Starting phenix.real_space_refine on Sun Jun 8 19:00:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cj8_45625/06_2025/9cj8_45625.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cj8_45625/06_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_45625/06_2025/9cj8_45625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cj8_45625/06_2025/9cj8_45625.map" model { file = "/net/cci-nas-00/data/ceres_data/9cj8_45625/06_2025/9cj8_45625.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cj8_45625/06_2025/9cj8_45625.cif" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.09, per 1000 atoms: 0.83 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: 2.80 Conformation dependent library (CDL) restraints added in 873.1 milliseconds 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: 1.00 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: 2.49 Time building geometry restraints manager: 3.28 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 259 or resid 301 throu \ gh 304)) selection = (chain 'B' and (resid 60 through 200 or resid 207 through 259 or resid 301 throu \ gh 304)) selection = (chain 'C' and (resid 60 through 259 or resid 301 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 414 or resid 701 through 702)) selection = chain 'b' selection = (chain 'c' and (resid 260 through 414 or resid 701 through 702)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 21.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.810 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.140 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (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 TRP 0.030 0.002 TRP B 227 HIS 0.028 0.002 HIS B 230 PHE 0.023 0.003 PHE A 233 TYR 0.032 0.002 TYR C 94 ARG 0.014 0.001 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00845 ( 33) link_NAG-ASN : angle 4.90568 ( 99) 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_ALPHA1-3 : bond 0.00220 ( 1) link_ALPHA1-3 : angle 4.14251 ( 3) hydrogen bonds : bond 0.17807 ( 337) hydrogen bonds : angle 7.62300 ( 906) link_BETA1-6 : bond 0.00186 ( 2) link_BETA1-6 : angle 1.17755 ( 6) SS BOND : bond 0.00395 ( 21) SS BOND : angle 3.07078 ( 42) covalent geometry : bond 0.00589 ( 9914) covalent geometry : angle 1.08480 (13453) Misc. bond : bond 0.08259 ( 1) *********************** 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 : 0.862 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: 0.2391 time to fit residues: 110.0226 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 : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3908 r_free = 0.3908 target = 0.140888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.122286 restraints weight = 21716.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.125487 restraints weight = 11665.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.127660 restraints weight = 7701.885| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9983 Z= 0.154 Angle : 0.873 15.275 13636 Z= 0.383 Chirality : 0.049 0.465 1682 Planarity : 0.004 0.034 1647 Dihedral : 10.251 79.800 2268 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.66 % Allowed : 14.86 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.27), residues: 955 helix: 0.36 (0.29), residues: 323 sheet: -1.34 (0.48), residues: 116 loop : -0.89 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP b 370 HIS 0.008 0.001 HIS B 230 PHE 0.020 0.002 PHE B 191 TYR 0.025 0.002 TYR B 129 ARG 0.005 0.001 ARG b 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00616 ( 33) link_NAG-ASN : angle 4.12872 ( 99) link_ALPHA1-6 : bond 0.01215 ( 2) link_ALPHA1-6 : angle 2.09251 ( 6) link_BETA1-4 : bond 0.00575 ( 9) link_BETA1-4 : angle 3.08863 ( 27) link_ALPHA1-3 : bond 0.02807 ( 1) link_ALPHA1-3 : angle 3.79274 ( 3) hydrogen bonds : bond 0.04223 ( 337) hydrogen bonds : angle 5.65757 ( 906) link_BETA1-6 : bond 0.00431 ( 2) link_BETA1-6 : angle 1.27844 ( 6) SS BOND : bond 0.00265 ( 21) SS BOND : angle 1.17726 ( 42) covalent geometry : bond 0.00342 ( 9914) covalent geometry : angle 0.78592 (13453) Misc. bond : bond 0.01068 ( 1) *********************** 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: 15 poor density : 301 time to evaluate : 0.977 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: 0.8297 (mm) cc_final: 0.8094 (mt) REVERT: C 194 MET cc_start: 0.8862 (tpp) cc_final: 0.7669 (tmm) REVERT: C 256 ARG cc_start: 0.6619 (tpt170) cc_final: 0.4894 (mmt180) REVERT: A 96 MET cc_start: 0.7105 (mmt) cc_final: 0.6859 (mmt) REVERT: A 234 SER cc_start: 0.8565 (t) cc_final: 0.8258 (p) REVERT: B 78 LEU cc_start: 0.8149 (mm) cc_final: 0.7935 (mm) REVERT: B 235 ARG cc_start: 0.8373 (mtm-85) cc_final: 0.6519 (mtt180) REVERT: B 256 ARG cc_start: 0.7122 (tpt-90) cc_final: 0.5794 (mtm180) REVERT: a 308 GLU cc_start: 0.8773 (mp0) cc_final: 0.8543 (mp0) REVERT: a 333 SER cc_start: 0.8661 (t) cc_final: 0.8138 (m) REVERT: c 317 ASP cc_start: 0.7825 (t70) cc_final: 0.7514 (t70) REVERT: c 406 GLN