Starting phenix.real_space_refine on Fri Feb 14 06:09:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cj8_45625/02_2025/9cj8_45625.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cj8_45625/02_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_45625/02_2025/9cj8_45625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cj8_45625/02_2025/9cj8_45625.map" model { file = "/net/cci-nas-00/data/ceres_data/9cj8_45625/02_2025/9cj8_45625.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cj8_45625/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 8.28, per 1000 atoms: 0.85 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: 3.13 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.08 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: 2.54 Time building geometry restraints manager: 3.54 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: 8.900 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: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 26.760 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.070 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.650 ------------------------------------------------------------------------------- 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 0.056 9914 Z= 0.374 Angle : 1.085 9.509 13453 Z= 0.529 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 *********************** 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 : 0.983 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: 0.2430 time to fit residues: 111.4026 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 : 1.039 ------------------------------------------------------------------------------- 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: 4.9990 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: 3.9990 chunk 107 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3899 r_free = 0.3899 target = 0.140070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.121404 restraints weight = 21703.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.124561 restraints weight = 11700.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.126693 restraints weight = 7781.041| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9914 Z= 0.242 Angle : 0.796 9.656 13453 Z= 0.368 Chirality : 0.049 0.467 1682 Planarity : 0.004 0.034 1647 Dihedral : 10.402 81.015 2268 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.00 % Allowed : 14.52 % 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: -0.84 (0.27), residues: 955 helix: 0.38 (0.29), residues: 323 sheet: -1.35 (0.48), residues: 116 loop : -0.93 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 227 HIS 0.009 0.001 HIS B 230 PHE 0.021 0.002 PHE B 191 TYR 0.026 0.002 TYR B 129 ARG 0.006 0.001 ARG b 282 *********************** 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 315 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 297 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 194 MET cc_start: 0.8902 (tpp) cc_final: 0.7689 (tmm) REVERT: C 256 ARG cc_start: 0.6572 (tpt170) cc_final: 0.4823 (mmt180) REVERT: A 96 MET cc_start: 0.7138 (mmt) cc_final: 0.6858 (mmt) REVERT: B 78 LEU cc_start: 0.8235 (mm) cc_final: 0.8023 (mm) REVERT: B 209 ASN cc_start: 0.8576 (t0) cc_final: 0.8366 (t0) REVERT: B 235 ARG cc_start: 0.8446 (mtm-85) cc_final: 0.6576 (mtt180) REVERT: B 256 ARG cc_start: 0.7111 (tpt-90) cc_final: 0.5722 (mtm180) REVERT: a 286 ILE cc_start: 0.7387 (tt) cc_final: 0.7087 (tt) REVERT: a 308 GLU cc_start: 0.8821 (mp0) cc_final: 0.8597 (mp0) REVERT: a 333 SER cc_start: 0.8688 (t) cc_final: 0.8187 (m) REVERT: b 404 GLU cc_start: 0.8202 (tp30) cc_final: 0.7940 (tp30) REVERT: c 317 ASP cc_start: 0.7935 (t70) cc_final: 0.7616 (t70) REVERT: c 406 GLN cc_start: 0.8931 (tp-100) cc_final: 0.8702 (tp-100) outliers start: 18 outliers final: 15 residues processed: 305 average time/residue: 0.2263 time to fit residues: 94.5491 Evaluate side-chains 294 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 279 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 a residue 403 ILE Chi-restraints excluded: chain b residue 281 THR Chi-restraints excluded: chain b residue 318 PHE Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain b residue 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: 0.9980 chunk 26 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 107 optimal weight: 0.3980 chunk 104 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN C 127 ASN A 185 ASN ** B 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 302 ASN ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 342 ASN c 354 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.133240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.114563 restraints weight = 21638.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.117781 restraints weight = 11554.