Starting phenix.real_space_refine on Wed Sep 17 16:51:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cj8_45625/09_2025/9cj8_45625.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cj8_45625/09_2025/9cj8_45625.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cj8_45625/09_2025/9cj8_45625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cj8_45625/09_2025/9cj8_45625.map" model { file = "/net/cci-nas-00/data/ceres_data/9cj8_45625/09_2025/9cj8_45625.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cj8_45625/09_2025/9cj8_45625.cif" } resolution = 3.74 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= -0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 6085 2.51 5 N 1614 2.21 5 O 1961 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9750 Number of models: 1 Model: "" Number of chains: 22 Chain: "H" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 585 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'TRANS': 116} Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 351 Unresolved non-hydrogen dihedrals: 117 Planarities with less than four sites: {'UNK:plan-1': 117} Unresolved non-hydrogen planarities: 117 Chain: "L" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 520 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'TRANS': 103} Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 312 Unresolved non-hydrogen dihedrals: 104 Planarities with less than four sites: {'UNK:plan-1': 104} Unresolved non-hydrogen planarities: 104 Chain: "C" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1481 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 180} Chain breaks: 2 Chain: "A" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1494 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 182} Chain breaks: 2 Chain: "B" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1520 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "a" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1167 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain breaks: 2 Chain: "b" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1167 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain breaks: 2 Chain: "c" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1167 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain breaks: 2 Chain: "D" 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, '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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" 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: "K" 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: "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: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} 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: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} 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: "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: "a" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "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 Time building chain proxies: 2.35, per 1000 atoms: 0.24 Number of scatterers: 9750 At special positions: 0 Unit cell: (117.45, 100.05, 92.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 1961 8.00 N 1614 7.00 C 6085 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.05 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.03 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.03 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=2.03 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=2.03 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 Atom "HETATM 9622 O5 NAG B 304 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Links applied ALPHA1-3 " BMA M 3 " - " MAN M 4 " ALPHA1-6 " BMA G 3 " - " MAN G 4 " " BMA M 3 " - " MAN M 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " BETA1-6 " NAG G 1 " - " FUC G 5 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG I 1 " - " FUC I 3 " NAG-ASN " NAG A 301 " - " ASN A 89 " " NAG A 302 " - " ASN A 99 " " NAG A 303 " - " ASN A 109 " " NAG A 304 " - " ASN A 119 " " NAG A 305 " - " ASN A 167 " " NAG A 306 " - " ASN A 224 " " NAG B 301 " - " ASN B 167 " " NAG B 302 " - " ASN B 89 " " NAG B 303 " - " ASN B 99 " " NAG B 304 " - " ASN B 224 " " NAG C 301 " - " ASN C 99 " " NAG C 302 " - " ASN C 109 " " NAG C 303 " - " ASN C 89 " " NAG C 304 " - " ASN C 167 " " NAG C 305 " - " ASN C 79 " " NAG C 306 " - " ASN C 224 " " NAG D 1 " - " ASN C 119 " " NAG E 1 " - " ASN A 79 " " NAG F 1 " - " ASN B 79 " " NAG G 1 " - " ASN B 109 " " NAG I 1 " - " ASN B 119 " " NAG J 1 " - " ASN a 373 " " NAG K 1 " - " ASN b 390 " " NAG M 1 " - " ASN b 365 " " NAG a 701 " - " ASN a 390 " " NAG a 702 " - " ASN a 395 " " NAG a 703 " - " ASN a 365 " " NAG b 701 " - " ASN b 373 " " NAG b 702 " - " ASN b 395 " " NAG c 701 " - " ASN c 390 " " NAG c 702 " - " ASN c 373 " " NAG c 703 " - " ASN c 365 " " NAG c 704 " - " ASN c 395 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 332.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2322 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 17 sheets defined 38.8% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'C' and resid 75 through 79 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 182 through 195 removed outlier: 3.783A pdb=" N GLY C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 246 removed outlier: 3.740A pdb=" N SER C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 80 removed outlier: 4.505A pdb=" N MET A 80 " --> pdb=" O THR A 77 " (cutoff:3.500A) 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 192 removed outlier: 3.578A pdb=" N GLY A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 245 Processing helix chain 'A' and resid 246 through 250 removed outlier: 4.357A pdb=" N THR A 249 " --> pdb=" O SER A 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.774A pdb=" N THR B 77 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN B 79 " --> pdb=" O GLU B 76 " (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 157 through 161 Processing helix chain 'B' and resid 182 through 195 removed outlier: 3.736A pdb=" N GLY B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 245 Processing helix chain 'a' and resid 294 through 299 Processing helix chain 'a' and resid 300 through 303 Processing helix chain 'a' and resid 308 through 326 Processing helix chain 'a' and resid 334 through 345 removed outlier: 5.988A pdb=" N ASN a 342 " --> pdb=" O ASN a 338 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ALA a 343 " --> pdb=" O LYS a 339 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU a 344 " --> pdb=" O ALA a 340 " (cutoff:3.500A) Processing helix chain 'a' and resid 346 through 359 removed outlier: 3.789A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 399 through 414 Processing helix chain 'b' and resid 281 through 285 Processing helix chain 'b' and resid 294 through 299 Processing helix chain 'b' and resid 299 through 304 removed