cc_start: 0.8901 (tp-100) cc_final: 0.8686 (tp-100) outliers start: 15 outliers final: 13 residues processed: 307 average time/residue: 0.2483 time to fit residues: 104.0321 Evaluate side-chains 293 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 280 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 13 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 112 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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 127 ASN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 321 GLN ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 342 ASN c 354 HIS c 406 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.122825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.104002 restraints weight = 21679.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.106706 restraints weight = 12601.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.108447 restraints weight = 8742.239| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3385 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3385 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.080 9983 Z= 0.451 Angle : 1.148 16.352 13636 Z= 0.523 Chirality : 0.058 0.509 1682 Planarity : 0.005 0.051 1647 Dihedral : 10.757 75.849 2268 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 5.10 % Allowed : 16.96 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.27), residues: 955 helix: -0.01 (0.28), residues: 332 sheet: -1.66 (0.47), residues: 118 loop : -1.20 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 227 HIS 0.011 0.003 HIS C 141 PHE 0.023 0.003 PHE A 157 TYR 0.025 0.003 TYR b 363 ARG 0.007 0.001 ARG a 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00777 ( 33) link_NAG-ASN : angle 4.67042 ( 99) link_ALPHA1-6 : bond 0.00659 ( 2) link_ALPHA1-6 : angle 1.73031 ( 6) link_BETA1-4 : bond 0.00607 ( 9) link_BETA1-4 : angle 3.11127 ( 27) link_ALPHA1-3 : bond 0.02703 ( 1) link_ALPHA1-3 : angle 3.50167 ( 3) hydrogen bonds : bond 0.04880 ( 337) hydrogen bonds : angle 5.96061 ( 906) link_BETA1-6 : bond 0.00469 ( 2) link_BETA1-6 : angle 1.64206 ( 6) SS BOND : bond 0.00634 ( 21) SS BOND : angle 1.69795 ( 42) covalent geometry : bond 0.01022 ( 9914) covalent geometry : angle 1.06896 (13453) Misc. bond : bond 0.00854 ( 1) *********************** 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 328 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 282 time to evaluate : 1.023 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 146 ASN cc_start: 0.8545 (m-40) cc_final: 0.8243 (m110) REVERT: C 162 ILE cc_start: 0.8573 (mm) cc_final: 0.8371 (mt) REVERT: C 194 MET cc_start: 0.9093 (tpp) cc_final: 0.8021 (tmm) REVERT: C 256 ARG cc_start: 0.6665 (tpt170) cc_final: 0.4665 (mmt180) REVERT: A 122 ASP cc_start: 0.7707 (t0) cc_final: 0.7474 (t0) REVERT: B 134 MET cc_start: 0.8767 (ttm) cc_final: 0.8483 (tpp) REVERT: B 209 ASN cc_start: 0.8916 (t0) cc_final: 0.8638 (t0) REVERT: B 235 ARG cc_start: 0.8661 (mtm-85) cc_final: 0.7087 (mtt180) REVERT: B 256 ARG cc_start: 0.7470 (tpt-90) cc_final: 0.5428 (mtp85) REVERT: a 333 SER cc_start: 0.8784 (t) cc_final: 0.8361 (m) REVERT: a 405 GLN cc_start: 0.9029 (tp40) cc_final: 0.8812 (tp-100) REVERT: a 410 MET cc_start: 0.8523 (tpp) cc_final: 0.7949 (tpp) REVERT: b 389 SER cc_start: 0.8868 (m) cc_final: 0.8541 (p) REVERT: b 393 TYR cc_start: 0.9199 (m-80) cc_final: 0.8981 (m-10) REVERT: b 404 GLU cc_start: 0.8420 (tp30) cc_final: 0.8104 (tp30) REVERT: c 261 THR cc_start: 0.8943 (t) cc_final: 0.8674 (p) REVERT: c 314 ARG cc_start: 0.8868 (mtm-85) cc_final: 0.8524 (mtt90) REVERT: c 317 ASP cc_start: 0.8035 (t70) cc_final: 0.7788 (t70) REVERT: c 342 ASN cc_start: 0.7621 (m-40) cc_final: 0.7376 (m110) REVERT: c 359 MET cc_start: 0.8610 (mtt) cc_final: 0.8303 (mtt) outliers start: 46 outliers final: 30 residues processed: 295 average time/residue: 0.2374 time to fit residues: 95.5886 Evaluate side-chains 300 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 270 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 164 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 188 LEU 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 239 ILE Chi-restraints excluded: chain B residue 254 ILE 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 46 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN A 141 HIS A 149 GLN B 69 GLN ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.133783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.115252 restraints weight = 21484.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.118438 restraints weight = 11456.