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.119879 restraints weight = 7574.952| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3631 r_free = 0.3631 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3631 r_free = 0.3631 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9914 Z= 0.341 Angle : 0.814 9.727 13453 Z= 0.383 Chirality : 0.051 0.487 1682 Planarity : 0.004 0.037 1647 Dihedral : 9.728 73.300 2268 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.66 % Allowed : 17.18 % Favored : 79.16 % 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: -0.90 (0.27), residues: 955 helix: 0.59 (0.29), residues: 324 sheet: -1.64 (0.43), residues: 142 loop : -1.04 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP b 370 HIS 0.009 0.002 HIS C 92 PHE 0.019 0.002 PHE a 262 TYR 0.023 0.002 TYR C 66 ARG 0.006 0.001 ARG b 282 *********************** 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 330 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 297 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 194 MET cc_start: 0.9029 (tpp) cc_final: 0.8027 (tmm) REVERT: C 256 ARG cc_start: 0.6657 (tpt170) cc_final: 0.4762 (mmt180) REVERT: B 76 GLU cc_start: 0.8044 (tp30) cc_final: 0.7805 (tp30) REVERT: B 134 MET cc_start: 0.8611 (ttm) cc_final: 0.8156 (tpp) REVERT: B 209 ASN cc_start: 0.8742 (t0) cc_final: 0.8452 (t0) REVERT: B 235 ARG cc_start: 0.8485 (mtm-85) cc_final: 0.6968 (mtt180) REVERT: B 256 ARG cc_start: 0.7299 (tpt-90) cc_final: 0.5499 (mtp85) REVERT: a 286 ILE cc_start: 0.7640 (tt) cc_final: 0.7343 (tt) REVERT: a 308 GLU cc_start: 0.8849 (mp0) cc_final: 0.8568 (mp0) REVERT: a 333 SER cc_start: 0.8642 (t) cc_final: 0.8177 (m) REVERT: a 410 MET cc_start: 0.8397 (tpp) cc_final: 0.7975 (tpt) outliers start: 33 outliers final: 23 residues processed: 306 average time/residue: 0.2386 time to fit residues: 100.0957 Evaluate side-chains 307 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 284 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain a residue 280 LEU Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 389 SER Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain b residue 281 THR Chi-restraints excluded: chain b residue 318 PHE Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain c residue 281 THR Chi-restraints excluded: chain c residue 284 MET 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 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: 1.9990 chunk 45 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 83 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN B 69 GLN ** B 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 GLN a 302 ASN a 348 GLN ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 342 ASN ** c 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 354 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.134823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.116430 restraints weight = 21770.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.119637 restraints weight = 11623.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.121736 restraints weight = 7628.877| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3639 r_free = 0.3639 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3639 r_free = 0.3639 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9914 Z= 0.225 Angle : 0.726 9.746 13453 Z= 0.341 Chirality : 0.047 0.480 1682 Planarity : 0.003 0.036 1647 Dihedral : 9.265 65.125 2268 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.99 % Allowed : 21.18 % Favored : 75.83 % 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: -0.66 (0.28), residues: 955 helix: 0.86 (0.30), residues: 326 sheet: -1.59 (0.42), residues: 144 loop : -0.93 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP b 370 HIS 0.008 0.001 HIS C 92 PHE 0.013 0.002 PHE C 140 TYR 0.019 0.002 TYR C 66 ARG 0.005 0.001 ARG a 314 *********************** 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 324 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 297 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 194 MET cc_start: 0.9039 (tpp) cc_final: 0.8000 (tmm) REVERT: C 223 GLN cc_start: 0.8520 (pm20) cc_final: 0.8295 (pm20) REVERT: C 256 ARG cc_start: 0.6561 (tpt170) cc_final: 0.4791 (mmt180) REVERT: A 153 MET cc_start: 0.8470 (tpt) cc_final: 0.8148 (tpt) REVERT: B 76 GLU cc_start: 0.8054 (tp30) cc_final: 0.7792 (tp30) REVERT: B 78 LEU cc_start: 0.8731 (mm) cc_final: 0.8453 (mm) REVERT: B 235 ARG cc_start: 0.8459 (mtm-85) cc_final: 0.6925 (mtt180) REVERT: B 256 ARG cc_start: 0.7247 (tpt-90) cc_final: 0.5436 (mtp85) REVERT: a 286 ILE cc_start: 0.7434 (tt) cc_final: 0.7176 (tt) REVERT: a 308 GLU cc_start: 0.8797 (mp0) cc_final: 0.8456 (mp0) REVERT: a 333 SER cc_start: 0.8632 (t) cc_final: 0.7549 (m) REVERT: a 363 TYR cc_start: 0.7450 (p90) cc_final: 0.7173 (p90) REVERT: c 324 GLN cc_start: 0.8503 (pt0) cc_final: 0.8282 (pt0) outliers start: 27 outliers final: 24 residues processed: 305 average time/residue: 0.2369 time to fit residues: 98.4486 Evaluate side-chains 310 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 