Starting phenix.real_space_refine on Sat Aug 23 09:34:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eji_28183/08_2025/8eji_28183.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eji_28183/08_2025/8eji_28183.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8eji_28183/08_2025/8eji_28183.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eji_28183/08_2025/8eji_28183.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eji_28183/08_2025/8eji_28183.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eji_28183/08_2025/8eji_28183.map" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.003 sd= 0.032 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 97 5.16 5 C 6886 2.51 5 N 1742 2.21 5 O 2298 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11023 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1516 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "a" Number of atoms: 1286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1286 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 4, 'TRANS': 154} Chain: "B" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1504 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain breaks: 1 Chain: "b" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1223 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 3, 'TRANS': 146} Chain breaks: 1 Chain: "H" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 923 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "C" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1504 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain breaks: 1 Chain: "c" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1232 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain breaks: 1 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: "E" 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: "F" 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: "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: "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: "M" 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: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 2.29, per 1000 atoms: 0.21 Number of scatterers: 11023 At special positions: 0 Unit cell: (125.4, 96.14, 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 97 16.00 O 2298 8.00 N 1742 7.00 C 6886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 360 " distance=2.04 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.04 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=2.01 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 360 " distance=2.08 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.03 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.03 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.02 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 105 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.04 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=2.08 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 ALPHA1-2 " MAN R 4 " - " MAN R 5 " " MAN W 4 " - " MAN W 5 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA G 3 " - " MAN G 4 " " BMA J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 5 " " BMA M 3 " - " MAN M 4 " " BMA R 3 " - " MAN R 4 " " BMA W 3 " - " MAN W 4 " ALPHA1-6 " MAN E 4 " - " MAN E 5 " " BMA G 3 " - " MAN G 5 " " BMA M 3 " - " MAN M 5 " " BMA R 3 " - " MAN R 6 " " BMA W 3 " - " MAN W 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " 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 M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG 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 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-ASN " NAG B 301 " - " ASN B 89 " " NAG B 302 " - " ASN B 99 " " NAG B 303 " - " ASN B 109 " " NAG B 304 " - " ASN B 119 " " NAG C 301 " - " ASN C 89 " " NAG C 302 " - " ASN C 99 " " NAG C 303 " - " ASN C 109 " " NAG C 304 " - " ASN C 119 " " NAG D 1 " - " ASN A 79 " " NAG E 1 " - " ASN A 89 " " NAG F 1 " - " ASN A 99 " " NAG G 1 " - " ASN A 109 " " NAG I 1 " - " ASN A 119 " " NAG J 1 " - " ASN A 167 " " NAG K 1 " - " ASN A 224 " " NAG M 1 " - " ASN a 365 " " NAG N 1 " - " ASN a 373 " " NAG O 1 " - " ASN B 79 " " 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 167 " " NAG V 1 " - " ASN C 224 " " NAG W 1 " - " ASN c 365 " " NAG X 1 " - " ASN c 373 " " 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 " Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 400.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2362 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 18 sheets defined 37.9% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 209 through 213 removed outlier: 3.946A pdb=" N ILE A 213 " --> pdb=" O TRP A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 245 removed outlier: 3.603A pdb=" N LEU A 245 " --> pdb=" O TYR A 241 " (cutoff:3.500A) Processing helix chain 'a' and resid 294 through 304 Processing helix chain 'a' and resid 307 through 326 Processing helix chain 'a' and resid 329 through 333 removed outlier: 3.541A pdb=" N SER a 333 " --> pdb=" O ALA a 330 " (cutoff:3.500A) Processing helix chain 'a' and resid 336 through 339 Processing helix chain 'a' and resid 340 through 345 Processing helix chain 'a' and resid 346 through 359 removed outlier: 3.587A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 395 through 418 removed outlier: 5.603A pdb=" N ASP a 401 " --> pdb=" O THR a 397 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ASP a 402 " --> pdb=" O HIS a 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 65 No H-bonds generated for 'chain 'B' and resid 63 through 65' Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.544A pdb=" N THR B 77 " --> pdb=" O ASN B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 130 through 143 Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 182 through 195 Processing helix chain 'B' and resid 195 through 203 removed outlier: 4.384A pdb=" N TYR B 200 " --> pdb=" O TRP B 196 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE B 201 " --> pdb=" O GLY B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 247 removed outlier: 3.819A pdb=" N SER B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLN B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) Processing helix chain 'b' and resid 281 through 285 Processing helix chain 'b' and resid 294 through 302 removed outlier: 3.559A pdb=" N ASN b 302 " --> pdb=" O VAL b 298 " (cutoff:3.500A) Processing helix chain 'b' and resid 307 through 326 Processing helix chain 'b' and resid 333 through 345 removed outlier: 3.894A pdb=" N LYS b 339 " --> pdb=" O GLN b 335 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ASN b 342 " --> pdb=" O ASN b 338 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA b 343 " --> pdb=" O LYS b 339 