Starting phenix.real_space_refine on Fri Feb 14 08:01:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ejf_28180/02_2025/8ejf_28180.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ejf_28180/02_2025/8ejf_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/cci-nas-00/data/ceres_data/8ejf_28180/02_2025/8ejf_28180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ejf_28180/02_2025/8ejf_28180.map" model { file = "/net/cci-nas-00/data/ceres_data/8ejf_28180/02_2025/8ejf_28180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ejf_28180/02_2025/8ejf_28180.cif" } 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. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.63, per 1000 atoms: 0.68 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " 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: 3.71 Conformation dependent library (CDL) restraints added in 971.3 milliseconds 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: 0.97 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: 2.70 Time building geometry restraints manager: 4.09 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: 0.00 - 2.90: 11867 2.90 - 5.81: 1434 5.81 - 8.71: 208 8.71 - 11.61: 24 11.61 - 14.52: 3 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 3.120 nonbonded pdb=" N ASP c 347 " pdb=" OD1 ASP c 347 " model vdw 2.379 3.120 ... (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 Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'L' selection = chain 'O' selection = chain 'R' selection = chain 'T' selection = chain 'W' selection = chain 'Z' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'U' selection = chain 'V' selection = chain 'Y' } ncs_group { reference = (chain 'H' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.550 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 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:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.970 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 1.142 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: 0.3144 time to fit residues: 89.7196 Evaluate side-chains 116 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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: 0.0010 chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 overall best weight: 1.2990 ------------------------------------------------------------------------------- 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 406 GLN B 92 HIS ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.054994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.043232 restraints weight = 55507.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.044655 restraints weight = 32477.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.045599 restraints weight = 23465.839| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 9993 Z= 0.348 Angle : 1.026 10.847 13536 Z= 0.511 Chirality : 0.052 0.304 1755 Planarity : 0.005 0.036 1587 Dihedral : 15.891 92.527 2988 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.67 % Favored : 89.23 % Rotamer: Outliers : 1.86 % Allowed : 7.14 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.23), residues: 1068 helix: -0.40 (0.26), residues: 381 sheet: -0.08 (0.58), residues: 87 loop : -2.18 (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 0.003 TYR c 419 ARG 0.006 0.001 ARG a 325 *********************** 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 155 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 1.154 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: A 134 MET cc_start: 0.7489 (ttp) cc_final: 0.7117 (tmt) REVERT: A 194 MET cc_start: 0.9098 (tpt) cc_final: 0.8671 (tpp) REVERT: a 359 MET cc_start: 0.8788 (tpp) cc_final: 0.8455 (mtp) REVERT: a 399 PHE cc_start: 0.8458 (t80) cc_final: 0.7921 (t80) REVERT: a 417 LYS cc_start: 0.9366 (tppp) cc_final: 0.9010 (mptt) REVERT: B 82 MET cc_start: 0.8937 (pmm) cc_final: 0.8185 (pmm) REVERT: B 210 TRP cc_start: 0.5573 (t-100) cc_final: 0.5260 (t-100) REVERT: b 414 MET cc_start: 0.9287 (tmm) cc_final: 0.8963 (mtt) REVERT: C 82 MET cc_start: 0.9111 (pmm) cc_final: 0.8432 (pmm) REVERT: C 134 MET cc_start: 0.8769 (tpp) cc_final: 0.8426 (tpp) REVERT: C 194 MET cc_start: 0.9054 (tpt) cc_final: 0.8719 (tpp) REVERT: c 399 PHE cc_start: 0.8175 (t80) cc_final: 0.7488 (t80) REVERT: c 414 MET cc_start: 0.9278 (tmm) cc_final: 0.8750 (tmm) outliers start: 18 outliers final: 10 residues processed: 152 average time/residue: 0.2565 time to fit residues: 52.7992 Evaluate side-chains 125 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 253 TYR 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 19 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 0.0570 chunk 70 optimal weight: 8.9990 chunk 34 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 overall best weight: 4.