286 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 185 ASN Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 353 ASN Chi-restraints excluded: chain a residue 389 SER 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 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 c residue 296 THR Chi-restraints excluded: chain c residue 318 PHE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 388 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 114 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 36 optimal weight: 0.1980 chunk 52 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 overall best weight: 5.4388 ------------------------------------------------------------------------------- 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** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 GLN a 302 ASN a 321 GLN ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 342 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.119423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.100660 restraints weight = 21778.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.103239 restraints weight = 12802.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.105025 restraints weight = 8937.264| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.081 9914 Z= 0.738 Angle : 1.139 10.726 13453 Z= 0.536 Chirality : 0.059 0.514 1682 Planarity : 0.005 0.053 1647 Dihedral : 10.867 64.714 2268 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 5.88 % Allowed : 20.18 % Favored : 73.95 % 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: -1.34 (0.26), residues: 955 helix: -0.03 (0.27), residues: 327 sheet: -1.73 (0.47), residues: 120 loop : -1.22 (0.27), residues: 508 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 0.025 0.004 PHE A 157 TYR 0.028 0.003 TYR b 363 ARG 0.006 0.001 ARG b 314 *********************** 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 328 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 275 time to evaluate : 1.038 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 104 GLU cc_start: 0.8290 (tp30) cc_final: 0.7966 (tp30) REVERT: C 194 MET cc_start: 0.9081 (tpp) cc_final: 0.8232 (tmm) REVERT: C 256 ARG cc_start: 0.6676 (tpt170) cc_final: 0.4760 (mtp85) REVERT: B 209 ASN cc_start: 0.9028 (t0) cc_final: 0.8698 (t0) REVERT: B 235 ARG cc_start: 0.8698 (mtm-85) cc_final: 0.7189 (mtt180) REVERT: B 256 ARG cc_start: 0.7554 (tpt-90) cc_final: 0.5490 (mtp85) REVERT: B 259 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7816 (tt) REVERT: a 333 SER cc_start: 0.8727 (t) cc_final: 0.8497 (m) REVERT: a 405 GLN cc_start: 0.9051 (tp40) cc_final: 0.8842 (tp-100) REVERT: a 410 MET cc_start: 0.8631 (tpp) cc_final: 0.8194 (tpp) REVERT: b 351 MET cc_start: 0.8455 (tmm) cc_final: 0.7933 (tmm) REVERT: b 355 LEU cc_start: 0.9359 (mp) cc_final: 0.8952 (mp) REVERT: c 261 THR cc_start: 0.8886 (t) cc_final: 0.8633 (p) REVERT: c 308 GLU cc_start: 0.8062 (mp0) cc_final: 0.7808 (pm20) REVERT: c 309 PHE cc_start: 0.8834 (t80) cc_final: 0.8578 (t80) REVERT: c 386 TRP cc_start: 0.9103 (t-100) cc_final: 0.8013 (m-90) outliers start: 53 outliers final: 39 residues processed: 296 average time/residue: 0.2405 time to fit residues: 98.3425 Evaluate side-chains 302 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 262 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 137 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 187 VAL 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 284 MET Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 350 ILE 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 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 369 TYR Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain c residue 296 THR Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 317 ASP Chi-restraints excluded: chain c residue 318 PHE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 376 THR Chi-restraints excluded: chain c residue 388 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 47 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 GLN A 218 GLN B 131 HIS B 189 GLN a 321 GLN ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 342 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.126413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.107551 restraints weight = 21077.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.110468 restraints weight = 11659.