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 359 removed outlier: 3.603A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 395 through 398 Processing helix chain 'b' and resid 399 through 417 Processing helix chain 'H' and resid 29 through 37 Processing helix chain 'H' and resid 96 through 100 Processing helix chain 'L' and resid 95 through 99 removed outlier: 4.017A pdb=" N PHE L 99 " --> pdb=" O PRO L 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 65 No H-bonds generated for 'chain 'C' and resid 63 through 65' Processing helix chain 'C' and resid 74 through 79 removed outlier: 3.543A pdb=" N THR C 77 " --> pdb=" O ASN C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 195 through 203 removed outlier: 4.385A pdb=" N TYR C 200 " --> pdb=" O TRP C 196 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 247 removed outlier: 3.818A pdb=" N SER C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLN C 247 " --> pdb=" O GLY C 243 " (cutoff:3.500A) Processing helix chain 'c' and resid 281 through 285 Processing helix chain 'c' and resid 294 through 302 removed outlier: 3.559A pdb=" N ASN c 302 " --> pdb=" O VAL c 298 " (cutoff:3.500A) Processing helix chain 'c' and resid 307 through 326 Processing helix chain 'c' and resid 333 through 345 removed outlier: 3.895A pdb=" N LYS c 339 " --> pdb=" O GLN c 335 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ASN c 342 " --> pdb=" O ASN c 338 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA c 343 " --> pdb=" O LYS c 339 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.604A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 395 through 398 Processing helix chain 'c' and resid 399 through 418 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 88 removed outlier: 3.628A pdb=" N GLY A 102 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 279 through 281 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 61 through 62 Processing sheet with id=AA6, first strand: chain 'B' and resid 71 through 72 removed outlier: 9.249A pdb=" N TYR b 366 " --> pdb=" O VAL b 388 " (cutoff:3.500A) removed outlier: 10.373A pdb=" N VAL b 388 " --> pdb=" O TYR b 366 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LYS b 368 " --> pdb=" O TRP b 386 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 84 through 87 Processing sheet with id=AA8, first strand: chain 'b' and resid 278 through 280 removed outlier: 3.635A pdb=" N LYS b 291 " --> pdb=" O LEU b 280 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.923A pdb=" N MET H 39 " --> pdb=" O TYR H 55 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N TYR H 55 " --> pdb=" O MET H 39 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP H 41 " --> pdb=" O VAL H 53 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 13 Processing sheet with id=AB3, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.563A pdb=" N LEU L 11 " --> pdb=" O ASP L 125 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU L 39 " --> pdb=" O ASN L 55 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASN L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.563A pdb=" N LEU L 11 " --> pdb=" O ASP L 125 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AB7, first strand: chain 'C' and resid 71 through 72 removed outlier: 9.249A pdb=" N TYR c 366 " --> pdb=" O VAL c 388 " (cutoff:3.500A) removed outlier: 10.372A pdb=" N VAL c 388 " --> pdb=" O TYR c 366 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LYS c 368 " --> pdb=" O TRP c 386 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 84 through 87 Processing sheet with id=AB9, first strand: chain 'c' and resid 278 through 280 removed outlier: 3.635A pdb=" N LYS c 291 " --> pdb=" O LEU c 280 " (cutoff:3.500A) 456 hydrogen bonds defined for protein. 1185 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: 1.12 Time building geometry restraints manager: 1.02 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: 2105 1.32 - 1.45: 3702 1.45 - 1.59: 5255 1.59 - 1.72: 36 1.72 - 1.86: 146 Bond restraints: 11244 Sorted by residual: bond pdb=" CB HIS A 170 " pdb=" CG HIS A 170 " ideal model delta sigma weight residual 1.497 1.407 0.090 1.40e-02 5.10e+03 4.16e+01 bond pdb=" CB HIS A 93 " pdb=" CG HIS A 93 " ideal model delta sigma weight residual 1.497 1.412 0.085 1.40e-02 5.10e+03 3.71e+01 bond pdb=" CB HIS a 354 " pdb=" CG HIS a 354 " ideal model delta sigma weight residual 1.497 1.414 0.083 1.40e-02 5.10e+03 3.55e+01 bond pdb=" CB LEU a 372 " pdb=" CG LEU a 372 " ideal model delta sigma weight residual 1.530 1.422 0.108 2.00e-02 2.50e+03 2.89e+01 bond pdb=" CB HIS H 40 " pdb=" CG HIS H 40 " ideal model delta sigma weight residual 1.497 1.423 0.074 1.40e-02 5.10e+03 2.76e+01 ... (remaining 11239 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 13396 2.73 - 5.47: 1597 5.47 - 8.20: 200 8.20 - 10.93: 27 10.93 - 13.66: 6 Bond angle restraints: 15226 Sorted by residual: angle pdb=" N LEU a 382 " pdb=" CA LEU a 382 " pdb=" C LEU a 382 " ideal model delta sigma weight residual 109.83 99.24 10.59 1.27e+00 6.20e-01 6.96e+01 angle pdb=" C SER a 267 " pdb=" CA SER a 267 " pdb=" CB SER a 267 " ideal model delta sigma weight residual 117.23 107.05 10.18 1.36e+00 5.41e-01 5.61e+01 angle pdb=" C TRP c 370 " pdb=" CA TRP c 370 " pdb=" CB TRP c 370 " ideal model delta sigma weight residual 110.85 98.41 12.44 1.70e+00 3.46e-01 5.36e+01 angle pdb=" C TRP b 370 " pdb=" CA TRP b 370 " pdb=" CB TRP b 370 " ideal model delta sigma weight residual 110.85 98.45 12.40 1.70e+00 3.46e-01 5.32e+01 angle pdb=" N LEU c 382 " pdb=" CA LEU c 382 " pdb=" C LEU c 382 " ideal model delta sigma weight residual 109.50 99.00 10.50 1.47e+00 4.63e-01 5.10e+01 ... (remaining 15221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.72: 7300 21.72 - 43.44: 225 43.44 - 65.16: 43 65.16 - 86.88: 75 86.88 - 108.60: 54 Dihedral angle restraints: 7697 sinusoidal: 4029 harmonic: 3668 Sorted by residual: dihedral pdb=" CB CYS H 23 " pdb=" SG CYS H 23 " pdb=" SG CYS H 105 " pdb=" CB CYS H 105 " ideal model delta sinusoidal sigma weight residual 93.00 166.90 -73.90 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CB CYS C 86 " pdb=" SG CYS C 86 " pdb=" SG CYS C 231 " pdb=" CB CYS C 231 " ideal model delta sinusoidal sigma weight residual -86.00 -158.57 72.57 1 1.00e+01 1.00e-02 6.72e+01 dihedral pdb=" CB CYS B 86 " pdb=" SG CYS B 86 " pdb=" SG CYS B 231 " pdb=" CB CYS B 231 " ideal model delta sinusoidal sigma weight residual -86.00 -158.53 72.53 1 1.00e+01 1.00e-02 6.72e+01 ... (remaining 7694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 1292 0.119 - 0.239: 409 0.239 - 0.358: 146 0.358 - 0.478: 62 0.478 - 0.597: 9 Chirality restraints: 1918 Sorted by residual: chirality pdb=" C1 BMA R 3 " pdb=" O4 NAG R 2 " pdb=" C2 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-02 