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 HIS B 209 ASN 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 = 0.051505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.039707 restraints weight = 57934.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.041040 restraints weight = 34180.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.041943 restraints weight = 25147.825| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 9993 Z= 0.413 Angle : 0.982 11.786 13536 Z= 0.484 Chirality : 0.051 0.311 1755 Planarity : 0.004 0.028 1587 Dihedral : 13.508 85.912 2988 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.99 % Favored : 87.92 % Rotamer: Outliers : 2.69 % Allowed : 8.59 % Favored : 88.72 % 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: -2.03 (0.24), residues: 1068 helix: -0.26 (0.27), residues: 384 sheet: -0.74 (0.57), residues: 87 loop : -2.28 (0.22), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 227 HIS 0.006 0.002 HIS A 131 PHE 0.017 0.002 PHE c 309 TYR 0.020 0.002 TYR C 150 ARG 0.009 0.001 ARG b 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 145 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8964 (pmm) cc_final: 0.8438 (pmm) REVERT: A 134 MET cc_start: 0.7920 (ttp) cc_final: 0.7491 (tmm) REVERT: a 417 LYS cc_start: 0.9381 (tppp) cc_final: 0.9158 (tppp) REVERT: B 82 MET cc_start: 0.8792 (pmm) cc_final: 0.8179 (pmm) REVERT: B 192 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7820 (mpp) REVERT: b 410 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7726 (ttm) REVERT: b 414 MET cc_start: 0.9340 (tmm) cc_final: 0.8796 (tmm) REVERT: C 82 MET cc_start: 0.9183 (pmm) cc_final: 0.8423 (pmm) REVERT: C 194 MET cc_start: 0.9102 (tpt) cc_final: 0.8532 (tpp) REVERT: c 359 MET cc_start: 0.8566 (mmm) cc_final: 0.8178 (mtp) REVERT: c 414 MET cc_start: 0.9340 (tmm) cc_final: 0.8841 (tmm) REVERT: c 417 LYS cc_start: 0.9248 (tppt) cc_final: 0.8950 (ttmm) outliers start: 26 outliers final: 20 residues processed: 132 average time/residue: 0.2327 time to fit residues: 42.5304 Evaluate side-chains 128 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 253 TYR Chi-restraints excluded: chain a residue 266 LEU Chi-restraints excluded: chain a residue 398 HIS Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 253 TYR Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain b residue 410 MET Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 212 CYS 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 355 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 26 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 76 optimal weight: 0.0570 chunk 16 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.4102 ------------------------------------------------------------------------------- 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 = 0.3484 r_free = 0.3484 target = 0.053241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.041438 restraints weight = 56100.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.042823 restraints weight = 32757.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.043793 restraints weight = 23905.873| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4665 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= 0.248 Angle : 0.814 8.272 13536 Z= 0.401 Chirality : 0.049 0.352 1755 Planarity : 0.004 0.049 1587 Dihedral : 11.910 80.880 2988 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.28 % Allowed : 13.01 % Favored : 86.70 % Rotamer: Outliers : 2.80 % Allowed : 10.46 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.24), residues: 1068 helix: -0.32 (0.27), residues: 387 sheet: -0.92 (0.56), residues: 87 loop : -2.34 (0.22), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 210 HIS 0.006 0.001 HIS C 179 PHE 0.013 0.001 PHE b 309 TYR 0.018 0.002 TYR c 419 ARG 0.007 0.001 ARG c 422 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 1.080 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 82 MET cc_start: 0.8768 (pmm) cc_final: 0.8386 (pmm) REVERT: A 134 MET cc_start: 0.7970 (ttp) cc_final: 0.7572 (tmm) REVERT: a 359 MET cc_start: 0.8983 (tpp) cc_final: 0.8708 (mtp) REVERT: a 414 MET cc_start: 0.9300 (tmm) cc_final: 0.8763 (tmm) REVERT: B 82 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.7854 (pmm) REVERT: b 414 MET cc_start: 0.9363 (tmm) cc_final: 0.8878 (tmm) REVERT: C 82 MET cc_start: 0.9044 (pmm) cc_final: 0.8259 (pmm) REVERT: C 194 MET cc_start: 0.9044 (tpt) cc_final: 0.8520 (tpp) REVERT: c 351 MET