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.120499 restraints weight = 7558.529| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3607 r_free = 0.3607 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3607 r_free = 0.3607 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9983 Z= 0.149 Angle : 0.843 16.829 13636 Z= 0.379 Chirality : 0.048 0.480 1682 Planarity : 0.003 0.039 1647 Dihedral : 9.695 66.794 2268 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.10 % Allowed : 21.40 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.27), residues: 955 helix: 0.64 (0.29), residues: 326 sheet: -1.88 (0.42), residues: 149 loop : -1.05 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP b 370 HIS 0.008 0.001 HIS C 92 PHE 0.016 0.002 PHE B 191 TYR 0.022 0.002 TYR a 371 ARG 0.007 0.001 ARG a 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00560 ( 33) link_NAG-ASN : angle 3.92527 ( 99) link_ALPHA1-6 : bond 0.00670 ( 2) link_ALPHA1-6 : angle 1.52947 ( 6) link_BETA1-4 : bond 0.00487 ( 9) link_BETA1-4 : angle 2.71816 ( 27) link_ALPHA1-3 : bond 0.02284 ( 1) link_ALPHA1-3 : angle 4.31164 ( 3) hydrogen bonds : bond 0.03832 ( 337) hydrogen bonds : angle 5.28633 ( 906) link_BETA1-6 : bond 0.00379 ( 2) link_BETA1-6 : angle 1.26283 ( 6) SS BOND : bond 0.00258 ( 21) SS BOND : angle 1.47432 ( 42) covalent geometry : bond 0.00336 ( 9914) covalent geometry : angle 0.76073 (13453) Misc. bond : bond 0.00134 ( 1) *********************** 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 320 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 292 time to evaluate : 1.050 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 162 ILE cc_start: 0.8373 (mm) cc_final: 0.8115 (mt) REVERT: C 194 MET cc_start: 0.9076 (tpp) cc_final: 0.8032 (tmm) REVERT: C 256 ARG cc_start: 0.6545 (tpt170) cc_final: 0.4726 (mmt180) REVERT: A 153 MET cc_start: 0.8483 (tpt) cc_final: 0.8156 (tpt) REVERT: A 217 TYR cc_start: 0.8133 (m-80) cc_final: 0.7905 (m-80) REVERT: A 248 ARG cc_start: 0.8476 (ttp80) cc_final: 0.7858 (ttp-170) REVERT: B 134 MET cc_start: 0.8689 (ttm) cc_final: 0.8161 (tpp) REVERT: B 209 ASN cc_start: 0.8800 (t0) cc_final: 0.8515 (t0) REVERT: B 235 ARG cc_start: 0.8430 (mtm-85) cc_final: 0.7022 (mtt180) REVERT: B 256 ARG cc_start: 0.7296 (tpt-90) cc_final: 0.5430 (mtp85) REVERT: a 333 SER cc_start: 0.8590 (t) cc_final: 0.8119 (m) REVERT: a 405 GLN cc_start: 0.9005 (tp40) cc_final: 0.8784 (tp-100) REVERT: b 348 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7941 (mm-40) REVERT: b 351 MET cc_start: 0.8168 (tmm) cc_final: 0.7852 (tmm) REVERT: b 355 LEU cc_start: 0.9210 (mp) cc_final: 0.9000 (mp) REVERT: b 404 GLU cc_start: 0.8268 (tp30) cc_final: 0.7901 (tp30) REVERT: c 261 THR cc_start: 0.8860 (t) cc_final: 0.8600 (p) REVERT: c 324 GLN cc_start: 0.8464 (pt0) cc_final: 0.8253 (pt0) REVERT: c 359 MET cc_start: 0.8320 (mtt) cc_final: 0.8043 (mtt) outliers start: 28 outliers final: 19 residues processed: 302 average time/residue: 0.2238 time to fit residues: 92.6639 Evaluate side-chains 294 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 275 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 B residue 137 ILE Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain b residue 286 ILE 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 318 PHE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 410 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 114 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 chunk 57 optimal weight: 8.9990 chunk 104 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 52 optimal weight: 0.0970 chunk 16 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN A 149 GLN ** A 218 GLN ** 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** c 354 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.123999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.105118 restraints weight = 21122.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.107960 restraints weight = 11666.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.109925 restraints weight = 7884.448| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3403 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3404 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 9983 Z= 0.292 Angle : 0.956 16.682 13636 Z= 0.433 Chirality : 0.052 0.495 1682 Planarity : 0.004 0.040 1647 Dihedral : 9.994 61.979 2268 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 5.10 % Allowed : 21.18 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.27), residues: 955 helix: 0.45 (0.29), residues: 330 sheet: -1.89 (0.42), residues: 147 loop : -1.07 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP b 370 HIS 0.010 0.002 HIS C 92 PHE 0.014 0.002 PHE A 157 TYR 0.023 0.002 TYR a 371 ARG 0.005 0.001 ARG a 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00605 ( 33) link_NAG-ASN : angle 4.15367 ( 99) link_ALPHA1-6 : bond 0.00582 ( 2) link_ALPHA1-6 : angle 1.61313 ( 6) link_BETA1-4 : bond 0.00378 ( 9) link_BETA1-4 : angle 2.75357 ( 27) link_ALPHA1-3 : bond 0.01881 ( 1) link_ALPHA1-3 : angle 3.85675 ( 3) hydrogen bonds : bond 0.04163 ( 337) hydrogen bonds : angle 5.49547 ( 906) link_BETA1-6 : bond 0.00343 ( 2) link_BETA1-6 : angle 1.35462 ( 6) SS BOND : bond 0.00424 ( 21) SS BOND : angle 1.50959 ( 42) covalent geometry : bond 0.00672 ( 9914) covalent