2.50e+03 6.36e+02 chirality pdb=" C1 BMA W 3 " pdb=" O4 NAG W 2 " pdb=" C2 BMA W 3 " pdb=" O5 BMA W 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-02 2.50e+03 4.47e+02 chirality pdb=" C1 MAN W 5 " pdb=" O2 MAN W 4 " pdb=" C2 MAN W 5 " pdb=" O5 MAN W 5 " both_signs ideal model delta sigma weight residual False 2.40 2.75 -0.35 2.00e-02 2.50e+03 3.00e+02 ... (remaining 1915 not shown) Planarity restraints: 1836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 2 " -0.355 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG S 2 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG S 2 " -0.131 2.00e-02 2.50e+03 pdb=" N2 NAG S 2 " 0.544 2.00e-02 2.50e+03 pdb=" O7 NAG S 2 " -0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 2 " 0.355 2.00e-02 2.50e+03 3.05e-01 1.17e+03 pdb=" C7 NAG X 2 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG X 2 " 0.131 2.00e-02 2.50e+03 pdb=" N2 NAG X 2 " -0.543 2.00e-02 2.50e+03 pdb=" O7 NAG X 2 " 0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 1 " -0.349 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG R 1 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG R 1 " -0.089 2.00e-02 2.50e+03 pdb=" N2 NAG R 1 " 0.537 2.00e-02 2.50e+03 pdb=" O7 NAG R 1 " -0.179 2.00e-02 2.50e+03 ... (remaining 1833 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3323 2.83 - 3.35: 10668 3.35 - 3.86: 18681 3.86 - 4.38: 22634 4.38 - 4.90: 35563 Nonbonded interactions: 90869 Sorted by model distance: nonbonded pdb=" O4 MAN J 4 " pdb=" O6 MAN J 4 " model vdw 2.309 3.040 nonbonded pdb=" NZ LYS a 339 " pdb=" OD2 ASP B 251 " model vdw 2.409 3.120 nonbonded pdb=" OD2 ASP H 82 " pdb=" NZ LYS H 85 " model vdw 2.410 3.120 nonbonded pdb=" OG SER L 26 " pdb=" OE1 GLN L 27 " model vdw 2.419 3.040 nonbonded pdb=" N ASP c 306 " pdb=" OD1 ASP c 306 " model vdw 2.419 3.120 ... (remaining 90864 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 59 through 171 or resid 179 through 255)) selection = (chain 'B' and resid 59 through 255) selection = (chain 'C' and resid 59 through 255) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'T' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'I' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'X' } ncs_group { reference = chain 'R' selection = chain 'W' } ncs_group { reference = (chain 'a' and (resid 260 through 268 or resid 277 through 417 or resid 701 thro \ ugh 702)) selection = chain 'b' selection = (chain 'c' and (resid 260 through 417 or resid 701 through 702)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.610 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 : 0.023 0.134 11345 Z= 1.213 Angle : 1.907 13.663 15506 Z= 1.172 Chirality : 0.148 0.597 1918 Planarity : 0.018 0.306 1803 Dihedral : 16.973 108.601 5266 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.23), residues: 1231 helix: -0.12 (0.25), residues: 358 sheet: 0.71 (0.33), residues: 232 loop : 0.27 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 248 TYR 0.056 0.009 TYR a 363 PHE 0.034 0.006 PHE L 118 TRP 0.034 0.009 TRP A 196 HIS 0.015 0.003 HIS c 374 Details of bonding type rmsd covalent geometry : bond 0.02204 (11244) covalent geometry : angle 1.84806 (15226) SS BOND : bond 0.01612 ( 23) SS BOND : angle 2.62679 ( 46) hydrogen bonds : bond 0.17826 ( 447) hydrogen bonds : angle 7.33024 ( 1185) link_ALPHA1-2 : bond 0.00488 ( 2) link_ALPHA1-2 : angle 5.91152 ( 6) link_ALPHA1-3 : bond 0.06881 ( 7) link_ALPHA1-3 : angle 4.50911 ( 21) link_ALPHA1-6 : bond 0.05289 ( 5) link_ALPHA1-6 : angle 2.76301 ( 15) link_BETA1-4 : bond 0.06286 ( 31) link_BETA1-4 : angle 4.77463 ( 93) link_NAG-ASN : bond 0.06888 ( 33) link_NAG-ASN : angle 3.47607 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 0.392 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: 0.9141 (ptp) cc_final: 0.8918 (ptp) REVERT: A 134 MET cc_start: 0.9087 (tpp) cc_final: 0.8265 (tpp) REVERT: a 284 MET cc_start: 0.9002 (mtp) cc_final: 0.8580 (mtt) REVERT: a 347 ASP cc_start: 0.8227 (p0) cc_final: 0.7864 (p0) REVERT: a 405 GLN cc_start: 0.8905 (tp40) cc_final: 0.8533 (tp-100) REVERT: a 408 ASP cc_start: 0.8508 (m-30) cc_final: 0.8102 (t70) REVERT: b 289 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7129 (pm20) REVERT: b 312 MET cc_start: 0.8916 (mmm) cc_final: 0.8693 (mmm) REVERT: H 39 MET cc_start: 0.8371 (mmm) cc_final: 0.8029 (mmt) REVERT: H 126 VAL cc_start: 0.9228 (t) cc_final: 0.9008 (p) REVERT: L 98 ASP cc_start: 0.8550 (m-30) cc_final: 0.8193 (m-30) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.0969 time to fit residues: 44.1420 Evaluate side-chains 145 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 GLN A 170 HIS A 179 HIS A 247 GLN ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN ** b 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.079241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.064984 restraints weight = 36409.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.067598 restraints weight = 19741.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.069400 restraints weight = 13310.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.070653 restraints weight = 10144.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.071555 restraints weight = 8303.711| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 11345 Z= 0.201 Angle : 1.017 16.279 15506 Z= 0.467 Chirality : 0.053 0.342 1918 Planarity : 0.004 0.034 1803 Dihedral : 14.445 89.552 2929 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.82 % Favored : 96.10 % Rotamer: Outliers : 2.40 % Allowed : 9.69 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.23), residues: 1231 helix: 0.59 (0.26), residues: 370 sheet: 1.05 (0.36), residues: 198 loop : -0.49 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 81 TYR 0.017 0.002 TYR A 66 PHE 0.023 0.002 PHE C 117 TRP 0.033 0.003 TRP c 370 HIS 0.008 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00425 (11244) covalent geometry : angle 0.89125 (15226) SS BOND : bond 0.00428 ( 23) SS BOND : angle 1.66470 ( 46) hydrogen bonds : bond 0.05610 ( 447) hydrogen bonds : angle 5.47318 ( 1185) link_ALPHA1-2 : bond 0.00339 ( 2) link_ALPHA1-2 : angle 2.35477 ( 6) link_ALPHA1-3 : bond 0.01012 ( 7) link_ALPHA1-3 : angle 2.94130 ( 21) link_ALPHA1-6 : bond 0.00682 ( 5) link_ALPHA1-6 : angle 1.77770 ( 15) link_BETA1-4 : bond 0.00857 ( 31) link_BETA1-4 : angle 3.94247 ( 93) link_NAG-ASN : bond 0.00907 ( 33) link_NAG-ASN : angle 4.62397 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9246 (tpp) cc_final: 0.7632 (tpp) REVERT: A 150 TYR cc_start: 0.8486 (OUTLIER) cc_final: 0.7828 (m-80) REVERT: A 192 MET cc_start: 0.8889 (tpp) cc_final: 0.8675 (tpp) REVERT: A 194 MET cc_start: 0.9065 (tpp) cc_final: 0.8772 (tpp) REVERT: A 210 TRP cc_start: 0.7146 (t60) cc_final: 0.6839 (t60) REVERT: a 278 TYR cc_start: 0.6960 (t80) cc_final: 0.6717 (t80) REVERT: a 284 MET cc_start: 0.8684 (mtp) cc_final: 0.8082 (mtt) REVERT: a 311 ASP cc_start: 0.9143 (m-30) cc_final: 0.8745 (t70) REVERT: a 332 MET cc_start: 0.8530 (tmm) cc_final: 0.7837 (tmm) REVERT: a 347 ASP cc_start: 0.8268 (p0) cc_final: 0.7562 (p0) REVERT: a 405 GLN cc_start: 0.8928 (tp40) cc_final: 0.8522 (tp40) REVERT: a 408 ASP cc_start: 0.8507 (m-30) cc_final: 0.8076 (t70) REVERT: B 140 PHE cc_start: 0.8636 (t80) cc_final: 0.8420 (t80) REVERT: B 189 GLN cc_start: 0.8772 (mt0) cc_final: 0.8438 (tt0) REVERT: B 192 MET cc_start: 0.8325 (tpt) cc_final: 0.8067 (tpp) REVERT: B 214 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.6953 (pmm) REVERT: b 284 MET cc_start: 0.7935 (mtm) cc_final: 0.7560 (mtm) REVERT: b 289 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7400 (mm-30) REVERT: b 347 ASP cc_start: 0.7930 (p0) cc_final: 0.7365 (p0) REVERT: L 98 ASP cc_start: 0.8481 (m-30) cc_final: 0.8035 (m-30) REVERT: L 106 GLN cc_start: 0.7598 (pp30) cc_final: 0.6924 (pp30) REVERT: c 312 MET cc_start: 0.8781 (mmm) cc_final: 0.8104 (mmm) REVERT: c 370 TRP cc_start: 0.7680 (m-10) cc_final: 0.7058 (m-10) outliers start: 27 outliers final: 13 residues processed: 206 average time/residue: 0.0889 time to fit residues: 26.5446 Evaluate side-chains 161 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 150 TYR Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 295 ASN Chi-restraints excluded: chain b residue 345 ILE Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain c residue 286 ILE Chi-restraints excluded: chain c residue 345 ILE Chi-restraints excluded: chain c residue 411 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 37 optimal weight: 0.0030 chunk 34 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 97 optimal weight: 0.0970 chunk 83 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 GLN A 179 HIS ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS B 185 ASN L 43 GLN ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.076868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.061809 restraints weight = 37673.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.064461 restraints weight = 19673.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.066273 restraints weight = 13206.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.067528 restraints weight = 10103.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.068401 restraints weight = 8339.454| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11345 Z= 0.192 Angle : 0.894 13.618 15506 Z= 0.407 Chirality : 0.049 0.321 1918 Planarity : 0.004 0.041 1803 Dihedral : 11.592 79.625 2929 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.67 % Allowed : 12.18 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.23), residues: 1231 helix: 0.81 (0.27), residues: 372 sheet: 0.95 (0.34), residues: 221 loop : -0.80 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG c 314 TYR 0.020 0.002 TYR A 62 PHE 0.022 0.002 PHE c 399 TRP 0.024 0.002 TRP b 283 HIS 0.015 0.002 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00424 (11244) covalent geometry : angle 0.79083 (15226) SS BOND : bond 0.00435 ( 23) SS BOND : angle 1.47493 ( 46) hydrogen bonds : bond 0.04676 ( 447) hydrogen bonds : angle 5.10005 ( 1185) link_ALPHA1-2 : bond 0.00602 ( 2) link_ALPHA1-2 : angle 2.36896 ( 6) link_ALPHA1-3 : bond 0.00982 ( 7) link_ALPHA1-3 : angle 2.56216 ( 21) link_ALPHA1-6 : bond 0.00736 ( 5) link_ALPHA1-6 : angle 1.85456 ( 15) link_BETA1-4 : bond 0.00692 ( 31) link_BETA1-4 : angle 3.10954 ( 93) link_NAG-ASN : bond 0.00584 ( 33) link_NAG-ASN : angle 4.08419 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.9168 (tpp) cc_final: 0.7598 (tpp) REVERT: a 284 MET cc_start: 0.8752 (mtp) cc_final: 0.8241 (mtt) REVERT: a 307 GLU cc_start: 0.8281 (mt-10) cc_final: 0.8056 (mt-10) REVERT: a 311 ASP cc_start: 0.9202 (m-30) cc_final: 0.8860 (t70) REVERT: a 332 MET cc_start: 0.8856 (tmm) cc_final: 0.7578 (tmm) REVERT: a 347 ASP cc_start: 0.8314 (p0) cc_final: 0.7866 (p0) REVERT: a 353 ASN cc_start: 0.9059 (m-40) cc_final: 0.8844 (m-40) REVERT: a 382 LEU cc_start: 0.9175 (tt) cc_final: 0.8833 (tt) REVERT: a 405 GLN cc_start: 0.8839 (tp40) cc_final: 0.8540 (tp40) REVERT: a 408 ASP cc_start: 0.8471 (m-30) cc_final: 0.8008 (t70) REVERT: B 134 MET cc_start: 0.8615 (tpp) cc_final: 0.8260 (tpp) REVERT: B 192 MET cc_start: 0.8260 (tpt) cc_final: 0.7927 (tpp) REVERT: b 284 MET cc_start: 0.7952 (mtm) cc_final: 0.7691 (mtm) REVERT: b 289 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7484 (mm-30) REVERT: b 347 ASP cc_start: 0.7849 (p0) cc_final: 0.7647 (p0) REVERT: L 87 PHE cc_start: 0.8227 (m-80) cc_final: 0.7756 (m-10) REVERT: L 89 LEU cc_start: 0.8515 (tp) cc_final: 0.8299 (tp) REVERT: L 98 ASP cc_start: 0.8545 (m-30) cc_final: 0.8148 (m-30) REVERT: L 106 GLN cc_start: 0.7793 (pp30) cc_final: 0.7391 (pp30) REVERT: c 304 LYS cc_start: 0.9000 (mmmt) cc_final: 0.8795 (mmmt) REVERT: c 361 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8454 (tp) REVERT: c 370 TRP cc_start: 0.7690 (m-10) cc_final: 0.7434 (m-10) outliers start: 30 outliers final: 20 residues processed: 180 average time/residue: 0.0899 time to fit residues: 23.2293 Evaluate side-chains 166 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 295 ASN Chi-restraints excluded: chain b residue 311 ASP Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain c residue 286 ILE Chi-restraints excluded: chain c residue 345 ILE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain c residue 415 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 40 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 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 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 335 GLN a 354 HIS b 335 GLN C 93 HIS ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.074755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.059740 restraints weight = 38422.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.062241 restraints weight = 20832.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.063906 restraints weight = 14277.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.065071 restraints weight = 11149.