cc_start: 0.9354 (mmm) cc_final: 0.8866 (mmm) REVERT: c 359 MET cc_start: 0.8543 (mmm) cc_final: 0.8249 (mtp) REVERT: c 414 MET cc_start: 0.9364 (tmm) cc_final: 0.8863 (tmm) outliers start: 27 outliers final: 16 residues processed: 131 average time/residue: 0.2276 time to fit residues: 41.8366 Evaluate side-chains 117 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 253 TYR Chi-restraints excluded: chain a residue 266 LEU Chi-restraints excluded: chain a residue 397 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 253 TYR Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 253 TYR Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 402 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 20 optimal weight: 0.5980 chunk 96 optimal weight: 0.0670 chunk 63 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN B 90 ASN b 354 HIS C 90 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.052690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.040959 restraints weight = 56708.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.042320 restraints weight = 33719.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.043268 restraints weight = 24556.312| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9993 Z= 0.248 Angle : 0.833 10.979 13536 Z= 0.408 Chirality : 0.049 0.344 1755 Planarity : 0.004 0.041 1587 Dihedral : 11.182 77.843 2988 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.56 % Allowed : 12.73 % Favored : 86.70 % Rotamer: Outliers : 2.69 % Allowed : 11.70 % Favored : 85.61 % 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: -2.26 (0.24), residues: 1068 helix: -0.43 (0.27), residues: 402 sheet: -0.64 (0.53), residues: 105 loop : -2.58 (0.22), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 196 HIS 0.003 0.001 HIS a 305 PHE 0.010 0.001 PHE c 309 TYR 0.016 0.002 TYR A 253 ARG 0.011 0.001 ARG c 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 132 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8299 (pmm) REVERT: A 134 MET cc_start: 0.8115 (ttp) cc_final: 0.7824 (tmm) REVERT: A 194 MET cc_start: 0.9205 (tpt) cc_final: 0.8803 (tpp) REVERT: a 320 LYS cc_start: 0.9450 (tptp) cc_final: 0.9176 (tptp) REVERT: a 335 GLN cc_start: 0.8767 (pm20) cc_final: 0.8558 (pm20) REVERT: a 351 MET cc_start: 0.9247 (mmm) cc_final: 0.8784 (mmm) REVERT: a 359 MET cc_start: 0.9122 (tpp) cc_final: 0.8719 (mmp) REVERT: a 414 MET cc_start: 0.9364 (tmm) cc_final: 0.8892 (tmm) REVERT: B 153 MET cc_start: 0.6171 (mpp) cc_final: 0.5913 (mpp) REVERT: B 203 LEU cc_start: 0.7730 (mt) cc_final: 0.7449 (tt) REVERT: b 414 MET cc_start: 0.9377 (tmm) cc_final: 0.8934 (tmm) REVERT: C 194 MET cc_start: 0.9103 (tpt) cc_final: 0.8725 (tpp) REVERT: C 210 TRP cc_start: 0.6501 (t-100) cc_final: 0.6161 (t-100) REVERT: c 414 MET cc_start: 0.9360 (tmm) cc_final: 0.8958 (tmm) REVERT: c 417 LYS cc_start: 0.9215 (tppt) cc_final: 0.8858 (ttmm) outliers start: 26 outliers final: 21 residues processed: 123 average time/residue: 0.2200 time to fit residues: 38.4207 Evaluate side-chains 120 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 253 TYR Chi-restraints excluded: chain a residue 266 LEU Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain a residue 397 THR Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 212 CYS 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 402 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 80 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.3462 r_free = 0.3462 target = 0.052671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.040834 restraints weight = 57030.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.042183 restraints weight = 34023.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.043119 restraints weight = 24830.403| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.5220 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= 0.251 Angle : 0.803 10.855 13536 Z= 0.390 Chirality : 0.049 0.349 1755 Planarity : 0.004 0.034 1587 Dihedral : 10.563 75.031 2988 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.56 % Allowed : 12.92 % Favored : 86.52 % Rotamer: Outliers : 2.59 % Allowed : 13.56 % Favored : 83.85 % 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: -2.26 (0.24), residues: 1068 helix: -0.35 (0.27), residues: 402 sheet: -0.95 (0.58), residues: 87 loop : -2.53 (0.22), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 210 HIS 0.004 0.001 HIS B 131 PHE 0.010 0.001 PHE a 309 TYR 0.015 0.002 TYR A 253 ARG 0.007 0.001 ARG c 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 to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.8000 (pmm) REVERT: A 134 MET cc_start: 0.8185 (ttp) cc_final: 