outlier: 4.374A pdb=" N GLU b 303 " --> pdb=" O ALA b 299 " (cutoff:3.500A) Processing helix chain 'b' and resid 307 through 324 removed outlier: 4.192A pdb=" N ASP b 311 " --> pdb=" O GLU b 307 " (cutoff:3.500A) Processing helix chain 'b' and resid 334 through 340 removed outlier: 3.879A pdb=" N ALA b 340 " --> pdb=" O LEU b 336 " (cutoff:3.500A) Processing helix chain 'b' and resid 340 through 345 Processing helix chain 'b' and resid 346 through 360 removed outlier: 3.871A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 399 through 411 Processing helix chain 'c' and resid 294 through 300 removed outlier: 4.393A pdb=" N LYS c 300 " --> pdb=" O THR c 296 " (cutoff:3.500A) Processing helix chain 'c' and resid 301 through 303 No H-bonds generated for 'chain 'c' and resid 301 through 303' Processing helix chain 'c' and resid 307 through 325 removed outlier: 3.789A pdb=" N ASP c 311 " --> pdb=" O GLU c 307 " (cutoff:3.500A) Processing helix chain 'c' and resid 334 through 345 removed outlier: 5.768A pdb=" N ASN c 342 " --> pdb=" O ASN c 338 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ALA c 343 " --> pdb=" O LYS c 339 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 359 removed outlier: 4.412A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 399 through 414 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 57 through 58 removed outlier: 6.826A pdb=" N UNK H 36 " --> pdb=" O UNK H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 66 through 70 Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA5, first strand: chain 'L' and resid 44 through 48 removed outlier: 5.382A pdb=" N UNK L 46 " --> pdb=" O UNK L 37 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N UNK L 37 " --> pdb=" O UNK L 46 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N UNK L 38 " --> pdb=" O UNK L 85 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 62 through 65 removed outlier: 3.595A pdb=" N UNK L 74 " --> pdb=" O UNK L 63 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 61 through 63 removed outlier: 6.957A pdb=" N TYR C 66 " --> pdb=" O TYR C 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 69 through 72 Processing sheet with id=AA9, first strand: chain 'C' and resid 84 through 86 removed outlier: 4.084A pdb=" N THR C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 84 through 86 removed outlier: 4.084A pdb=" N THR C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 157 through 158 removed outlier: 3.828A pdb=" N ASN C 158 " --> pdb=" O LYS C 161 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 66 through 68 Processing sheet with id=AB4, first strand: chain 'A' and resid 71 through 72 removed outlier: 4.272A pdb=" N ASN a 365 " --> pdb=" O TRP a 386 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N TRP a 386 " --> pdb=" O ASN a 365 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N SER a 367 " --> pdb=" O LYS a 384 " (cutoff:3.500A) removed outlier: 10.496A pdb=" N LYS a 384 " --> pdb=" O SER a 367 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 84 through 87 Processing sheet with id=AB6, first strand: chain 'B' and resid 67 through 72 Processing sheet with id=AB7, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AB8, first strand: chain 'c' and resid 388 through 389 346 hydrogen bonds defined for protein. 906 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: 1.41 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3040 1.34 - 1.47: 2615 1.47 - 1.60: 4121 1.60 - 1.73: 0 1.73 - 1.86: 138 Bond restraints: 9914 Sorted by residual: bond pdb=" N ILE c 286 " pdb=" CA ILE c 286 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.14e-02 7.69e+03 7.60e+00 bond pdb=" N PHE c 318 " pdb=" CA PHE c 318 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.25e-02 6.40e+03 4.98e+00 bond pdb=" N ALA c 288 " pdb=" CA ALA c 288 " ideal model delta sigma weight residual 1.455 1.481 -0.026 1.25e-02 6.40e+03 4.26e+00 bond pdb=" N GLU c 287 " pdb=" CA GLU c 287 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.52e-02 4.33e+03 4.16e+00 bond pdb=" C PHE B 117 " pdb=" N CYS B 118 " ideal model delta sigma weight residual 1.324 1.369 -0.044 2.56e-02 1.53e+03 3.01e+00 ... (remaining 9909 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 12482 1.90 - 3.80: 782 3.80 - 5.71: 143 5.71 - 7.61: 33 7.61 - 9.51: 13 Bond angle restraints: 13453 Sorted by residual: angle pdb=" CA MET a 410 " pdb=" CB MET a 410 " pdb=" CG MET a 410 " ideal model delta sigma weight residual 114.10 121.84 -7.74 2.00e+00 2.50e-01 1.50e+01 angle pdb=" C UNK L 55 " pdb=" N UNK L 56 " pdb=" CA UNK L 56 " ideal model delta sigma weight residual 121.70 128.64 -6.94 1.80e+00 3.09e-01 1.49e+01 angle pdb=" C UNK H 27 " pdb=" N UNK H 28 " pdb=" CA UNK H 28 " ideal model delta sigma weight residual 121.70 128.60 -6.90 1.80e+00 3.09e-01 1.47e+01 angle pdb=" N SER C 246 " pdb=" CA SER C 246 " pdb=" C SER C 246 " ideal model delta sigma weight residual 110.55 105.41 5.14 1.35e+00 5.49e-01 1.45e+01 angle pdb=" C UNK H 25 " pdb=" N UNK H 26 " pdb=" CA UNK H 26 " ideal model delta sigma weight residual 121.70 128.24 -6.54 1.80e+00 3.09e-01 1.32e+01 ... (remaining 13448 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.30: 6106 22.30 - 44.59: 353 44.59 - 66.89: 50 66.89 - 89.18: 31 89.18 - 111.47: 9 Dihedral angle restraints: 6549 sinusoidal: 2985 harmonic: 3564 Sorted by residual: dihedral pdb=" CB CYS c 364 " pdb=" SG CYS c 364 " pdb=" SG CYS c 385 " pdb=" CB CYS c 385 " ideal model delta sinusoidal sigma weight residual 93.00 -179.50 -87.50 1 1.00e+01 1.00e-02 9.18e+01 dihedral pdb=" CB CYS a 364 " pdb=" SG CYS a 364 " pdb=" SG CYS a 385 " pdb=" CB CYS a 385 " ideal model delta sinusoidal sigma weight residual -86.00 -170.18 84.18 1 1.00e+01 1.00e-02 8.63e+01 dihedral pdb=" CB CYS A 180 " pdb=" SG CYS A 180 " pdb=" SG CYS A 212 " pdb=" CB CYS A 212 " ideal model delta sinusoidal sigma weight residual 93.00 173.60 -80.60 1 1.00e+01 1.00e-02 8.03e+01 ... (remaining 6546 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.166: 1652 0.166 - 0.333: 22 0.333 - 0.499: 5 0.499 - 0.665: 1 0.665 - 0.832: 2 Chirality restraints: 1682 Sorted by residual: chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.57 -0.83 2.00e-02 2.50e+03 1.73e+03 chirality pdb=" C1 MAN M 4 " pdb=" O3 BMA M 3 " pdb=" C2 MAN M 4 " pdb=" O5 MAN M 4 " both_signs ideal model delta sigma weight residual False 2.40 1.92 0.48 2.00e-02 2.50e+03 5.78e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-02 2.50e+03 2.59e+02 ... (remaining 1679 not shown) Planarity restraints: 1680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " -0.342 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG M 2 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " -0.153 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " 0.522 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " -0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 302 " -0.320 2.00e-02 2.50e+03 