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.065894 restraints weight = 9355.090| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11345 Z= 0.225 Angle : 0.882 13.641 15506 Z= 0.402 Chirality : 0.048 0.332 1918 Planarity : 0.004 0.042 1803 Dihedral : 10.256 71.599 2929 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.76 % Allowed : 12.98 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.23), residues: 1231 helix: 1.06 (0.28), residues: 367 sheet: 0.71 (0.34), residues: 226 loop : -1.00 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 81 TYR 0.020 0.002 TYR B 241 PHE 0.015 0.002 PHE L 87 TRP 0.026 0.002 TRP B 210 HIS 0.011 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00507 (11244) covalent geometry : angle 0.78760 (15226) SS BOND : bond 0.00445 ( 23) SS BOND : angle 1.19219 ( 46) hydrogen bonds : bond 0.04376 ( 447) hydrogen bonds : angle 4.98549 ( 1185) link_ALPHA1-2 : bond 0.00343 ( 2) link_ALPHA1-2 : angle 2.34865 ( 6) link_ALPHA1-3 : bond 0.00938 ( 7) link_ALPHA1-3 : angle 2.47991 ( 21) link_ALPHA1-6 : bond 0.00767 ( 5) link_ALPHA1-6 : angle 2.01830 ( 15) link_BETA1-4 : bond 0.00576 ( 31) link_BETA1-4 : angle 2.86521 ( 93) link_NAG-ASN : bond 0.00523 ( 33) link_NAG-ASN : angle 3.97580 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7575 (mtp) cc_final: 0.7127 (mtt) REVERT: a 284 MET cc_start: 0.8684 (mtp) cc_final: 0.8269 (mtt) REVERT: a 303 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7790 (tm-30) REVERT: a 311 ASP cc_start: 0.9276 (m-30) cc_final: 0.8963 (t70) REVERT: a 332 MET cc_start: 0.9016 (tmm) cc_final: 0.8506 (tmm) REVERT: a 347 ASP cc_start: 0.8422 (p0) cc_final: 0.7850 (p0) REVERT: a 405 GLN cc_start: 0.8869 (tp40) cc_final: 0.8606 (tp40) REVERT: a 408 ASP cc_start: 0.8372 (m-30) cc_final: 0.8017 (t70) REVERT: B 134 MET cc_start: 0.8618 (tpp) cc_final: 0.7828 (tpp) REVERT: B 189 GLN cc_start: 0.8757 (mt0) cc_final: 0.8555 (mt0) REVERT: B 192 MET cc_start: 0.8386 (tpt) cc_final: 0.7978 (tpp) REVERT: b 347 ASP cc_start: 0.7923 (p0) cc_final: 0.7610 (p0) REVERT: L 87 PHE cc_start: 0.8242 (m-80) cc_final: 0.7610 (m-10) REVERT: L 89 LEU cc_start: 0.8597 (tp) cc_final: 0.8296 (tp) REVERT: L 98 ASP cc_start: 0.8515 (m-30) cc_final: 0.8088 (m-30) REVERT: L 106 GLN cc_start: 0.8008 (pp30) cc_final: 0.7600 (pp30) REVERT: C 228 GLU cc_start: 0.8109 (pp20) cc_final: 0.7572 (tp30) REVERT: c 361 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8382 (tp) REVERT: c 370 TRP cc_start: 0.7692 (m-10) cc_final: 0.7339 (m-10) outliers start: 31 outliers final: 20 residues processed: 169 average time/residue: 0.0811 time to fit residues: 20.1465 Evaluate side-chains 158 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain a residue 335 GLN Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 295 ASN Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain c residue 286 ILE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain c residue 417 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 1 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 chunk 55 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 GLN ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.072551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.057839 restraints weight = 38024.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.060255 restraints weight = 20293.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.061911 restraints weight = 13818.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.063049 restraints weight = 10696.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.063844 restraints weight = 8921.186| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.5000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 11345 Z= 0.267 Angle : 0.909 13.478 15506 Z= 0.418 Chirality : 0.050 0.353 1918 Planarity : 0.004 0.044 1803 Dihedral : 9.698 59.824 2929 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.29 % Allowed : 13.33 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.23), residues: 1231 helix: 0.96 (0.27), residues: 376 sheet: 0.57 (0.34), residues: 221 loop : -1.13 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG c 325 TYR 0.022 0.002 TYR L 107 PHE 0.017 0.002 PHE L 87 TRP 0.018 0.002 TRP H 52 HIS 0.011 0.002 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00603 (11244) covalent geometry : angle 0.82447 (15226) SS BOND : bond 0.00462 ( 23) SS BOND : angle 1.14139 ( 46) hydrogen bonds : bond 0.04527 ( 447) hydrogen bonds : angle 5.02239 ( 1185) link_ALPHA1-2 : bond 0.00350 ( 2) link_ALPHA1-2 : angle 2.37745 ( 6) link_ALPHA1-3 : bond 0.00873 ( 7) link_ALPHA1-3 : angle 2.43313 ( 21) link_ALPHA1-6 : bond 0.00817 ( 5) link_ALPHA1-6 : angle 2.04824 ( 15) link_BETA1-4 : bond 0.00553 ( 31) link_BETA1-4 : angle 2.66011 ( 93) link_NAG-ASN : bond 0.00544 ( 33) link_NAG-ASN : angle 3.94064 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.8880 (mpp) REVERT: A 96 MET cc_start: 0.7649 (mtp) cc_final: 0.7246 (mtt) REVERT: A 134 MET cc_start: 0.9281 (tpp) cc_final: 0.7476 (tpp) REVERT: A 192 MET cc_start: 0.9020 (tpp) cc_final: 0.8808 (tpp) REVERT: a 284 MET cc_start: 0.8780 (mtp) cc_final: 0.8361 (mtt) REVERT: a 303 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7705 (tm-30) REVERT: a 311 ASP cc_start: 0.9284 (m-30) cc_final: 0.8981 (t70) REVERT: a 348 GLN cc_start: 0.8949 (mm-40) cc_final: 0.8561 (mm-40) REVERT: a 408 ASP cc_start: 0.8439 (m-30) cc_final: 0.8172 (p0) REVERT: B 134 MET cc_start: 0.8641 (tpp) cc_final: 0.7495 (tpp) REVERT: B 189 GLN cc_start: 0.8693 (mt0) cc_final: 0.8440 (mt0) REVERT: B 192 MET cc_start: 0.8469 (tpt) cc_final: 0.8028 (tpp) REVERT: b 312 MET cc_start: 0.8864 (mmm) cc_final: 0.8596 (mmp) REVERT: b 347 ASP cc_start: 0.7983 (p0) cc_final: 0.7752 (p0) REVERT: L 87 PHE cc_start: 0.8180 (m-80) cc_final: 0.7893 (m-10) REVERT: L 89 LEU cc_start: 0.8636 (tp) cc_final: 0.8312 (tp) REVERT: L 98 ASP cc_start: 0.8438 (m-30) cc_final: 0.8110 (m-30) REVERT: L 106 GLN cc_start: 0.8284 (pp30) cc_final: 0.7930 (pp30) REVERT: L 120 GLN cc_start: 0.8371 (pm20) cc_final: 0.8141 (pm20) REVERT: C 228 GLU cc_start: 0.8020 (pp20) cc_final: 0.7575 (tp30) REVERT: c 284 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8373 (ptp) REVERT: c 348 GLN cc_start: 0.8864 (mm-40) cc_final: 0.8558 (mm110) REVERT: c 370 TRP cc_start: 0.7841 (m-10) cc_final: 0.7557 (m-10) outliers start: 37 outliers final: 25 residues processed: 168 average time/residue: 0.0811 time to fit residues: 20.1534 Evaluate side-chains 161 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 355 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain c residue 284 MET Chi-restraints excluded: chain c residue 345 ILE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain c residue 417 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 21 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 54 optimal weight: 0.0770 chunk 59 optimal weight: 3.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 335 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.075289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.060281 restraints weight = 37867.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.062786 restraints weight = 20449.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.064478 restraints weight = 14013.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.065667 restraints weight = 10895.