0.7851 (tmm) REVERT: A 194 MET cc_start: 0.9197 (tpt) cc_final: 0.8791 (tpp) REVERT: A 210 TRP cc_start: 0.6147 (t-100) cc_final: 0.5845 (t-100) REVERT: a 320 LYS cc_start: 0.9469 (tptp) cc_final: 0.9169 (tptp) REVERT: a 359 MET cc_start: 0.9106 (tpp) cc_final: 0.8752 (mtp) REVERT: B 82 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.7782 (pmm) REVERT: B 203 LEU cc_start: 0.7701 (mt) cc_final: 0.7449 (tt) REVERT: b 399 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8611 (t80) REVERT: b 414 MET cc_start: 0.9394 (tmm) cc_final: 0.8993 (tmm) REVERT: C 134 MET cc_start: 0.8390 (ttm) cc_final: 0.7843 (tmm) REVERT: C 194 MET cc_start: 0.9122 (tpt) cc_final: 0.8753 (tpp) REVERT: c 351 MET cc_start: 0.9282 (mmm) cc_final: 0.8848 (mmm) REVERT: c 414 MET cc_start: 0.9404 (tmm) cc_final: 0.9024 (tmm) outliers start: 25 outliers final: 18 residues processed: 119 average time/residue: 0.2519 time to fit residues: 43.7021 Evaluate side-chains 120 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain a residue 266 LEU Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain b residue 399 PHE Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 212 CYS 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 355 LEU Chi-restraints excluded: chain c residue 402 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 55 optimal weight: 0.0770 chunk 76 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 overall best weight: 4.0146 ------------------------------------------------------------------------------- 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 = 0.3410 r_free = 0.3410 target = 0.051021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.039440 restraints weight = 57483.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.040733 restraints weight = 34122.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.041648 restraints weight = 24785.937| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 9993 Z= 0.369 Angle : 0.873 9.071 13536 Z= 0.421 Chirality : 0.049 0.335 1755 Planarity : 0.004 0.031 1587 Dihedral : 10.527 73.796 2988 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.56 % Allowed : 12.83 % Favored : 86.61 % Rotamer: Outliers : 2.90 % Allowed : 14.49 % Favored : 82.61 % 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: -2.33 (0.24), residues: 1068 helix: -0.49 (0.26), residues: 402 sheet: 0.35 (0.57), residues: 75 loop : -2.71 (0.22), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 210 HIS 0.005 0.001 HIS B 131 PHE 0.013 0.002 PHE a 309 TYR 0.015 0.002 TYR B 241 ARG 0.005 0.001 ARG c 422 *********************** 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 125 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8073 (pmm) REVERT: A 134 MET cc_start: 0.8267 (ttp) cc_final: 0.7842 (tmm) REVERT: A 210 TRP cc_start: 0.6458 (t-100) cc_final: 0.6246 (t-100) REVERT: a 320 LYS cc_start: 0.9519 (tptp) cc_final: 0.9242 (tptp) REVERT: a 359 MET cc_start: 0.9160 (tpp) cc_final: 0.8798 (mtp) REVERT: a 414 MET cc_start: 0.9301 (tmm) cc_final: 0.8779 (tmm) REVERT: B 82 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.7729 (pmm) REVERT: B 134 MET cc_start: 0.8962 (tpp) cc_final: 0.8629 (tpp) REVERT: B 203 LEU cc_start: 0.7649 (mt) cc_final: 0.7350 (tt) REVERT: b 399 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.8604 (t80) REVERT: b 414 MET cc_start: 0.9404 (tmm) cc_final: 0.9008 (tmm) REVERT: C 82 MET cc_start: 0.8900 (pmm) cc_final: 0.8517 (pmm) REVERT: C 134 MET cc_start: 0.8431 (ttm) cc_final: 0.7798 (tmm) REVERT: C 194 MET cc_start: 0.9176 (tpt) cc_final: 0.8788 (tpp) REVERT: c 311 ASP cc_start: 0.9287 (m-30) cc_final: 0.8656 (m-30) REVERT: c 414 MET cc_start: 0.9414 (tmm) cc_final: 0.8858 (tmm) outliers start: 28 outliers final: 19 residues processed: 116 average time/residue: 0.1991 time to fit residues: 34.0538 Evaluate side-chains 115 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain a residue 266 LEU Chi-restraints excluded: chain a residue 347 ASP Chi-restraints excluded: chain a residue 403 ILE Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain b residue 399 PHE 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 212 CYS Chi-restraints excluded: chain C residue 253 TYR 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 82 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.052562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.040988 restraints weight = 56335.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.042344 restraints weight = 32924.