2.71e-01 9.19e+02 pdb=" C7 NAG B 302 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG B 302 " -0.184 2.00e-02 2.50e+03 pdb=" N2 NAG B 302 " 0.471 2.00e-02 2.50e+03 pdb=" O7 NAG B 302 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 304 " 0.293 2.00e-02 2.50e+03 2.42e-01 7.30e+02 pdb=" C7 NAG B 304 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG B 304 " 0.192 2.00e-02 2.50e+03 pdb=" N2 NAG B 304 " -0.404 2.00e-02 2.50e+03 pdb=" O7 NAG B 304 " -0.001 2.00e-02 2.50e+03 ... (remaining 1677 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 5 2.13 - 2.82: 2845 2.82 - 3.51: 13473 3.51 - 4.21: 21407 4.21 - 4.90: 37026 Nonbonded interactions: 74756 Sorted by model distance: nonbonded pdb=" O4 NAG G 1 " pdb=" C1 NAG G 2 " model vdw 1.437 3.470 nonbonded pdb=" O ALA B 195 " pdb=" OG SER B 199 " model vdw 2.071 3.040 nonbonded pdb=" OE2 GLU A 72 " pdb=" OG SER a 367 " model vdw 2.105 3.040 nonbonded pdb=" C4 NAG G 1 " pdb=" O7 NAG G 2 " model vdw 2.107 2.776 nonbonded pdb=" O6 NAG G 1 " pdb=" C7 NAG G 2 " model vdw 2.123 2.616 ... (remaining 74751 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 60 through 200 or resid 207 through 304)) selection = (chain 'B' and (resid 60 through 200 or resid 207 through 304)) selection = (chain 'C' and resid 60 through 304) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'J' selection = chain 'K' } ncs_group { reference = (chain 'G' and resid 1 through 4) selection = (chain 'M' and resid 1 through 4) } ncs_group { reference = (chain 'H' and resid 14 through 109) selection = chain 'L' } ncs_group { reference = (chain 'a' and resid 260 through 702) selection = chain 'b' selection = (chain 'c' and resid 260 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=0.94 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: 12.480 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.630 Find NCS groups from input model: 0.240 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: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 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 : 0.006 0.083 9983 Z= 0.278 Angle : 1.186 23.758 13636 Z= 0.554 Chirality : 0.062 0.832 1682 Planarity : 0.013 0.294 1647 Dihedral : 14.814 111.475 4164 Min Nonbonded Distance : 1.437 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.31 (0.27), residues: 955 helix: -0.29 (0.28), residues: 322 sheet: -1.55 (0.48), residues: 113 loop : -1.02 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG b 282 TYR 0.032 0.002 TYR C 94 PHE 0.023 0.003 PHE A 233 TRP 0.030 0.002 TRP B 227 HIS 0.028 0.002 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00589 ( 9914) covalent geometry : angle 1.08480 (13453) SS BOND : bond 0.00395 ( 21) SS BOND : angle 3.07078 ( 42) hydrogen bonds : bond 0.17807 ( 337) hydrogen bonds : angle 7.62300 ( 906) Misc. bond : bond 0.08259 ( 1) link_ALPHA1-3 : bond 0.00220 ( 1) link_ALPHA1-3 : angle 4.14251 ( 3) link_ALPHA1-6 : bond 0.00300 ( 2) link_ALPHA1-6 : angle 1.14884 ( 6) link_BETA1-4 : bond 0.00879 ( 9) link_BETA1-4 : angle 4.36079 ( 27) link_BETA1-6 : bond 0.00186 ( 2) link_BETA1-6 : angle 1.17755 ( 6) link_NAG-ASN : bond 0.00845 ( 33) link_NAG-ASN : angle 4.90568 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 126 LYS cc_start: 0.8911 (mttp) cc_final: 0.8381 (mttp) REVERT: C 230 HIS cc_start: 0.5729 (m90) cc_final: 0.5521 (m-70) REVERT: C 256 ARG cc_start: 0.6290 (tpt170) cc_final: 0.4599 (mmt180) REVERT: A 234 SER cc_start: 0.8585 (t) cc_final: 0.8269 (p) REVERT: A 256 ARG cc_start: 0.8219 (mtm-85) cc_final: 0.7861 (mmt180) REVERT: B 69 GLN cc_start: 0.8284 (mt0) cc_final: 0.7908 (mt0) REVERT: B 209 ASN cc_start: 0.8584 (t0) cc_final: 0.8372 (t0) REVERT: B 235 ARG cc_start: 0.8389 (mtm-85) cc_final: 0.6537 (mtt-85) REVERT: B 256 ARG cc_start: 0.7222 (tpt-90) cc_final: 0.5428 (mtm180) REVERT: a 282 ARG cc_start: 0.8478 (mtp-110) cc_final: 0.8267 (mtp-110) REVERT: a 321 GLN cc_start: 0.8771 (mm110) cc_final: 0.8549 (mm-40) REVERT: a 333 SER cc_start: 0.8665 (t) cc_final: 0.8295 (m) REVERT: b 355 LEU cc_start: 0.9282 (mp) cc_final: 0.8985 (mp) REVERT: b 410 MET cc_start: 0.8220 (tpp) cc_final: 0.8017 (tpt) REVERT: c 317 ASP cc_start: 0.7921 (t70) cc_final: 0.7489 (t70) REVERT: c 394 LEU cc_start: 0.8386 (tp) cc_final: 0.8183 (tp) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.1063 time to fit residues: 48.9991 Evaluate side-chains 283 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS A 189 GLN B 189 GLN a 302 ASN ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 342 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.140455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.121845 restraints weight = 21721.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.125036 restraints weight = 11669.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.127175 restraints weight = 7697.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.128616 restraints weight = 5771.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.129444 restraints weight = 4692.231| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3737 r_free = 0.3737 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3736 r_free = 0.3736 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9983 Z= 0.168 Angle : 0.883 15.221 13636 Z= 0.388 Chirality : 0.049 0.463 1682 Planarity : 0.004 0.034 1647 Dihedral : 10.357 80.715 2268 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.77 % Allowed : 14.86 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.83 (0.27), residues: 955 helix: 0.36 (0.29), residues: 323 sheet: -1.35 (0.48), residues: 116 loop : -0.91 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG b 282 TYR 0.025 0.002 TYR B 129 PHE 0.021 0.002 PHE B 191 TRP 0.021 0.002 TRP b 370 HIS 0.008 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 9914) covalent geometry : angle 0.79541 (13453) SS BOND : bond 0.00293 ( 21) SS BOND : angle 1.22584 ( 42) hydrogen bonds : bond 0.04386 ( 337) hydrogen bonds : angle 5.69812 ( 906) Misc. bond : bond 0.00271 ( 1) link_ALPHA1-3 : bond 0.03372 ( 1) link_ALPHA1-3 : angle 3.72304 ( 3) link_ALPHA1-6 : bond 0.01128 ( 2) link_ALPHA1-6 : angle 2.17372 ( 6) link_BETA1-4 : bond 0.00830 ( 9) link_BETA1-4 : angle 3.12555 ( 27) link_BETA1-6 : bond 0.00281 ( 2) link_BETA1-6 : angle 1.37595 ( 6) link_NAG-ASN : bond 0.00611 ( 33) link_NAG-ASN : angle 4.14766 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 300 time to evaluate : 0.360 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: C 162 ILE cc_start: 0.8307 (mm) cc_final: 0.8091 (mt) REVERT: C 194 MET cc_start: 0.8896 (tpp) cc_final: 0.7682 (tmm) REVERT: C 256 ARG cc_start: 0.6635 (tpt170) cc_final: 0.4922 (mmt180) REVERT: A 96 MET cc_start: 0.7056 (mmt) cc_final: 0.6759 (mmt) REVERT: B 78 LEU cc_start: 0.8187 (mm) cc_final: 0.7971 (mm) REVERT: B 235 ARG cc_start: 0.8430 (mtm-85) cc_final: 0.6525 (mtt180) REVERT: B 256 ARG cc_start: 0.7146 (tpt-90) cc_final: 0.5818 (mtm180) REVERT: a 286 ILE