================================================================== Job complete usr+sys time: 1779.91 seconds wall clock time: 33 minutes 52.98 seconds (2032.98 seconds total)