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.043295 restraints weight = 23696.798| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.5649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9993 Z= 0.222 Angle : 0.803 10.908 13536 Z= 0.385 Chirality : 0.048 0.366 1755 Planarity : 0.003 0.030 1587 Dihedral : 9.771 69.645 2988 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.56 % Allowed : 12.17 % Favored : 87.27 % Rotamer: Outliers : 2.07 % Allowed : 15.42 % Favored : 82.51 % 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: -2.16 (0.24), residues: 1068 helix: -0.09 (0.27), residues: 387 sheet: -0.15 (0.60), residues: 57 loop : -2.60 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 210 HIS 0.003 0.001 HIS C 124 PHE 0.011 0.001 PHE a 309 TYR 0.015 0.001 TYR c 366 ARG 0.005 0.001 ARG c 422 *********************** 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 126 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7890 (pmm) REVERT: A 134 MET cc_start: 0.8228 (ttp) cc_final: 0.7763 (tmm) REVERT: a 320 LYS cc_start: 0.9492 (tptp) cc_final: 0.9187 (tptp) REVERT: a 359 MET cc_start: 0.9042 (tpp) cc_final: 0.8733 (mtp) REVERT: a 414 MET cc_start: 0.9318 (tmm) cc_final: 0.8825 (tmm) REVERT: B 82 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7774 (pmm) REVERT: B 134 MET cc_start: 0.8934 (tpp) cc_final: 0.8586 (tpp) REVERT: b 399 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8599 (t80) REVERT: b 414 MET cc_start: 0.9400 (tmm) cc_final: 0.8895 (tmm) REVERT: C 82 MET cc_start: 0.8802 (pmm) cc_final: 0.8424 (pmm) REVERT: C 134 MET cc_start: 0.8470 (ttm) cc_final: 0.7651 (tmm) REVERT: C 194 MET cc_start: 0.9082 (tpt) cc_final: 0.8705 (tpp) REVERT: c 311 ASP cc_start: 0.9235 (m-30) cc_final: 0.8574 (m-30) REVERT: c 414 MET cc_start: 0.9408 (tmm) cc_final: 0.8880 (tmm) outliers start: 20 outliers final: 13 residues processed: 120 average time/residue: 0.2331 time to fit residues: 39.5037 Evaluate side-chains 109 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain a residue 266 LEU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain b residue 399 PHE Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 212 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.9990 chunk 84 optimal weight: 0.1980 chunk 74 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 79 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN c 398 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.052963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.041742 restraints weight = 56015.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.043142 restraints weight = 31685.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.044098 restraints weight = 22402.395| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.5835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9993 Z= 0.216 Angle : 0.817 10.101 13536 Z= 0.395 Chirality : 0.048 0.357 1755 Planarity : 0.004 0.052 1587 Dihedral : 9.396 67.409 2988 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.66 % Allowed : 12.55 % Favored : 86.80 % Rotamer: Outliers : 1.97 % Allowed : 16.25 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.05 (0.24), residues: 1068 helix: -0.03 (0.27), residues: 387 sheet: 0.21 (0.55), residues: 75 loop : -2.61 (0.22), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 210 HIS 0.007 0.001 HIS c 305 PHE 0.039 0.001 PHE C 147 TYR 0.011 0.001 TYR c 419 ARG 0.015 0.001 ARG b 314 *********************** 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 120 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.8321 (ttp) cc_final: 0.8009 (tmm) REVERT: a 311 ASP cc_start: 0.9206 (m-30) cc_final: 0.8729 (m-30) REVERT: a 320 LYS cc_start: 0.9496 (tptp) cc_final: 0.9184 (tptp) REVERT: a 359 MET cc_start: 0.8987 (tpp) cc_final: 0.8670 (mtp) REVERT: a 414 MET cc_start: 0.9300 (tmm) cc_final: 0.8827 (tmm) REVERT: B 82 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7740 (pmm) REVERT: B 134 MET cc_start: 0.8896 (tpp) cc_final: 0.8394 (ttm) REVERT: b 332 MET cc_start: 0.8735 (tpp) cc_final: 0.8334 (tpp) REVERT: b 399 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8582 (t80) REVERT: b 414 MET cc_start: 0.9396 (tmm) cc_final: 0.8967 (tmm) REVERT: C 82 MET cc_start: 0.8699 (pmm) cc_final: 0.8258 (pmm) REVERT: C 134 MET cc_start: 0.8428 (ttm) cc_final: 0.7693 (tmm) REVERT: C 151 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8307 (tt0) REVERT: C 194 MET cc_start: 0.9025 (tpt) cc_final: 0.8634 (tpp) REVERT: c 303 GLU cc_start: 0.8986 (pm20) cc_final: 0.8464 (tp30) REVERT: c 311 ASP cc_start: 0.9220 (m-30) cc_final: 0.8590 (m-30) REVERT: c 414 MET cc_start: 0.9395 (tmm) cc_final: 0.8871 (tmm) outliers start: 19 outliers final: 13 residues processed: 117 average time/residue: 0.1959 time to fit residues: 33.9634 Evaluate side-chains 109 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 212 CYS Chi-restraints excluded: chain a residue 266 LEU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain b residue 399 PHE Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 355 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 4 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 101 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 15 optimal weight: 0.0020 chunk 63 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.052533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.041259 restraints weight = 56495.