cc_start: 0.7344 (tt) cc_final: 0.7041 (tt) REVERT: a 308 GLU cc_start: 0.8773 (mp0) cc_final: 0.8550 (mp0) REVERT: a 333 SER cc_start: 0.8628 (t) cc_final: 0.8118 (m) REVERT: c 317 ASP cc_start: 0.7824 (t70) cc_final: 0.7522 (t70) outliers start: 16 outliers final: 13 residues processed: 306 average time/residue: 0.1062 time to fit residues: 44.7002 Evaluate side-chains 295 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 282 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain a residue 400 SER Chi-restraints excluded: chain b residue 318 PHE Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain b residue 367 SER Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain c residue 318 PHE Chi-restraints excluded: chain c residue 388 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 83 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 59 optimal weight: 0.0970 chunk 99 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 ASN A 185 ASN a 302 ASN ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 342 ASN c 354 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.136776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.118006 restraints weight = 21958.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.121232 restraints weight = 11780.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.123383 restraints weight = 7785.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.124790 restraints weight = 5833.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.125637 restraints weight = 4765.318| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3700 r_free = 0.3700 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3700 r_free = 0.3700 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9983 Z= 0.180 Angle : 0.832 15.418 13636 Z= 0.370 Chirality : 0.048 0.471 1682 Planarity : 0.003 0.036 1647 Dihedral : 9.599 75.602 2268 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.88 % Allowed : 17.18 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.78 (0.27), residues: 955 helix: 0.70 (0.30), residues: 323 sheet: -1.63 (0.43), residues: 143 loop : -0.95 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG a 314 TYR 0.019 0.002 TYR C 66 PHE 0.015 0.002 PHE a 262 TRP 0.021 0.002 TRP b 370 HIS 0.008 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 9914) covalent geometry : angle 0.74751 (13453) SS BOND : bond 0.00908 ( 21) SS BOND : angle 1.17723 ( 42) hydrogen bonds : bond 0.03914 ( 337) hydrogen bonds : angle 5.30923 ( 906) Misc. bond : bond 0.00176 ( 1) link_ALPHA1-3 : bond 0.02585 ( 1) link_ALPHA1-3 : angle 4.01813 ( 3) link_ALPHA1-6 : bond 0.00827 ( 2) link_ALPHA1-6 : angle 1.59653 ( 6) link_BETA1-4 : bond 0.00373 ( 9) link_BETA1-4 : angle 2.81916 ( 27) link_BETA1-6 : bond 0.00557 ( 2) link_BETA1-6 : angle 1.16719 ( 6) link_NAG-ASN : bond 0.00531 ( 33) link_NAG-ASN : angle 3.98715 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 298 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 194 MET cc_start: 0.8972 (tpp) cc_final: 0.7867 (tmm) REVERT: C 256 ARG cc_start: 0.6567 (tpt170) cc_final: 0.4788 (mmt180) REVERT: B 63 LYS cc_start: 0.7086 (mmtm) cc_final: 0.6800 (mmtt) REVERT: B 76 GLU cc_start: 0.7913 (tp30) cc_final: 0.7697 (tp30) REVERT: B 78 LEU cc_start: 0.8493 (mm) cc_final: 0.8234 (mm) REVERT: B 212 CYS cc_start: 0.5910 (m) cc_final: 0.5665 (m) REVERT: B 235 ARG cc_start: 0.8377 (mtm-85) cc_final: 0.6691 (mtt180) REVERT: B 256 ARG cc_start: 0.7220 (tpt-90) cc_final: 0.5838 (mtm180) REVERT: a 286 ILE cc_start: 0.7404 (tt) cc_final: 0.7132 (tt) REVERT: a 308 GLU cc_start: 0.8800 (mp0) cc_final: 0.8521 (mp0) REVERT: a 333 SER cc_start: 0.8600 (t) cc_final: 0.8100 (m) REVERT: a 410 MET cc_start: 0.8404 (tpp) cc_final: 0.8084 (tpp) REVERT: b 404 GLU cc_start: 0.8207 (tp30) cc_final: 0.7843 (tp30) REVERT: c 317 ASP cc_start: 0.7875 (t70) cc_final: 0.7635 (t70) outliers start: 26 outliers final: 20 residues processed: 305 average time/residue: 0.1077 time to fit residues: 45.2503 Evaluate side-chains 299 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 279 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain b residue 281 THR Chi-restraints excluded: chain b residue 318 PHE Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain c residue 281 THR Chi-restraints excluded: chain c residue 296 THR Chi-restraints excluded: chain c residue 318 PHE Chi-restraints excluded: chain c residue 352 LYS Chi-restraints excluded: chain c residue 376 THR Chi-restraints excluded: chain c residue 388 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 23 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 302 ASN ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 342 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.126275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.107623 restraints weight = 21513.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.110342 restraints weight = 12384.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.112291 restraints weight = 8578.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.113571 restraints weight = 6584.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.114338 restraints weight = 5463.380| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 9983 Z= 0.275 Angle : 0.938 16.027 13636 Z= 0.424 Chirality : 0.052 0.506 1682 Planarity : 0.004 0.039 1647 Dihedral : 9.786 63.916 2268 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.10 % Allowed : 18.85 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.98 (0.27), residues: 955 helix: 0.53 (0.29), residues: 326 sheet: -1.70 (0.43), residues: 145 loop : -1.08 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG b 379 TYR 0.022 0.002 TYR b 363 PHE 0.014 0.003 PHE A 157 TRP 0.025 0.002 TRP b 370 HIS 0.009 0.002 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00630 ( 9914) covalent geometry : angle 0.86182 (13453) SS BOND : bond 0.00441 ( 21) SS BOND : angle 1.46985 ( 42) hydrogen bonds : bond 0.04110 ( 337) hydrogen bonds : angle 5.48626 ( 906) Misc. bond : bond 0.00263 ( 1) link_ALPHA1-3 : bond 0.02453 ( 1) link_ALPHA1-3 : angle 4.02405 ( 3) link_ALPHA1-6 : bond 0.00567 ( 2) link_ALPHA1-6 : angle 1.54433 ( 6) link_BETA1-4 : bond 0.00382 ( 9) link_BETA1-4 : angle 2.71910 ( 27) link_BETA1-6 : bond 0.00384 ( 2) link_BETA1-6 : angle 1.32737 ( 6) link_NAG-ASN : bond 0.00599 ( 33) link_NAG-ASN : angle 4.07185 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 291 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 146 ASN cc_start: 0.8410 (m-40) cc_final: 0.8196 (m110) REVERT: C 194 MET cc_start: 0.9056 (tpp) cc_final: 0.8044 (tmm) REVERT: C 223 GLN cc_start: 0.8753 (pm20) cc_final: 0.8461 (pm20) REVERT: C 256 ARG cc_start: 0.6603 (tpt170) cc_final: 0.4706 (mmt180) REVERT: A 153 MET cc_start: 0.8589 (tpt) cc_final: 0.8245 (tpt) REVERT: A 218 GLN cc_start: 0.7764 (mp10) cc_final: 0.7481 (mp10) REVERT: B 235 ARG cc_start: 0.8576 (mtm-85) cc_final: 0.7094 (mtt180) REVERT: B 256 ARG cc_start: 0.7378 (tpt-90) cc_final: 0.5475 (mtp85) REVERT: a 286 ILE cc_start: 0.7712 (tt) cc_final: 0.7455 (tt) REVERT: a 308 GLU cc_start: 0.8880 (mp0) cc_final: 0.8670 (mp0) REVERT: a 333 SER cc_start: 0.8664 (t) cc_final: 0.8218 (m) REVERT: a 371 TYR cc_start: 0.7087 (p90) cc_final: 0.6644 (p90) REVERT: b 393 TYR cc_start: 0.9093 (m-80) cc_final: 0.8791 (m-10) REVERT: b 404 GLU cc_start: 0.8302 (tp30) cc_final: 0.7942 (tp30) REVERT: c 261 THR cc_start: 0.8908 (t) cc_final: 0.8656 (p) REVERT: c 308 GLU cc_start: 0.7918 (mp0) cc_final: 0.7414 (pm20) REVERT: c 359 MET cc_start: 0.8462 (mtt) cc_final: 0.8161 (mtt) outliers start: 37 outliers final: 28 residues processed: 303 average time/residue: 0.1089 time to fit residues: 45.2886 Evaluate side-chains 303 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 275 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain a residue 280 LEU Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 403 ILE Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain b residue 281 THR Chi-restraints excluded: chain b residue 318 PHE Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 367 SER Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain c residue 265 THR Chi-restraints excluded: chain c residue 281 THR Chi-restraints excluded: chain c residue 296 THR Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 318 PHE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 376 THR Chi-restraints excluded: chain c residue 388 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 41 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 HIS B 69 GLN ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.134225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.115877 restraints weight = 21488.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.118920 restraints weight = 11738.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.121048 restraints weight = 7881.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.122323 restraints weight = 5925.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.123268 restraints weight = 4893.633| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3630 r_free = 0.3630 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9983 Z= 0.170 Angle : 0.833 16.386 13636 Z= 0.378 Chirality : 0.048 0.476 1682 Planarity : 0.003 0.038 1647 Dihedral : 9.446 59.574 2268 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.33 % Allowed : 22.84 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.81 (0.27), residues: 955 helix: 0.67 (0.29), residues: 330 sheet: -1.69 (0.42), residues: 144 loop : -0.96 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG c 314 TYR 0.021 0.002 TYR C 129 PHE 0.014 0.002 PHE c 309 TRP 0.026 0.002 TRP b 370 HIS 0.009 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 9914) covalent geometry : angle 0.75689 (13453) SS BOND : bond 0.00455 ( 21) SS BOND : angle 1.40388 ( 42) hydrogen bonds : bond 0.03768 ( 337) hydrogen bonds : angle 5.23291 ( 906) Misc. bond : bond 0.00137 ( 1) link_ALPHA1-3 : bond 0.02761 ( 1) link_ALPHA1-3 : angle 4.25212 ( 3) link_ALPHA1-6 : bond 0.00644 ( 2) link_ALPHA1-6 : angle 1.55457 ( 6) link_BETA1-4 : bond 0.00329 ( 9) link_BETA1-4 : angle 2.58697 ( 27) link_BETA1-6 : bond 0.00315 ( 2) link_BETA1-6 : angle 1.29707 ( 6) link_NAG-ASN : bond 0.00533 ( 33) link_NAG-ASN : angle 3.76749 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 294 time to evaluate : 0.350 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: C 194 MET cc_start: 0.9068 (tpp) cc_final: 0.8043 (tmm) REVERT: C 223 GLN cc_start: 0.8614 (pm20) cc_final: 0.8333 (pm20) REVERT: C 256 ARG cc_start: 0.6535 (tpt170) cc_final: 0.4761 (mmt180) REVERT: A 153 MET cc_start: 0.8521 (tpt) cc_final: 0.8166 (tpt) REVERT: A 218 GLN cc_start: 0.7770 (mp10) cc_final: 0.7541 (mp10) REVERT: B 235 ARG cc_start: 0.8496 (mtm-85) cc_final: 0.7005 (mtt180) REVERT: B 256 ARG cc_start: 0.7261 (tpt-90) cc_final: 0.5439 (mtp85) REVERT: a 286 ILE cc_start: 0.7557 (tt) cc_final: 0.7342 (tt) REVERT: a 308 GLU cc_start: 0.8844 (mp0) cc_final: 0.8557 (mp0) REVERT: a 333 SER cc_start: 0.8556 (t) cc_final: 0.8117 (m) REVERT: a 363 TYR cc_start: 0.7480 (p90) cc_final: 0.7260 (p90) REVERT: a 371 TYR cc_start: 0.6873 (p90) cc_final: 0.6536 (p90) REVERT: b 393 TYR cc_start: 0.9027 (m-80) cc_final: 0.8623 (m-10) REVERT: b 404 GLU cc_start: 0.8241 (tp30) cc_final: 0.7871 (tp30) REVERT: c 261 THR cc_start: 0.8854 (t) cc_final: 0.8590 (p) REVERT: c 308 GLU cc_start: 0.7838 (mp0) cc_final: 0.7635 (mp0) REVERT: c 332 MET cc_start: 0.6376 (mmm) cc_final: 0.6024 (mmm) REVERT: c 359 MET cc_start: 0.8419 (mtt) cc_final: 0.8142 (mtt) outliers start: 30 outliers final: 23 residues processed: 304 average time/residue: 0.1079 time to fit residues: 45.1531 Evaluate side-chains 300 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 277 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 389 SER Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain b residue 281 THR Chi-restraints excluded: chain b residue 318 PHE Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 367 SER Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain c residue 281 THR Chi-restraints excluded: chain c residue 296 THR Chi-restraints excluded: chain c residue 318 PHE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 388 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 39 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 302 ASN ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 338 ASN ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.124334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.105237 restraints weight = 21637.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.108079 restraints weight = 12051.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.110079 restraints weight = 8082.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.111400 restraints weight = 6140.