geometry : angle 0.87854 (13453) Misc. bond : bond 0.00284 ( 1) *********************** 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 333 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 287 time to evaluate : 0.914 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 162 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8322 (mt) REVERT: C 194 MET cc_start: 0.9073 (tpp) cc_final: 0.8065 (tmm) REVERT: C 256 ARG cc_start: 0.6516 (tpt170) cc_final: 0.4617 (mmt180) REVERT: A 82 MET cc_start: 0.9090 (pmm) cc_final: 0.8877 (pmm) REVERT: A 122 ASP cc_start: 0.7563 (t0) cc_final: 0.7282 (t0) REVERT: A 153 MET cc_start: 0.8575 (tpt) cc_final: 0.8137 (tpt) REVERT: A 218 GLN cc_start: 0.7905 (mp10) cc_final: 0.7528 (mp10) REVERT: A 245 LEU cc_start: 0.9087 (mt) cc_final: 0.8864 (mt) REVERT: A 248 ARG cc_start: 0.8574 (ttp80) cc_final: 0.7900 (ttp-170) REVERT: B 134 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8248 (tpp) REVERT: B 209 ASN cc_start: 0.8866 (t0) cc_final: 0.8603 (t0) REVERT: B 235 ARG cc_start: 0.8621 (mtm-85) cc_final: 0.7147 (mtt180) REVERT: B 256 ARG cc_start: 0.7414 (tpt-90) cc_final: 0.5419 (mtp85) REVERT: B 259 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7674 (tt) REVERT: a 333 SER cc_start: 0.8704 (t) cc_final: 0.8334 (m) REVERT: a 363 TYR cc_start: 0.7754 (p90) cc_final: 0.7451 (p90) REVERT: a 405 GLN cc_start: 0.9046 (tp40) cc_final: 0.8830 (tp-100) REVERT: a 410 MET cc_start: 0.8535 (tpp) cc_final: 0.8034 (tpp) REVERT: b 348 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8428 (mm-40) REVERT: b 389 SER cc_start: 0.8838 (m) cc_final: 0.8506 (p) REVERT: b 393 TYR cc_start: 0.9134 (m-80) cc_final: 0.8814 (m-10) REVERT: b 404 GLU cc_start: 0.8400 (tp30) cc_final: 0.7996 (tp30) REVERT: c 261 THR cc_start: 0.8859 (t) cc_final: 0.8621 (p) REVERT: c 284 MET cc_start: 0.8450 (ptp) cc_final: 0.8113 (ptp) REVERT: c 308 GLU cc_start: 0.7976 (mp0) cc_final: 0.7530 (pm20) REVERT: c 324 GLN cc_start: 0.8600 (pt0) cc_final: 0.8400 (pt0) REVERT: c 359 MET cc_start: 0.8691 (mtt) cc_final: 0.8383 (mtt) REVERT: c 386 TRP cc_start: 0.9038 (t-100) cc_final: 0.7999 (m-90) outliers start: 46 outliers final: 31 residues processed: 307 average time/residue: 0.2202 time to fit residues: 92.3684 Evaluate side-chains 307 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 273 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 137 ILE Chi-restraints excluded: chain C residue 162 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 212 CYS Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 224 ASN 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 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 Chi-restraints excluded: chain c residue 410 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 47 optimal weight: 0.6980 chunk 90 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 149 GLN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 321 GLN ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.131821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.113191 restraints weight = 21431.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.116378 restraints weight = 11446.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.118468 restraints weight = 7523.320| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9983 Z= 0.146 Angle : 0.836 16.727 13636 Z= 0.378 Chirality : 0.047 0.475 1682 Planarity : 0.003 0.039 1647 Dihedral : 9.561 59.203 2268 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.33 % Allowed : 23.73 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.27), residues: 955 helix: 0.85 (0.30), residues: 323 sheet: -1.56 (0.47), residues: 119 loop : -0.89 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP b 370 HIS 0.011 0.001 HIS C 92 PHE 0.012 0.001 PHE b 318 TYR 0.030 0.002 TYR B 150 ARG 0.007 0.001 ARG c 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00542 ( 33) link_NAG-ASN : angle 3.76074 ( 99) link_ALPHA1-6 : bond 0.00742 ( 2) link_ALPHA1-6 : angle 1.54785 ( 6) link_BETA1-4 : bond 0.00425 ( 9) link_BETA1-4 : angle 2.58598 ( 27) link_ALPHA1-3 : bond 0.02009 ( 1) link_ALPHA1-3 : angle 4.22256 ( 3) hydrogen bonds : bond 0.03684 ( 337) hydrogen bonds : angle 5.19978 ( 906) link_BETA1-6 : bond 0.00242 ( 2) link_BETA1-6 : angle 1.16534 ( 6) SS BOND : bond 0.00269 ( 21) SS BOND : angle 1.55044 ( 42) covalent geometry : bond 0.00339 ( 9914) covalent geometry : angle 0.76031 (13453) Misc. bond : bond 0.00071 ( 1) *********************** 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 324 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 294 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 162 ILE cc_start: 0.8378 (mm) cc_final: 0.8137 (mt) REVERT: C 194 MET cc_start: 0.9067 (tpp) cc_final: 0.8070 (tmm) REVERT: C 256 ARG cc_start: 0.6425 (tpt170) cc_final: 0.4658 (mmt180) REVERT: A 153 MET cc_start: 0.8477 (tpt) cc_final: 0.8187 (tpt) REVERT: A 193 ARG cc_start: 0.8902 (mtp180) cc_final: 