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.066502 restraints weight = 9090.304| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11345 Z= 0.140 Angle : 0.790 13.195 15506 Z= 0.361 Chirality : 0.047 0.336 1918 Planarity : 0.003 0.045 1803 Dihedral : 8.553 50.884 2929 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.40 % Allowed : 15.02 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.24), residues: 1231 helix: 1.13 (0.28), residues: 374 sheet: 0.75 (0.34), residues: 219 loop : -1.04 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG c 314 TYR 0.019 0.001 TYR B 219 PHE 0.013 0.001 PHE c 399 TRP 0.016 0.001 TRP b 283 HIS 0.014 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00307 (11244) covalent geometry : angle 0.70964 (15226) SS BOND : bond 0.00282 ( 23) SS BOND : angle 0.85434 ( 46) hydrogen bonds : bond 0.03780 ( 447) hydrogen bonds : angle 4.80154 ( 1185) link_ALPHA1-2 : bond 0.00272 ( 2) link_ALPHA1-2 : angle 2.06306 ( 6) link_ALPHA1-3 : bond 0.01016 ( 7) link_ALPHA1-3 : angle 2.22451 ( 21) link_ALPHA1-6 : bond 0.00818 ( 5) link_ALPHA1-6 : angle 1.88679 ( 15) link_BETA1-4 : bond 0.00587 ( 31) link_BETA1-4 : angle 2.40643 ( 93) link_NAG-ASN : bond 0.00512 ( 33) link_NAG-ASN : angle 3.56731 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8783 (mpp) REVERT: A 96 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7163 (mtt) REVERT: A 134 MET cc_start: 0.9224 (tpp) cc_final: 0.7476 (tpp) REVERT: A 192 MET cc_start: 0.8988 (tpp) cc_final: 0.8781 (tpp) REVERT: a 284 MET cc_start: 0.8727 (mtp) cc_final: 0.8320 (mtp) REVERT: a 303 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7577 (tm-30) REVERT: a 311 ASP cc_start: 0.9300 (m-30) cc_final: 0.8931 (t70) REVERT: a 332 MET cc_start: 0.9119 (tmm) cc_final: 0.8640 (tmm) REVERT: a 347 ASP cc_start: 0.8202 (p0) cc_final: 0.7855 (p0) REVERT: a 408 ASP cc_start: 0.8356 (m-30) cc_final: 0.8009 (t70) REVERT: B 134 MET cc_start: 0.8596 (tpp) cc_final: 0.7414 (tpp) REVERT: B 192 MET cc_start: 0.8394 (tpt) cc_final: 0.7917 (tpp) REVERT: b 284 MET cc_start: 0.7709 (mtm) cc_final: 0.7445 (mtm) REVERT: b 311 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8512 (t0) REVERT: b 347 ASP cc_start: 0.8056 (p0) cc_final: 0.7654 (p0) REVERT: L 87 PHE cc_start: 0.8078 (m-80) cc_final: 0.7674 (m-10) REVERT: L 89 LEU cc_start: 0.8639 (tp) cc_final: 0.8318 (tp) REVERT: L 98 ASP cc_start: 0.8418 (m-30) cc_final: 0.8138 (m-30) REVERT: L 106 GLN cc_start: 0.8048 (pp30) cc_final: 0.7647 (pp30) REVERT: L 120 GLN cc_start: 0.8296 (pm20) cc_final: 0.8076 (pm20) REVERT: C 170 HIS cc_start: 0.6697 (t-90) cc_final: 0.6392 (t-170) REVERT: c 282 ARG cc_start: 0.8152 (tpt90) cc_final: 0.7813 (tpt90) REVERT: c 289 GLU cc_start: 0.7646 (mp0) cc_final: 0.7408 (mt-10) REVERT: c 361 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8457 (tt) REVERT: c 370 TRP cc_start: 0.7555 (m-10) cc_final: 0.7210 (m-10) outliers start: 27 outliers final: 12 residues processed: 170 average time/residue: 0.0863 time to fit residues: 21.5561 Evaluate side-chains 154 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 311 ASP Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain c residue 361 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 117 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 405 GLN ** c 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.072757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.057727 restraints weight = 38149.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.060085 restraints weight = 21018.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.061689 restraints weight = 14595.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.062798 restraints weight = 11457.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.063531 restraints weight = 9673.769| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.5476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11345 Z= 0.242 Angle : 0.867 13.196 15506 Z= 0.398 Chirality : 0.049 0.362 1918 Planarity : 0.004 0.047 1803 Dihedral : 8.411 53.484 2929 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.49 % Allowed : 15.38 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.24), residues: 1231 helix: 1.11 (0.28), residues: 376 sheet: 0.62 (0.35), residues: 219 loop : -1.14 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG c 314 TYR 0.018 0.002 TYR L 107 PHE 0.015 0.002 PHE L 118 TRP 0.017 0.002 TRP H 52 HIS 0.012 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00549 (11244) covalent geometry : angle 0.78854 (15226) SS BOND : bond 0.00433 ( 23) SS BOND : angle 1.06487 ( 46) hydrogen bonds : bond 0.04266 ( 447) hydrogen bonds : angle 4.93546 ( 1185) link_ALPHA1-2 : bond 0.00387 ( 2) link_ALPHA1-2 : angle 2.32307 ( 6) link_ALPHA1-3 : bond 0.00935 ( 7) link_ALPHA1-3 : angle 2.17708 ( 21) link_ALPHA1-6 : bond 0.00665 ( 5) link_ALPHA1-6 : angle 2.01804 ( 15) link_BETA1-4 : bond 0.00506 ( 31) link_BETA1-4 : angle 2.52520 ( 93) link_NAG-ASN : bond 0.00543 ( 33) link_NAG-ASN : angle 3.69831 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7642 (mtp) cc_final: 0.7298 (mtp) REVERT: A 192 MET cc_start: 0.9030 (tpp) cc_final: 0.8816 (tpp) REVERT: a 284 MET cc_start: 0.8725 (mtp) cc_final: 0.8278 (mtt) REVERT: a 303 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7542 (tm-30) REVERT: a 311 ASP cc_start: 0.9321 (m-30) cc_final: 0.9014 (t0) REVERT: a 347 ASP cc_start: 0.8287 (p0) cc_final: 0.7868 (p0) REVERT: a 408 ASP cc_start: 0.8394 (m-30) cc_final: 0.8021 (t70) REVERT: a 410 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7129 (mpp) REVERT: B 134 MET cc_start: 0.8630 (tpp) cc_final: 0.7416 (tpp) REVERT: B 192 MET cc_start: 0.8523 (tpt) cc_final: 0.8093 (tpp) REVERT: b 284 MET cc_start: 0.7909 (mtm) cc_final: 0.7604 (mtm) REVERT: b 311 ASP cc_start: 0.8879 (OUTLIER) cc_final: 0.8550 (t0) REVERT: b 312 MET cc_start: 0.8816 (mmm) cc_final: 0.8513 (mmp) REVERT: b 347 ASP cc_start: 0.8074 (p0) cc_final: 0.7789 (p0) REVERT: H 39 MET cc_start: 0.8812 (mmm) cc_final: 0.8426 (mmm) REVERT: H 96 ARG cc_start: 0.8340 (mmm-85) cc_final: 0.8110 (mmm-85) REVERT: L 87 PHE cc_start: 0.8231 (m-80) cc_final: 0.7913 (m-10) REVERT: L 89 LEU cc_start: 0.8623 (tp) cc_final: 0.8312 (tp) REVERT: L 98 ASP cc_start: 0.8407 (m-30) cc_final: 0.8109 (m-30) REVERT: L 106 GLN cc_start: 0.8374 (pp30) cc_final: 0.8060 (pp30) REVERT: c 282 ARG cc_start: 0.8224 (tpt90) cc_final: 0.7878 (tpt90) REVERT: c 370 TRP cc_start: 0.7890 (m-10) cc_final: 0.7587 (m-10) outliers start: 28 outliers final: 19 residues processed: 160 average time/residue: 0.0833 time to fit residues: 19.9791 Evaluate side-chains 148 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain a residue 410 MET Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 311 ASP Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 408 ASP Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain c residue 345 ILE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain c residue 417 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 113 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 37 optimal weight: 0.0050 chunk 89 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 348 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.074491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.060116 restraints weight = 36761.