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.112194 restraints weight = 5072.868| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3445 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3445 r_free = 0.3445 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3445 r_free = 0.3445 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3445 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 9983 Z= 0.276 Angle : 0.939 16.366 13636 Z= 0.426 Chirality : 0.051 0.484 1682 Planarity : 0.004 0.038 1647 Dihedral : 9.786 59.611 2268 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 5.21 % Allowed : 21.62 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.94 (0.27), residues: 955 helix: 0.57 (0.29), residues: 330 sheet: -1.90 (0.41), residues: 147 loop : -0.99 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG c 314 TYR 0.022 0.002 TYR b 363 PHE 0.016 0.002 PHE C 147 TRP 0.028 0.002 TRP b 370 HIS 0.010 0.002 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00633 ( 9914) covalent geometry : angle 0.86559 (13453) SS BOND : bond 0.00441 ( 21) SS BOND : angle 1.48435 ( 42) hydrogen bonds : bond 0.04194 ( 337) hydrogen bonds : angle 5.45301 ( 906) Misc. bond : bond 0.00201 ( 1) link_ALPHA1-3 : bond 0.02044 ( 1) link_ALPHA1-3 : angle 3.88509 ( 3) link_ALPHA1-6 : bond 0.00615 ( 2) link_ALPHA1-6 : angle 1.61862 ( 6) link_BETA1-4 : bond 0.00427 ( 9) link_BETA1-4 : angle 2.65169 ( 27) link_BETA1-6 : bond 0.00292 ( 2) link_BETA1-6 : angle 1.41921 ( 6) link_NAG-ASN : bond 0.00571 ( 33) link_NAG-ASN : angle 3.99318 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 281 time to evaluate : 0.358 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: C 194 MET cc_start: 0.9078 (tpp) cc_final: 0.8086 (tmm) REVERT: C 223 GLN cc_start: 0.8741 (pm20) cc_final: 0.8444 (pm20) REVERT: C 256 ARG cc_start: 0.6456 (tpt170) cc_final: 0.4502 (mmt180) REVERT: A 122 ASP cc_start: 0.7566 (t0) cc_final: 0.7261 (t0) REVERT: A 153 MET cc_start: 0.8620 (tpt) cc_final: 0.8205 (tpt) REVERT: A 248 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.7524 (ttp-170) REVERT: B 235 ARG cc_start: 0.8651 (mtm-85) cc_final: 0.7160 (mtt180) REVERT: B 256 ARG cc_start: 0.7393 (tpt-90) cc_final: 0.5365 (mtp85) REVERT: B 259 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7533 (tt) REVERT: a 308 GLU cc_start: 0.8940 (mp0) cc_final: 0.8707 (mp0) REVERT: a 333 SER cc_start: 0.8652 (t) cc_final: 0.7652 (m) REVERT: a 363 TYR cc_start: 0.7835 (p90) cc_final: 0.7552 (p90) REVERT: a 371 TYR cc_start: 0.7131 (p90) cc_final: 0.6765 (p90) REVERT: b 348 GLN cc_start: 0.8246 (mm-40) cc_final: 0.8039 (tm-30) REVERT: b 351 MET cc_start: 0.8435 (tmm) cc_final: 0.8218 (tmm) REVERT: b 393 TYR cc_start: 0.9132 (m-80) cc_final: 0.8798 (m-10) REVERT: b 404 GLU cc_start: 0.8396 (tp30) cc_final: 0.7984 (tp30) REVERT: c 284 MET cc_start: 0.8432 (ptp) cc_final: 0.8033 (ptp) REVERT: c 308 GLU cc_start: 0.7931 (mp0) cc_final: 0.7352 (mp0) REVERT: c 359 MET cc_start: 0.8700 (mtt) cc_final: 0.8402 (mtt) outliers start: 47 outliers final: 34 residues processed: 298 average time/residue: 0.1072 time to fit residues: 43.9553 Evaluate side-chains 312 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 276 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain b residue 281 THR Chi-restraints excluded: chain b residue 318 PHE Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 347 ASP Chi-restraints excluded: chain b residue 367 SER Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain c residue 263 THR Chi-restraints excluded: chain c residue 281 THR Chi-restraints excluded: chain c residue 296 THR Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 317 ASP Chi-restraints excluded: chain c residue 318 PHE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 376 THR Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 397 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 109 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 88 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 17 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 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 = 0.3796 r_free = 0.3796 target = 0.132499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.114052 restraints weight = 21485.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.117194 restraints weight = 11305.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.119266 restraints weight = 7372.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.120520 restraints weight = 5488.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.121467 restraints weight = 4516.569| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3625 r_free = 0.3625 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9983 Z= 0.152 Angle : 0.838 16.654 13636 Z= 0.380 Chirality : 0.047 0.472 1682 Planarity : 0.003 0.038 1647 Dihedral : 9.307 58.609 2268 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.33 % Allowed : 24.39 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.66 (0.27), residues: 955 helix: 0.79 (0.29), residues: 330 sheet: -1.72 (0.44), residues: 120 loop : -0.91 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG a 314 TYR 0.016 0.002 TYR b 363 PHE 0.012 0.002 PHE b 318 TRP 0.031 0.002 TRP b 370 HIS 0.011 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 9914) covalent geometry : angle 0.76651 (13453) SS BOND : bond 0.00393 ( 21) SS BOND : angle 1.51717 ( 42) hydrogen bonds : bond 0.03730 ( 337) hydrogen bonds : angle 5.21127 ( 906) Misc. bond : bond 0.00047 ( 1) link_ALPHA1-3 : bond 0.01962 ( 1) link_ALPHA1-3 : angle 4.19740 ( 3) link_ALPHA1-6 : bond 0.00764 ( 2) link_ALPHA1-6 : angle 1.50003 ( 6) link_BETA1-4 : bond 0.00422 ( 9) link_BETA1-4 : angle 2.50084 ( 27) link_BETA1-6 : bond 0.00365 ( 2) link_BETA1-6 : angle 1.23185 ( 6) link_NAG-ASN : bond 0.00533 ( 33) link_NAG-ASN : angle 3.66835 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 293 time to evaluate : 0.366 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: C 194 MET cc_start: 0.9047 (tpp) cc_final: 0.8054 (tmm) REVERT: C 223 GLN cc_start: 0.8554 (pm20) cc_final: 0.8283 (pm20) REVERT: C 256 ARG cc_start: 0.6378 (tpt170) cc_final: 0.4629 (mmt180) REVERT: A 153 MET cc_start: 0.8553 (tpt) cc_final: 0.8254 (tpt) REVERT: A 193 ARG cc_start: 0.8875 (mtp180) cc_final: 0.8327 (mtp180) REVERT: A 248 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.7505 (ttp-110) REVERT: B 235 ARG cc_start: 0.8423 (mtm-85) cc_final: 0.7070 (mtt180) REVERT: B 256 ARG cc_start: 0.7328 (tpt-90) cc_final: 0.5392 (mtp85) REVERT: a 308 GLU cc_start: 0.8850 (mp0) cc_final: 0.8550 (mp0) REVERT: a 333 SER cc_start: 0.8347 (t) cc_final: 0.8054 (m) REVERT: a 370 TRP cc_start: 0.7317 (p-90) cc_final: 0.7019 (p-90) REVERT: a 371 TYR cc_start: 0.6823 (p90) cc_final: 0.6500 (p90) REVERT: b 348 GLN cc_start: 0.8125 (mm-40) cc_final: 0.7701 (mm-40) REVERT: b 368 LYS cc_start: 0.8613 (ttpt) cc_final: 0.8128 (ttpt) REVERT: b 393 TYR cc_start: 0.9026 (m-80) cc_final: 0.8736 (m-10) REVERT: b 404 GLU cc_start: 0.8280 (tp30) cc_final: 0.8077 (tp30) REVERT: c 284 MET cc_start: 0.8385 (ptp) cc_final: 0.8060 (ptp) REVERT: c 359 MET cc_start: 0.8443 (mtt) cc_final: 0.8178 (mtt) outliers start: 30 outliers final: 22 residues processed: 304 average time/residue: 0.1120 time to fit residues: 46.6823 Evaluate side-chains 303 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 280 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain b residue 281 THR Chi-restraints excluded: chain b residue 318 PHE Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain c residue 281 THR Chi-restraints excluded: chain c residue 296 THR Chi-restraints excluded: chain c residue 318 PHE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 388 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 50 optimal weight: 0.0770 chunk 45 optimal weight: 0.0570 chunk 109 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.8858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 ASN A 185 ASN ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 319 ASN ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 342 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.134261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.115989 restraints weight = 21529.