0.8671 (mtp180) REVERT: A 248 ARG cc_start: 0.8441 (ttp80) cc_final: 0.7927 (ttp-170) REVERT: B 113 ILE cc_start: 0.8771 (mp) cc_final: 0.8549 (tt) REVERT: B 134 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8151 (tpp) REVERT: B 209 ASN cc_start: 0.8821 (t0) cc_final: 0.8605 (t0) REVERT: B 235 ARG cc_start: 0.8431 (mtm-85) cc_final: 0.7120 (mtt180) REVERT: B 256 ARG cc_start: 0.7359 (tpt-90) cc_final: 0.5399 (mtp85) REVERT: a 333 SER cc_start: 0.8547 (t) cc_final: 0.8151 (m) REVERT: a 363 TYR cc_start: 0.7562 (p90) cc_final: 0.7359 (p90) REVERT: a 405 GLN cc_start: 0.9036 (tp40) cc_final: 0.8814 (tp-100) REVERT: b 348 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8323 (mm-40) REVERT: b 404 GLU cc_start: 0.8312 (tp30) cc_final: 0.8092 (tp30) REVERT: c 261 THR cc_start: 0.8827 (t) cc_final: 0.8613 (p) REVERT: c 284 MET cc_start: 0.8444 (ptp) cc_final: 0.8072 (ptp) REVERT: c 308 GLU cc_start: 0.7921 (mp0) cc_final: 0.7454 (pm20) REVERT: c 359 MET cc_start: 0.8402 (mtt) cc_final: 0.8172 (mtt) outliers start: 30 outliers final: 20 residues processed: 304 average time/residue: 0.2309 time to fit residues: 95.2615 Evaluate side-chains 298 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 277 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 255 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain b residue 266 LEU 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 318 PHE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 410 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 61 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 28 optimal weight: 0.4980 chunk 1 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN A 149 GLN a 321 GLN ** 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** ** c 354 HIS ** 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 = 0.3637 r_free = 0.3637 target = 0.124249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.105217 restraints weight = 21753.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.108182 restraints weight = 11614.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.110213 restraints weight = 7683.780| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3408 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3408 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 9983 Z= 0.250 Angle : 0.921 16.557 13636 Z= 0.419 Chirality : 0.050 0.479 1682 Planarity : 0.004 0.039 1647 Dihedral : 9.664 59.255 2268 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.99 % Allowed : 25.17 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.28), residues: 955 helix: 0.71 (0.29), residues: 329 sheet: -1.63 (0.47), residues: 121 loop : -0.98 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP b 370 HIS 0.009 0.001 HIS C 92 PHE 0.012 0.002 PHE b 318 TYR 0.024 0.002 TYR B 150 ARG 0.010 0.001 ARG c 356 Details of bonding type rmsd link_NAG-ASN : bond 0.00554 ( 33) link_NAG-ASN : angle 3.94619 ( 99) link_ALPHA1-6 : bond 0.00682 ( 2) link_ALPHA1-6 : angle 1.55813 ( 6) link_BETA1-4 : bond 0.00400 ( 9) link_BETA1-4 : angle 2.59992 ( 27) link_ALPHA1-3 : bond 0.02090 ( 1) link_ALPHA1-3 : angle 3.75800 ( 3) hydrogen bonds : bond 0.03958 ( 337) hydrogen bonds : angle 5.37013 ( 906) link_BETA1-6 : bond 0.00362 ( 2) link_BETA1-6 : angle 1.34425 ( 6) SS BOND : bond 0.00378 ( 21) SS BOND : angle 1.53525 ( 42) covalent geometry : bond 0.00580 ( 9914) covalent geometry : angle 0.84848 (13453) Misc. bond : bond 0.00169 ( 1) *********************** 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 318 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 282 time to evaluate : 0.890 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 162 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8331 (mt) REVERT: C 194 MET cc_start: 0.9101 (tpp) cc_final: 0.8055 (tmm) REVERT: C 256 ARG cc_start: 0.6359 (tpt170) cc_final: 0.4537 (mmt180) REVERT: A 122 ASP cc_start: 0.7595 (t0) cc_final: 0.7286 (t0) REVERT: A 153 MET cc_start: 0.8605 (tpt) cc_final: 0.8238 (tpt) REVERT: A 193 ARG cc_start: 0.8951 (mtp180) cc_final: 0.8155 (mtp180) REVERT: B 134 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8230 (tpp) REVERT: B 209 ASN cc_start: 0.8821 (t0) cc_final: 0.8382 (t0) REVERT: B 235 ARG cc_start: 0.8601 (mtm-85) cc_final: 0.7159 (mtt180) REVERT: B 256 ARG cc_start: 0.7394 (tpt-90) cc_final: 0.5354 (mtp85) REVERT: B 259 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7655 (tt) REVERT: a 291 LYS cc_start: 0.8588 (mttt) cc_final: 0.8379 (mttt) REVERT: a 333 SER cc_start: 0.8665 (t) cc_final: 0.7744 (m) REVERT: a 363 TYR cc_start: 0.7825 (p90) cc_final: 0.7595 (p90) REVERT: a 405 GLN cc_start: 0.9019 (tp40) cc_final: 0.8796 (tp-100) REVERT: b 393 TYR cc_start: 0.9126 (m-80) cc_final: 0.8761 (m-10) REVERT: b 404 GLU cc_start: 0.8467 (tp30) cc_final: 0.8242 (tp30) REVERT: c 284 MET cc_start: 0.8522 (ptp) cc_final: 0.7912 (ptp) REVERT: c 308 GLU cc_start: 0.8048 (mp0) cc_final: 0.7385 (pm20) REVERT: c 332 