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.062531 restraints weight = 19924.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.064178 restraints weight = 13616.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.065321 restraints weight = 10546.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.066136 restraints weight = 8780.599| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.5637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11345 Z= 0.147 Angle : 0.788 13.055 15506 Z= 0.364 Chirality : 0.046 0.348 1918 Planarity : 0.003 0.045 1803 Dihedral : 7.994 59.376 2929 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.04 % Allowed : 16.18 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.24), residues: 1231 helix: 1.23 (0.28), residues: 366 sheet: 0.68 (0.35), residues: 219 loop : -0.96 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG c 314 TYR 0.017 0.001 TYR B 219 PHE 0.016 0.002 PHE c 262 TRP 0.015 0.001 TRP A 210 HIS 0.014 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00333 (11244) covalent geometry : angle 0.71319 (15226) SS BOND : bond 0.00268 ( 23) SS BOND : angle 0.78919 ( 46) hydrogen bonds : bond 0.03717 ( 447) hydrogen bonds : angle 4.84388 ( 1185) link_ALPHA1-2 : bond 0.00129 ( 2) link_ALPHA1-2 : angle 2.08643 ( 6) link_ALPHA1-3 : bond 0.00930 ( 7) link_ALPHA1-3 : angle 2.10138 ( 21) link_ALPHA1-6 : bond 0.00777 ( 5) link_ALPHA1-6 : angle 1.88977 ( 15) link_BETA1-4 : bond 0.00530 ( 31) link_BETA1-4 : angle 2.32971 ( 93) link_NAG-ASN : bond 0.00498 ( 33) link_NAG-ASN : angle 3.46535 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7640 (mtp) cc_final: 0.7305 (mtp) REVERT: A 134 MET cc_start: 0.9130 (tpp) cc_final: 0.7576 (tpp) REVERT: A 192 MET cc_start: 0.8999 (tpp) cc_final: 0.8785 (tpp) REVERT: a 284 MET cc_start: 0.8768 (mtp) cc_final: 0.8165 (mtp) REVERT: a 303 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7585 (tm-30) REVERT: a 311 ASP cc_start: 0.9257 (m-30) cc_final: 0.9013 (t0) REVERT: a 347 ASP cc_start: 0.8313 (p0) cc_final: 0.7995 (p0) REVERT: a 408 ASP cc_start: 0.8321 (m-30) cc_final: 0.7967 (t70) REVERT: B 134 MET cc_start: 0.8605 (tpp) cc_final: 0.7457 (tpp) REVERT: B 192 MET cc_start: 0.8457 (tpt) cc_final: 0.7951 (tpp) REVERT: b 284 MET cc_start: 0.7822 (mtm) cc_final: 0.7494 (mtm) REVERT: b 311 ASP cc_start: 0.8837 (OUTLIER) cc_final: 0.8509 (t0) REVERT: b 312 MET cc_start: 0.8624 (mmm) cc_final: 0.8367 (mmp) REVERT: b 347 ASP cc_start: 0.8130 (p0) cc_final: 0.7805 (p0) REVERT: H 39 MET cc_start: 0.8877 (mmm) cc_final: 0.8532 (mmm) REVERT: H 96 ARG cc_start: 0.8380 (mmm-85) cc_final: 0.8134 (mmm-85) REVERT: L 87 PHE cc_start: 0.8146 (m-80) cc_final: 0.7809 (m-10) REVERT: L 89 LEU cc_start: 0.8633 (tp) cc_final: 0.8302 (tp) REVERT: L 98 ASP cc_start: 0.8258 (m-30) cc_final: 0.8026 (m-30) REVERT: L 106 GLN cc_start: 0.8115 (pp30) cc_final: 0.7613 (pp30) REVERT: L 120 GLN cc_start: 0.8415 (pm20) cc_final: 0.8139 (pm20) REVERT: c 282 ARG cc_start: 0.8090 (tpt90) cc_final: 0.7740 (tpt90) REVERT: c 361 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8255 (tt) REVERT: c 370 TRP cc_start: 0.7700 (m-10) cc_final: 0.7224 (m-90) outliers start: 23 outliers final: 18 residues processed: 154 average time/residue: 0.0830 time to fit residues: 19.1534 Evaluate side-chains 150 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 311 ASP Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 411 ILE Chi-restraints excluded: chain c residue 417 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 36 optimal weight: 0.5980 chunk 76 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.074093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.059064 restraints weight = 37915.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.061496 restraints weight = 20747.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.063156 restraints weight = 14313.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.064288 restraints weight = 11179.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.065092 restraints weight = 9408.014| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.5764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11345 Z= 0.174 Angle : 0.802 13.026 15506 Z= 0.371 Chirality : 0.046 0.353 1918 Planarity : 0.004 0.046 1803 Dihedral : 7.820 56.294 2929 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.78 % Allowed : 16.98 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.24), residues: 1231 helix: 1.26 (0.28), residues: 367 sheet: 0.66 (0.37), residues: 195 loop : -0.96 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG c 314 TYR 0.017 0.001 TYR B 219 PHE 0.012 0.002 PHE a 309 TRP 0.021 0.002 TRP b 370 HIS 0.014 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00395 (11244) covalent geometry : angle 0.72890 (15226) SS BOND : bond 0.00331 ( 23) SS BOND : angle 0.86203 ( 46) hydrogen bonds : bond 0.03810 ( 447) hydrogen bonds : angle 4.85768 ( 1185) link_ALPHA1-2 : bond 0.00161 ( 2) link_ALPHA1-2 : angle 2.17803 ( 6) link_ALPHA1-3 : bond 0.00930 ( 7) link_ALPHA1-3 : angle 2.01369 ( 21) link_ALPHA1-6 : bond 0.00771 ( 5) link_ALPHA1-6 : angle 1.93252 ( 15) link_BETA1-4 : bond 0.00498 ( 31) link_BETA1-4 : angle 2.35481 ( 93) link_NAG-ASN : bond 0.00494 ( 33) link_NAG-ASN : angle 3.43388 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7689 (mtp) cc_final: 0.7398 (mtp) REVERT: A 134 MET cc_start: 0.9178 (tpp) cc_final: 0.7475 (tpp) REVERT: A 192 MET cc_start: 0.8943 (tpp) cc_final: 0.8723 (tpp) REVERT: a 262 PHE cc_start: 0.7218 (p90) cc_final: 0.6812 (p90) REVERT: a 284 MET cc_start: 0.8751 (mtp) cc_final: 0.8171 (mtp) REVERT: a 303 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7577 (tm-30) REVERT: a 311 ASP cc_start: 0.9264 (m-30) cc_final: 0.9014 (t0) REVERT: a 347 ASP cc_start: 0.8322 (p0) cc_final: 0.7968 (p0) REVERT: a 408 ASP cc_start: 0.8358 (m-30) cc_final: 0.8011 (t70) REVERT: B 134 MET cc_start: 0.8605 (tpp) cc_final: 0.7454 (tpp) REVERT: B 192 MET cc_start: 0.8562 (tpt) cc_final: 0.8120 (tpp) REVERT: b 284 MET cc_start: 0.7863 (mtm) cc_final: 0.7548 (mtm) REVERT: b 312 MET cc_start: 0.8727 (mmm) cc_final: 0.8479 (mmp) REVERT: H 39 MET cc_start: 0.8874 (mmm) cc_final: 0.8607 (mmm) REVERT: H 96 ARG cc_start: 0.8507 (mmm-85) cc_final: 0.8304 (mmm-85) REVERT: L 87 PHE