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.118912 restraints weight = 12202.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.120906 restraints weight = 8351.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.122188 restraints weight = 6400.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.122925 restraints weight = 5329.001| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9983 Z= 0.152 Angle : 0.841 16.295 13636 Z= 0.382 Chirality : 0.048 0.467 1682 Planarity : 0.003 0.040 1647 Dihedral : 9.090 59.877 2268 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.22 % Allowed : 26.39 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.61 (0.27), residues: 955 helix: 0.88 (0.29), residues: 330 sheet: -1.63 (0.45), residues: 120 loop : -0.94 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG a 282 TYR 0.025 0.002 TYR a 363 PHE 0.012 0.002 PHE a 262 TRP 0.033 0.002 TRP b 370 HIS 0.010 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 9914) covalent geometry : angle 0.77323 (13453) SS BOND : bond 0.00254 ( 21) SS BOND : angle 1.52929 ( 42) hydrogen bonds : bond 0.03656 ( 337) hydrogen bonds : angle 5.16435 ( 906) Misc. bond : bond 0.00029 ( 1) link_ALPHA1-3 : bond 0.01998 ( 1) link_ALPHA1-3 : angle 4.01201 ( 3) link_ALPHA1-6 : bond 0.00806 ( 2) link_ALPHA1-6 : angle 1.41512 ( 6) link_BETA1-4 : bond 0.00390 ( 9) link_BETA1-4 : angle 2.44485 ( 27) link_BETA1-6 : bond 0.00389 ( 2) link_BETA1-6 : angle 1.18537 ( 6) link_NAG-ASN : bond 0.00526 ( 33) link_NAG-ASN : angle 3.58573 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 299 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 194 MET cc_start: 0.9015 (tpp) cc_final: 0.8045 (tmm) REVERT: C 223 GLN cc_start: 0.8536 (pm20) cc_final: 0.8280 (pm20) REVERT: C 256 ARG cc_start: 0.6492 (tpt170) cc_final: 0.4736 (mmt180) REVERT: A 153 MET cc_start: 0.8499 (tpt) cc_final: 0.8246 (tpt) REVERT: A 193 ARG cc_start: 0.8810 (mtp180) cc_final: 0.8269 (mtp180) REVERT: A 248 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7498 (ttp-110) REVERT: B 235 ARG cc_start: 0.8470 (mtm-85) cc_final: 0.7004 (mtt180) REVERT: B 256 ARG cc_start: 0.7401 (tpt-90) cc_final: 0.5493 (mtp85) REVERT: a 308 GLU cc_start: 0.8751 (mp0) cc_final: 0.8443 (mp0) REVERT: a 333 SER cc_start: 0.8357 (t) cc_final: 0.8082 (m) REVERT: a 370 TRP cc_start: 0.7223 (p-90) cc_final: 0.6928 (p-90) REVERT: a 371 TYR cc_start: 0.6725 (p90) cc_final: 0.6372 (p90) REVERT: a 410 MET cc_start: 0.8536 (tpp) cc_final: 0.8223 (tpt) REVERT: b 348 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7672 (mm-40) REVERT: c 284 MET cc_start: 0.8425 (ptp) cc_final: 0.8092 (ptp) REVERT: c 332 MET cc_start: 0.6401 (mmm) cc_final: 0.6193 (mmm) REVERT: c 359 MET cc_start: 0.8471 (mtt) cc_final: 0.8245 (mtt) outliers start: 29 outliers final: 22 residues processed: 307 average time/residue: 0.1129 time to fit residues: 47.3062 Evaluate side-chains 304 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 281 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 353 ASN Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain b residue 281 THR Chi-restraints excluded: chain b residue 318 PHE Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain c residue 281 THR Chi-restraints excluded: chain c residue 296 THR Chi-restraints excluded: chain c residue 318 PHE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 388 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 48 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 8 optimal weight: 10.0000 chunk 117 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 65 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 chunk 47 optimal weight: 0.0170 chunk 5 optimal weight: 9.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 ASN A 185 ASN B 131 HIS b 409 ASN ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 342 ASN ** c 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.133145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.114119 restraints weight = 21741.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.117246 restraints weight = 11632.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.119359 restraints weight = 7734.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.120712 restraints weight = 5821.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.121557 restraints weight = 4794.599| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3633 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3633 r_free = 0.3633 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3633 r_free = 0.3633 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9983 Z= 0.149 Angle : 0.833 16.021 13636 Z= 0.382 Chirality : 0.047 0.463 1682 Planarity : 0.003 0.040 1647 Dihedral : 8.835 58.178 2268 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.44 % Allowed : 26.83 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.56 (0.27), residues: 955 helix: 0.94 (0.30), residues: 329 sheet: -1.41 (0.46), residues: 116 loop : -0.98 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG c 314 TYR 0.022 0.002 TYR b 363 PHE 0.012 0.001 PHE b 318 TRP 0.034 0.002 TRP b 370 HIS 0.009 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9914) covalent geometry : angle 0.76714 (13453) SS BOND : bond 0.00220 ( 21) SS BOND : angle 1.50824 ( 42) hydrogen bonds : bond 0.03642 ( 337) hydrogen bonds : angle 5.18690 ( 906) Misc. bond : bond 0.00028 ( 1) link_ALPHA1-3 : bond 0.01920 ( 1) link_ALPHA1-3 : angle 3.94992 ( 3) link_ALPHA1-6 : bond 0.00863 ( 2) link_ALPHA1-6 : angle 1.35017 ( 6) link_BETA1-4 : bond 0.00434 ( 9) link_BETA1-4 : angle 2.36214 ( 27) link_BETA1-6 : bond 0.00394 ( 2) link_BETA1-6 : angle 1.17093 ( 6) link_NAG-ASN : bond 0.00521 ( 33) link_NAG-ASN : angle 3.51764 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 295 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 194 MET cc_start: 0.9033 (tpp) cc_final: 0.8041 (tmm) REVERT: C 223 GLN cc_start: 0.8541 (pm20) cc_final: 0.8203 (pm20) REVERT: C 256 ARG cc_start: 0.6405 (tpt170) cc_final: 0.4858 (mmm160) REVERT: A 153 MET cc_start: 0.8545 (tpt) cc_final: 0.8269 (tpt) REVERT: A 193 ARG cc_start: 0.8823 (mtp180) cc_final: 0.8006 (mtp180) REVERT: A 248 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7478 (ttp-110) REVERT: B 235 ARG cc_start: 0.8501 (mtm-85) cc_final: 0.7064 (mtt-85) REVERT: B 256 ARG cc_start: 0.7343 (tpt-90) cc_final: 0.5401 (mtp85) REVERT: a 308 GLU cc_start: 0.8814 (mp0) cc_final: 0.8443 (mp0) REVERT: a 333 SER cc_start: 0.8385 (t) cc_final: 0.8130 (m) REVERT: a 371 TYR cc_start: 0.6880 (p90) cc_final: 0.6398 (p90) REVERT: a 410 MET cc_start: 0.8531 (tpp) cc_final: 0.8210 (tpt) REVERT: b 348 