MET cc_start: 0.6507 (mmm) cc_final: 0.6232 (mmm) REVERT: c 386 TRP cc_start: 0.9007 (t-100) cc_final: 0.8026 (m-90) outliers start: 36 outliers final: 28 residues processed: 297 average time/residue: 0.2167 time to fit residues: 88.4166 Evaluate side-chains 303 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 272 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 134 MET 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 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 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 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 410 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 36 optimal weight: 0.0070 chunk 14 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 6 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 overall best weight: 2.5202 ------------------------------------------------------------------------------- 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 149 GLN B 131 HIS ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.123659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.105249 restraints weight = 21825.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.108028 restraints weight = 12047.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.109962 restraints weight = 8104.102| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9983 Z= 0.252 Angle : 0.929 16.744 13636 Z= 0.423 Chirality : 0.050 0.489 1682 Planarity : 0.004 0.037 1647 Dihedral : 9.638 59.402 2268 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 5.43 % Allowed : 24.61 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.27), residues: 955 helix: 0.60 (0.29), residues: 329 sheet: -1.69 (0.46), residues: 121 loop : -1.05 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP b 370 HIS 0.009 0.001 HIS C 92 PHE 0.018 0.002 PHE a 262 TYR 0.042 0.002 TYR C 129 ARG 0.008 0.001 ARG b 356 Details of bonding type rmsd link_NAG-ASN : bond 0.00543 ( 33) link_NAG-ASN : angle 3.91978 ( 99) link_ALPHA1-6 : bond 0.00719 ( 2) link_ALPHA1-6 : angle 1.51772 ( 6) link_BETA1-4 : bond 0.00448 ( 9) link_BETA1-4 : angle 2.56558 ( 27) link_ALPHA1-3 : bond 0.02103 ( 1) link_ALPHA1-3 : angle 3.68793 ( 3) hydrogen bonds : bond 0.03969 ( 337) hydrogen bonds : angle 5.40964 ( 906) link_BETA1-6 : bond 0.00259 ( 2) link_BETA1-6 : angle 1.41566 ( 6) SS BOND : bond 0.00401 ( 21) SS BOND : angle 1.58130 ( 42) covalent geometry : bond 0.00581 ( 9914) covalent geometry : angle 0.85806 (13453) Misc. bond : bond 0.00089 ( 1) *********************** 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 332 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 283 time to evaluate : 1.223 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 162 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8313 (mt) REVERT: C 194 MET cc_start: 0.9094 (tpp) cc_final: 0.8086 (tmm) REVERT: C 256 ARG cc_start: 0.6448 (tpt170) cc_final: 0.4657 (mmt180) REVERT: A 122 ASP cc_start: 0.7554 (t0) cc_final: 0.7259 (t0) REVERT: A 153 MET cc_start: 0.8585 (tpt) cc_final: 0.8245 (tpt) REVERT: A 193 ARG cc_start: 0.8935 (mtp180) cc_final: 0.8346 (mtp180) REVERT: B 134 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8205 (tpp) REVERT: B 155 CYS cc_start: 0.7014 (OUTLIER) cc_final: 0.6686 (p) REVERT: B 209 ASN cc_start: 0.8847 (t0) cc_final: 0.8569 (t0) REVERT: B 235 ARG cc_start: 0.8598 (mtm-85) cc_final: 0.7181 (mtt180) REVERT: B 256 ARG cc_start: 0.7432 (tpt-90) cc_final: 0.5439 (mtp85) REVERT: B 259 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7643 (tt) REVERT: a 333 SER cc_start: 0.8569 (t) cc_final: 0.8300 (m) REVERT: a 405 GLN cc_start: 0.9026 (tp40) cc_final: 0.8818 (tp-100) REVERT: b 282 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8211 (tmm-80) REVERT: b 393 TYR cc_start: 0.9120 (m-80) cc_final: 0.8805 (m-10) REVERT: b 404 GLU cc_start: 0.8489 (tp30) cc_final: 0.8287 (tp30) REVERT: c 284 MET cc_start: 0.8602 (ptp) cc_final: 0.7998 (ptp) REVERT: c 308 GLU cc_start: 0.7927 (mp0) cc_final: 0.7466 (pm20) REVERT: c 332 MET cc_start: 0.6453 (mmm) cc_final: 0.6076 (mmm) REVERT: c 386 TRP cc_start: 0.8950 (t-100) cc_final: 0.8118 (m-90) outliers start: 49 outliers final: 35 residues processed: 304 average time/residue: 0.2322 time to fit residues: 96.9644 Evaluate side-chains 315 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 275 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 134 MET 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 a residue 358 ILE Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain b residue 281 THR Chi-restraints excluded: chain b residue 282 ARG 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 349 LEU 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 b residue 396 GLU 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 371 TYR Chi-restraints excluded: chain c residue 376 THR Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 410 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 17 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 354 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.123709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.104776 restraints weight = 21574.