cc_start: 0.8198 (m-80) cc_final: 0.7851 (m-10) REVERT: L 89 LEU cc_start: 0.8560 (tp) cc_final: 0.8245 (tp) REVERT: L 106 GLN cc_start: 0.8229 (pp30) cc_final: 0.7905 (pp30) REVERT: c 282 ARG cc_start: 0.8147 (tpt90) cc_final: 0.7780 (tpt90) REVERT: c 348 GLN cc_start: 0.8844 (mm-40) cc_final: 0.8498 (mm110) REVERT: c 361 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8292 (tt) REVERT: c 370 TRP cc_start: 0.7802 (m-10) cc_final: 0.7379 (m-10) outliers start: 20 outliers final: 15 residues processed: 146 average time/residue: 0.1023 time to fit residues: 22.1151 Evaluate side-chains 144 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain c residue 262 PHE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 417 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 33 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 84 optimal weight: 0.0770 chunk 120 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 319 ASN ** a 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.074456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.059490 restraints weight = 38097.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.061899 restraints weight = 21037.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.063557 restraints weight = 14577.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.064694 restraints weight = 11407.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.065503 restraints weight = 9571.582| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.5873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11345 Z= 0.161 Angle : 0.795 13.050 15506 Z= 0.371 Chirality : 0.046 0.351 1918 Planarity : 0.004 0.045 1803 Dihedral : 7.610 56.101 2929 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.12 % Favored : 94.80 % Rotamer: Outliers : 1.69 % Allowed : 17.42 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.24), residues: 1231 helix: 1.21 (0.28), residues: 366 sheet: 0.70 (0.37), residues: 194 loop : -0.95 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG c 314 TYR 0.017 0.001 TYR B 219 PHE 0.012 0.001 PHE a 309 TRP 0.020 0.002 TRP b 370 HIS 0.015 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00367 (11244) covalent geometry : angle 0.72298 (15226) SS BOND : bond 0.00310 ( 23) SS BOND : angle 1.05637 ( 46) hydrogen bonds : bond 0.03748 ( 447) hydrogen bonds : angle 4.91028 ( 1185) link_ALPHA1-2 : bond 0.00137 ( 2) link_ALPHA1-2 : angle 2.12221 ( 6) link_ALPHA1-3 : bond 0.00913 ( 7) link_ALPHA1-3 : angle 1.96974 ( 21) link_ALPHA1-6 : bond 0.00755 ( 5) link_ALPHA1-6 : angle 1.84592 ( 15) link_BETA1-4 : bond 0.00509 ( 31) link_BETA1-4 : angle 2.30559 ( 93) link_NAG-ASN : bond 0.00477 ( 33) link_NAG-ASN : angle 3.38061 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7758 (mtp) cc_final: 0.7421 (mtp) REVERT: A 134 MET cc_start: 0.9168 (tpp) cc_final: 0.7466 (tpp) REVERT: A 192 MET cc_start: 0.8941 (tpp) cc_final: 0.8731 (tpp) REVERT: a 262 PHE cc_start: 0.7220 (p90) cc_final: 0.6804 (p90) REVERT: a 284 MET cc_start: 0.8776 (mtp) cc_final: 0.8186 (mtp) REVERT: a 311 ASP cc_start: 0.9255 (m-30) cc_final: 0.9009 (t0) REVERT: a 347 ASP cc_start: 0.8302 (p0) cc_final: 0.7929 (p0) REVERT: a 408 ASP cc_start: 0.8352 (m-30) cc_final: 0.8008 (t70) REVERT: B 134 MET cc_start: 0.8624 (tpp) cc_final: 0.7481 (tpp) REVERT: B 192 MET cc_start: 0.8538 (tpt) cc_final: 0.8073 (tpp) REVERT: b 284 MET cc_start: 0.7856 (mtm) cc_final: 0.7530 (mtm) REVERT: b 312 MET cc_start: 0.8671 (mmm) cc_final: 0.8402 (mmp) REVERT: H 39 MET cc_start: 0.8905 (mmm) cc_final: 0.8631 (mmm) REVERT: H 48 LYS cc_start: 0.8221 (tptt) cc_final: 0.7997 (tptt) REVERT: L 87 PHE cc_start: 0.8157 (m-80) cc_final: 0.7935 (m-10) REVERT: L 89 LEU cc_start: 0.8549 (tp) cc_final: 0.8227 (tp) REVERT: L 106 GLN cc_start: 0.8196 (pp30) cc_final: 0.7868 (pp30) REVERT: L 120 GLN cc_start: 0.8387 (pm20) cc_final: 0.8067 (pm20) REVERT: c 282 ARG cc_start: 0.8121 (tpt90) cc_final: 0.7754 (tpt90) REVERT: c 348 GLN cc_start: 0.8844 (mm-40) cc_final: 0.8453 (mm110) REVERT: c 361 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8285 (tt) REVERT: c 370 TRP cc_start: 0.7768 (m-10) cc_final: 0.7352 (m-10) REVERT: c 417 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8895 (ptmm) outliers start: 19 outliers final: 15 residues processed: 148 average time/residue: 0.1012 time to fit residues: 22.1537 Evaluate side-chains 146 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 227 TRP Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain c residue 262 PHE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 417 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 34 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 37 optimal weight: 0.0970 chunk 75 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 100 optimal weight: 20.0000 chunk 114 optimal weight: 2.9990 overall best weight: 1.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** L 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.074956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.059997 restraints weight = 38071.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.062455 restraints weight = 20781.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.064124 restraints weight = 14311.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.065286 restraints weight = 11158.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.066106 restraints weight = 9335.432| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.5989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11345 Z= 0.145 Angle : 0.783 12.975 15506 Z= 0.363 Chirality : 0.045 0.349 1918 Planarity : 0.004 0.045 1803 Dihedral : 7.219 53.976 2929 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.63 % Favored : 95.29 % Rotamer: Outliers : 1.60 % Allowed : 17.69 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.24), residues: 1231 helix: 1.29 (0.28), residues: 366 sheet: 0.78 (0.38), residues: 194 loop : -0.93 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG c 314 TYR 0.016 0.001 TYR B 219 PHE 0.011 0.001 PHE a 309 TRP 0.028 0.002 TRP C 227 HIS 0.016 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00329 (11244) covalent geometry : angle 0.71433 (15226) SS BOND : bond 0.00293 ( 23) SS BOND : angle 0.85997 ( 46) hydrogen bonds : bond 0.03589 ( 447) hydrogen bonds : angle 4.83142 ( 1185) link_ALPHA1-2 : bond 0.00085 ( 2) link_ALPHA1-2 : angle 2.08909 ( 6) link_ALPHA1-3 : bond 0.00920 ( 7) link_ALPHA1-3 : angle 1.93110 ( 21) link_ALPHA1-6 : bond 0.00858 ( 5) link_ALPHA1-6 : angle 1.75682 ( 15) link_BETA1-4 : bond 0.00504 ( 31) link_BETA1-4 : angle 2.26241 ( 93) link_NAG-ASN : bond 0.00471 ( 33) link_NAG-ASN : angle 3.30548 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1505.37 seconds wall clock time: 27 minutes 11.12 seconds (1631.12 seconds total)