GLN cc_start: 0.8115 (mm-40) cc_final: 0.7673 (mm-40) REVERT: b 404 GLU cc_start: 0.8585 (tp30) cc_final: 0.8126 (tp30) REVERT: c 284 MET cc_start: 0.8418 (ptp) cc_final: 0.8029 (ptp) REVERT: c 332 MET cc_start: 0.6365 (mmm) cc_final: 0.6147 (mmm) REVERT: c 359 MET cc_start: 0.8518 (mtt) cc_final: 0.8292 (mtt) outliers start: 31 outliers final: 26 residues processed: 303 average time/residue: 0.1077 time to fit residues: 44.7919 Evaluate side-chains 314 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 287 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 353 ASN Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain b residue 281 THR Chi-restraints excluded: chain b residue 318 PHE Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain c residue 281 THR Chi-restraints excluded: chain c residue 296 THR Chi-restraints excluded: chain c residue 318 PHE Chi-restraints excluded: chain c residue 352 LYS Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 371 TYR Chi-restraints excluded: chain c residue 388 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 77 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 342 ASN ** c 354 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 = 0.3794 r_free = 0.3794 target = 0.132990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.113977 restraints weight = 21736.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.117090 restraints weight = 11652.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.119181 restraints weight = 7683.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.120368 restraints weight = 5812.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.121325 restraints weight = 4841.530| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9983 Z= 0.174 Angle : 0.876 15.741 13636 Z= 0.405 Chirality : 0.048 0.469 1682 Planarity : 0.004 0.040 1647 Dihedral : 8.800 58.761 2268 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.99 % Allowed : 28.27 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.63 (0.27), residues: 955 helix: 0.92 (0.30), residues: 331 sheet: -1.55 (0.46), residues: 120 loop : -1.02 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG b 356 TYR 0.029 0.002 TYR B 150 PHE 0.013 0.002 PHE b 318 TRP 0.036 0.002 TRP b 370 HIS 0.010 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 9914) covalent geometry : angle 0.81414 (13453) SS BOND : bond 0.00258 ( 21) SS BOND : angle 1.43349 ( 42) hydrogen bonds : bond 0.03838 ( 337) hydrogen bonds : angle 5.25791 ( 906) Misc. bond : bond 0.00013 ( 1) link_ALPHA1-3 : bond 0.01773 ( 1) link_ALPHA1-3 : angle 3.71144 ( 3) link_ALPHA1-6 : bond 0.00804 ( 2) link_ALPHA1-6 : angle 1.33000 ( 6) link_BETA1-4 : bond 0.00415 ( 9) link_BETA1-4 : angle 2.30947 ( 27) link_BETA1-6 : bond 0.00355 ( 2) link_BETA1-6 : angle 1.17871 ( 6) link_NAG-ASN : bond 0.00508 ( 33) link_NAG-ASN : angle 3.54606 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 289 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 194 MET cc_start: 0.9040 (tpp) cc_final: 0.8028 (tmm) REVERT: C 223 GLN cc_start: 0.8612 (pm20) cc_final: 0.8257 (pm20) REVERT: C 256 ARG cc_start: 0.6510 (tpt170) cc_final: 0.4554 (mmt180) REVERT: A 153 MET cc_start: 0.8558 (tpt) cc_final: 0.8153 (tpt) REVERT: A 193 ARG cc_start: 0.8842 (mtp180) cc_final: 0.8273 (mtp180) REVERT: A 248 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.7412 (ttp-110) REVERT: B 235 ARG cc_start: 0.8537 (mtm-85) cc_final: 0.7044 (mtt180) REVERT: B 256 ARG cc_start: 0.7412 (tpt-90) cc_final: 0.5448 (mtp85) REVERT: a 308 GLU cc_start: 0.8824 (mp0) cc_final: 0.8453 (mp0) REVERT: a 333 SER cc_start: 0.8414 (t) cc_final: 0.8143 (m) REVERT: a 370 TRP cc_start: 0.7342 (p-90) cc_final: 0.6954 (p-90) REVERT: a 371 TYR cc_start: 0.6789 (p90) cc_final: 0.6505 (p90) REVERT: a 410 MET cc_start: 0.8574 (tpp) cc_final: 0.8247 (tpt) REVERT: b 393 TYR cc_start: 0.8951 (m-80) cc_final: 0.8709 (m-10) REVERT: b 404 GLU cc_start: 0.8653 (tp30) cc_final: 0.8146 (tp30) REVERT: c 284 MET cc_start: 0.8467 (ptp) cc_final: 0.7915 (ptp) REVERT: c 332 MET cc_start: 0.6398 (mmm) cc_final: 0.6075 (mmm) REVERT: c 359 MET cc_start: 0.8563 (mtt) cc_final: 0.8358 (mtt) outliers start: 27 outliers final: 24 residues processed: 300 average time/residue: 0.1075 time to fit residues: 44.2460 Evaluate side-chains 310 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 285 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 353 ASN Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain b residue 281 THR Chi-restraints excluded: chain b residue 318 PHE Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain c residue 281 THR Chi-restraints excluded: chain c residue 296 THR Chi-restraints excluded: chain c residue 318 PHE Chi-restraints excluded: chain c residue 352 LYS Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 388 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 6 optimal weight: 10.0000 chunk 101 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 342 ASN ** c 354 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 = 0.3676 r_free = 0.3676 target = 0.127905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.109215 restraints weight = 21167.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.112180 restraints weight = 11482.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.114182 restraints weight = 7600.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.115429 restraints weight = 5726.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.116311 restraints weight = 4742.743| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3498 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3498 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 9983 Z= 0.195 Angle : 0.898 15.805 13636 Z= 0.416 Chirality : 0.049 0.481 1682 Planarity : 0.004 0.041 1647 Dihedral : 8.855 59.311 2268 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.10 % Allowed : 28.38 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.69 (0.27), residues: 955 helix: 0.84 (0.30), residues: 331 sheet: -1.54 (0.47), residues: 120 loop : -1.03 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG c 314 TYR 0.040 0.002 TYR C 94 PHE 0.012 0.002 PHE c 309 TRP 0.038 0.002 TRP b 370 HIS 0.008 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 9914) covalent geometry : angle 0.83830 (13453) SS BOND : bond 0.00287 ( 21) SS BOND : angle 1.38092 ( 42) hydrogen bonds : bond 0.04085 ( 337) hydrogen bonds : angle 5.35330 ( 906) Misc. bond : bond 0.00032 ( 1) link_ALPHA1-3 : bond 0.01859 ( 1) link_ALPHA1-3 : angle 3.54972 ( 3) link_ALPHA1-6 : bond 0.00814 ( 2) link_ALPHA1-6 : angle 1.34038 ( 6) link_BETA1-4 : bond 0.00404 ( 9) link_BETA1-4 : angle 2.29797 ( 27) link_BETA1-6 : bond 0.00326 ( 2) link_BETA1-6 : angle 1.21147 ( 6) link_NAG-ASN : bond 0.00508 ( 33) link_NAG-ASN : angle 3.55814 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2035.35 seconds wall clock time: 36 minutes 12.16 seconds (2172.16 seconds total)