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.107610 restraints weight = 11918.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.109621 restraints weight = 7989.815| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3402 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 9983 Z= 0.246 Angle : 0.937 16.764 13636 Z= 0.428 Chirality : 0.050 0.483 1682 Planarity : 0.004 0.038 1647 Dihedral : 9.636 58.985 2268 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 5.10 % Allowed : 25.61 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.28), residues: 955 helix: 0.58 (0.29), residues: 331 sheet: -1.74 (0.46), residues: 121 loop : -1.08 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP b 370 HIS 0.009 0.001 HIS C 92 PHE 0.014 0.002 PHE b 318 TYR 0.025 0.002 TYR a 363 ARG 0.009 0.001 ARG b 356 Details of bonding type rmsd link_NAG-ASN : bond 0.00549 ( 33) link_NAG-ASN : angle 3.91807 ( 99) link_ALPHA1-6 : bond 0.00729 ( 2) link_ALPHA1-6 : angle 1.49013 ( 6) link_BETA1-4 : bond 0.00443 ( 9) link_BETA1-4 : angle 2.46784 ( 27) link_ALPHA1-3 : bond 0.01959 ( 1) link_ALPHA1-3 : angle 3.53664 ( 3) hydrogen bonds : bond 0.03963 ( 337) hydrogen bonds : angle 5.47161 ( 906) link_BETA1-6 : bond 0.00257 ( 2) link_BETA1-6 : angle 1.41216 ( 6) SS BOND : bond 0.00385 ( 21) SS BOND : angle 1.50799 ( 42) covalent geometry : bond 0.00572 ( 9914) covalent geometry : angle 0.86792 (13453) Misc. bond : bond 0.00072 ( 1) *********************** 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 328 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 282 time to evaluate : 1.098 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 162 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8306 (mt) REVERT: C 194 MET cc_start: 0.9115 (tpp) cc_final: 0.8484 (tmm) REVERT: C 256 ARG cc_start: 0.6325 (tpt170) cc_final: 0.4498 (mmt180) REVERT: A 122 ASP cc_start: 0.7566 (t0) cc_final: 0.7270 (t0) REVERT: A 153 MET cc_start: 0.8634 (tpt) cc_final: 0.8307 (tpt) REVERT: A 193 ARG cc_start: 0.8944 (mtp180) cc_final: 0.8330 (mtp180) REVERT: B 134 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8348 (tpp) REVERT: B 155 CYS cc_start: 0.7221 (OUTLIER) cc_final: 0.6792 (p) REVERT: B 209 ASN cc_start: 0.8837 (t0) cc_final: 0.8528 (t0) REVERT: B 235 ARG cc_start: 0.8634 (mtm-85) cc_final: 0.7184 (mtt180) REVERT: B 256 ARG cc_start: 0.7423 (tpt-90) cc_final: 0.5334 (mtp85) REVERT: B 259 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7746 (tt) REVERT: a 333 SER cc_start: 0.8688 (t) cc_final: 0.8430 (m) REVERT: b 282 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8289 (tmm-80) REVERT: b 351 MET cc_start: 0.8443 (tmm) cc_final: 0.8212 (tmm) REVERT: b 393 TYR cc_start: 0.9137 (m-80) cc_final: 0.8809 (m-10) REVERT: c 284 MET cc_start: 0.8627 (ptp) cc_final: 0.8024 (ptp) REVERT: c 308 GLU cc_start: 0.7934 (mp0) cc_final: 0.7570 (pm20) REVERT: c 332 MET cc_start: 0.6433 (mmm) cc_final: 0.6132 (mmm) REVERT: c 386 TRP cc_start: 0.8944 (t-100) cc_final: 0.8119 (m-90) outliers start: 46 outliers final: 32 residues processed: 298 average time/residue: 0.2328 time to fit residues: 95.5488 Evaluate side-chains 311 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 274 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 153 MET 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 282 ARG 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 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 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 371 TYR Chi-restraints excluded: chain c residue 376 THR Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 410 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 17 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 36 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 149 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.126238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.107442 restraints weight = 21661.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.110464 restraints weight = 11503.