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.042579 restraints weight = 32374.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.043496 restraints weight = 23291.220| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.5942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 9993 Z= 0.245 Angle : 0.827 10.846 13536 Z= 0.401 Chirality : 0.048 0.351 1755 Planarity : 0.004 0.053 1587 Dihedral : 9.274 65.956 2988 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.56 % Allowed : 12.64 % Favored : 86.80 % Rotamer: Outliers : 1.55 % Allowed : 16.87 % Favored : 81.57 % 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: -2.03 (0.25), residues: 1068 helix: 0.04 (0.27), residues: 387 sheet: 0.17 (0.56), residues: 75 loop : -2.64 (0.22), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP C 210 HIS 0.005 0.001 HIS c 305 PHE 0.035 0.001 PHE C 147 TYR 0.022 0.001 TYR B 150 ARG 0.014 0.001 ARG b 314 ********************** 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 110 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8478 (pmm) cc_final: 0.7791 (pmm) REVERT: A 134 MET cc_start: 0.8304 (ttp) cc_final: 0.8027 (tmm) REVERT: a 311 ASP cc_start: 0.9199 (m-30) cc_final: 0.8763 (m-30) REVERT: a 320 LYS cc_start: 0.9517 (tptp) cc_final: 0.9230 (tptp) REVERT: a 332 MET cc_start: 0.8024 (ttt) cc_final: 0.7261 (tpp) REVERT: a 359 MET cc_start: 0.8998 (tpp) cc_final: 0.8650 (mtp) REVERT: a 414 MET cc_start: 0.9307 (tmm) cc_final: 0.8853 (tmm) REVERT: B 82 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7504 (pmm) REVERT: B 134 MET cc_start: 0.8887 (tpp) cc_final: 0.8502 (tpp) REVERT: b 332 MET cc_start: 0.8770 (tpp) cc_final: 0.8333 (tpp) REVERT: b 399 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8597 (t80) REVERT: b 414 MET cc_start: 0.9404 (tmm) cc_final: 0.8922 (tmm) REVERT: C 80 MET cc_start: 0.9483 (tpp) cc_final: 0.9039 (tpp) REVERT: C 82 MET cc_start: 0.8795 (pmm) cc_final: 0.8429 (pmm) REVERT: C 134 MET cc_start: 0.8393 (ttm) cc_final: 0.7669 (tmm) REVERT: C 151 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8299 (tt0) REVERT: C 194 MET cc_start: 0.9034 (tpt) cc_final: 0.8641 (tpp) REVERT: c 311 ASP cc_start: 0.9200 (m-30) cc_final: 0.8560 (m-30) REVERT: c 414 MET cc_start: 0.9426 (tmm) cc_final: 0.8960 (tmm) REVERT: c 417 LYS cc_start: 0.9193 (tppt) cc_final: 0.8876 (ttmm) outliers start: 15 outliers final: 11 residues processed: 108 average time/residue: 0.2037 time to fit residues: 32.6485 Evaluate side-chains 108 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 212 CYS Chi-restraints excluded: chain a residue 266 LEU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain b residue 399 PHE Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 355 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 67 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN B 69 GLN ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.051772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.040698 restraints weight = 57535.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.042023 restraints weight = 32981.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.042950 restraints weight = 23548.596| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.6078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9993 Z= 0.274 Angle : 0.843 10.154 13536 Z= 0.408 Chirality : 0.048 0.345 1755 Planarity : 0.004 0.049 1587 Dihedral : 9.238 63.850 2988 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.56 % Allowed : 12.55 % Favored : 86.89 % Rotamer: Outliers : 1.66 % Allowed : 16.87 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.24), residues: 1068 helix: -0.17 (0.27), residues: 405 sheet: 0.04 (0.56), residues: 75 loop : -2.75 (0.22), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP C 210 HIS 0.004 0.001 HIS a 305 PHE 0.033 0.002 PHE C 147 TYR 0.019 0.002 TYR B 150 ARG 0.013 0.001 ARG b 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2540.87 seconds wall clock time: 47 minutes 8.52 seconds (2828.52 seconds total)