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.112546 restraints weight = 7494.103| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- 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 = 0.87 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 = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3445 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9983 Z= 0.164 Angle : 0.886 16.667 13636 Z= 0.405 Chirality : 0.048 0.482 1682 Planarity : 0.004 0.040 1647 Dihedral : 9.250 58.169 2268 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.77 % Allowed : 26.72 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.27), residues: 955 helix: 0.72 (0.30), residues: 330 sheet: -1.73 (0.45), residues: 119 loop : -1.07 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP b 370 HIS 0.016 0.001 HIS B 230 PHE 0.013 0.002 PHE b 318 TYR 0.041 0.002 TYR C 94 ARG 0.008 0.001 ARG b 356 Details of bonding type rmsd link_NAG-ASN : bond 0.00533 ( 33) link_NAG-ASN : angle 3.69080 ( 99) link_ALPHA1-6 : bond 0.00828 ( 2) link_ALPHA1-6 : angle 1.40029 ( 6) link_BETA1-4 : bond 0.00440 ( 9) link_BETA1-4 : angle 2.35242 ( 27) link_ALPHA1-3 : bond 0.01899 ( 1) link_ALPHA1-3 : angle 3.70163 ( 3) hydrogen bonds : bond 0.03773 ( 337) hydrogen bonds : angle 5.30893 ( 906) link_BETA1-6 : bond 0.00395 ( 2) link_BETA1-6 : angle 1.20270 ( 6) SS BOND : bond 0.00278 ( 21) SS BOND : angle 1.29044 ( 42) covalent geometry : bond 0.00384 ( 9914) covalent geometry : angle 0.82083 (13453) Misc. bond : bond 0.00002 ( 1) ********************** 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 317 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 283 time to evaluate : 0.998 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 162 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8162 (mt) REVERT: C 194 MET cc_start: 0.9091 (tpp) cc_final: 0.8488 (tmm) REVERT: C 256 ARG cc_start: 0.6188 (tpt170) cc_final: 0.4465 (mmt180) REVERT: A 153 MET cc_start: 0.8681 (tpt) cc_final: 0.8308 (tpt) REVERT: A 193 ARG cc_start: 0.8899 (mtp180) cc_final: 0.8013 (mtp180) REVERT: B 134 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8287 (tpp) REVERT: B 209 ASN cc_start: 0.8818 (t0) cc_final: 0.8541 (t0) REVERT: B 235 ARG cc_start: 0.8523 (mtm-85) cc_final: 0.7107 (mtt180) REVERT: B 256 ARG cc_start: 0.7361 (tpt-90) cc_final: 0.5280 (mtp85) REVERT: a 333 SER cc_start: 0.8605 (t) cc_final: 0.8352 (m) REVERT: a 410 MET cc_start: 0.8561 (tpp) cc_final: 0.8271 (tpt) REVERT: b 282 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8283 (tmm-80) REVERT: b 351 MET cc_start: 0.8286 (tmm) cc_final: 0.8065 (tmm) REVERT: b 393 TYR cc_start: 0.9060 (m-80) cc_final: 0.8652 (m-10) REVERT: c 284 MET cc_start: 0.8587 (ptp) cc_final: 0.7973 (ptp) REVERT: c 308 GLU cc_start: 0.8036 (mp0) cc_final: 0.7527 (pm20) REVERT: c 332 MET cc_start: 0.6385 (mmm) cc_final: 0.6097 (mmm) REVERT: c 386 TRP cc_start: 0.8884 (t-100) cc_final: 0.8152 (m-90) REVERT: c 414 MET cc_start: 0.7222 (tpp) cc_final: 0.6827 (tpp) outliers start: 34 outliers final: 26 residues processed: 295 average time/residue: 0.2370 time to fit residues: 95.0212 Evaluate side-chains 302 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 273 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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 162 ILE 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 81 THR Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 134 MET 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 282 ARG 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 b residue 414 MET 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 376 THR 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 113 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 88 optimal weight: 0.0770 chunk 76 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- 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 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.126088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.107910 restraints weight = 21581.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.110716 restraints weight = 11919.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.112646 restraints weight = 7958.152| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3463 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3463 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9983 Z= 0.158 Angle : 0.872 16.364 13636 Z= 0.403 Chirality : 0.048 0.471 1682 Planarity : 0.003 0.042 1647 Dihedral : 9.070 58.252 2268 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.55 % Allowed : 27.16 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.27), residues: 955 helix: 0.75 (0.30), residues: 331 sheet: -1.81 (0.43), residues: 120 loop : -1.00 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP b 370 HIS 0.014 0.001 HIS C 92 PHE 0.013 0.002 PHE b 318 TYR 0.023 0.002 TYR C 94 ARG 0.004 0.001 ARG C 250 Details of bonding type rmsd link_NAG-ASN : bond 0.00512 ( 33) link_NAG-ASN : angle 3.61020 ( 99) link_ALPHA1-6 : bond 0.00823 ( 2) link_ALPHA1-6 : angle 1.33104 ( 6) link_BETA1-4 : bond 0.00518 ( 9) link_BETA1-4 : angle 2.21831 ( 27) link_ALPHA1-3 : bond 0.01907 ( 1) link_ALPHA1-3 : angle 3.59215 ( 3) hydrogen bonds : bond 0.03721 ( 337) hydrogen bonds : angle 5.27724 ( 906) link_BETA1-6 : bond 0.00386 ( 2) link_BETA1-6 : angle 1.14395 ( 6) SS BOND : bond 0.00263 ( 21) SS BOND : angle 1.28640 ( 42) covalent geometry : bond 0.00370 ( 9914) covalent geometry : angle 0.80961 (13453) Misc. bond : bond 0.00003 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4182.89 seconds wall clock time: 74 minutes 57.69 seconds (4497.69 seconds total)