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.112531 restraints weight = 7807.031| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3438 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3438 r_free = 0.3438 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3438 r_free = 0.3438 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3438 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9914 Z= 0.235 Angle : 0.784 9.885 13453 Z= 0.371 Chirality : 0.048 0.488 1682 Planarity : 0.004 0.036 1647 Dihedral : 9.833 59.314 2268 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.88 % Allowed : 24.17 % Favored : 71.95 % 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: -0.81 (0.27), residues: 955 helix: 0.62 (0.29), residues: 323 sheet: -1.59 (0.47), residues: 120 loop : -1.00 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP b 370 HIS 0.011 0.001 HIS C 92 PHE 0.013 0.002 PHE b 318 TYR 0.021 0.002 TYR b 363 ARG 0.006 0.001 ARG a 314 *********************** 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 322 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 287 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 194 MET cc_start: 0.9100 (tpp) cc_final: 0.8088 (tmm) REVERT: C 256 ARG cc_start: 0.6318 (tpt170) cc_final: 0.4554 (mmt180) REVERT: A 248 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.7570 (ttp-110) REVERT: B 113 ILE cc_start: 0.8807 (mp) cc_final: 0.8562 (tt) REVERT: B 209 ASN cc_start: 0.8911 (t0) cc_final: 0.8531 (t0) REVERT: B 235 ARG cc_start: 0.8518 (mtm-85) cc_final: 0.7116 (mtt180) REVERT: B 256 ARG cc_start: 0.7321 (tpt-90) cc_final: 0.5271 (mtp85) REVERT: a 333 SER cc_start: 0.8693 (t) cc_final: 0.8397 (m) REVERT: a 363 TYR cc_start: 0.7782 (p90) cc_final: 0.7533 (p90) REVERT: a 405 GLN cc_start: 0.9052 (tp40) cc_final: 0.8844 (tp-100) REVERT: b 351 MET cc_start: 0.8365 (tmm) cc_final: 0.7873 (tmm) REVERT: b 355 LEU cc_start: 0.9351 (mp) cc_final: 0.8954 (mp) REVERT: b 404 GLU cc_start: 0.8509 (tp30) cc_final: 0.8183 (tp30) REVERT: c 261 THR cc_start: 0.8866 (t) cc_final: 0.8621 (p) REVERT: c 308 GLU cc_start: 0.7819 (mp0) cc_final: 0.7361 (pm20) REVERT: c 332 MET cc_start: 0.6524 (mmm) cc_final: 0.6088 (mmm) outliers start: 35 outliers final: 23 residues processed: 303 average time/residue: 0.2365 time to fit residues: 98.0966 Evaluate side-chains 298 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 274 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain 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 349 LEU Chi-restraints excluded: chain b residue 367 SER Chi-restraints excluded: chain b residue 369 TYR 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 61 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 HIS ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 302 ASN ** 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.125476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.106590 restraints weight = 21369.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.109500 restraints weight = 11763.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.111592 restraints weight = 7829.392| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3426 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3426 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9914 Z= 0.306 Angle : 0.802 9.866 13453 Z= 0.382 Chirality : 0.049 0.477 1682 Planarity : 0.003 0.037 1647 Dihedral : 9.657 58.540 2268 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.77 % Allowed : 25.39 % 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: -0.86 (0.27), residues: 955 helix: 0.56 (0.29), residues: 330 sheet: -1.64 (0.46), residues: 120 loop : -1.03 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP b 370 HIS 0.009 0.001 HIS C 92 PHE 0.012 0.002 PHE b 318 TYR 0.027 0.002 TYR b 393 ARG 0.004 0.001 ARG a 314 *********************** 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 320 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 286 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 194 MET cc_start: 0.9105 (tpp) cc_final: 0.8097 (tmm) REVERT: C 256 ARG cc_start: 0.6314 (tpt170) cc_final: 0.4578 (mmt180) REVERT: A 122 ASP cc_start: 0.7410 (t0) cc_final: 0.7139 (t0) REVERT: A 248 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.7573 (ttp-110) REVERT: B 113 ILE cc_start: 0.8807 (mp) cc_final: 0.8555 (tt) REVERT: B 209 ASN cc_start: 0.8900 (t0) cc_final: 0.8484 (t0) REVERT: B 235 ARG cc_start: 0.8582 (mtm-85) cc_final: 0.7140 (mtt180) REVERT: B 256 ARG cc_start: 0.7354 (tpt-90) cc_final: 0.5295 (mtp85) REVERT: a 333 SER cc_start: 0.8655 (t) cc_final: 0.8360 (m) REVERT: a 363 TYR cc_start: 0.7812 (p90) cc_final: 0.7559 (p90) REVERT: a 405 GLN cc_start: 0.9046 (tp40) cc_final: 0.8835 (tp-100) REVERT: a 410 MET cc_start: 0.8571 (tpp) cc_final: 0.8273 (tpt) REVERT: b 351 MET cc_start: 0.8345 (tmm) cc_final: 0.8015 (tmm) REVERT: c 261 THR cc_start: 0.8840 (t) cc_final: 0.8627 (p) REVERT: c 286 ILE cc_start: 0.7335 (OUTLIER) cc_final: 0.6559 (tp) REVERT: c 308 GLU cc_start: 0.7923 (mp0) cc_final: 0.7475 (pm20) REVERT: c 332 MET cc_start: 0.6436 (mmm) cc_final: 0.6050 (mmm) REVERT: c 410 MET cc_start: 0.7669 (ptm) cc_final: 0.6971 (ptm) outliers start: 34 outliers final: 27 residues processed: 301 average time/residue: 0.2369 time to fit residues: 98.3395 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 : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain 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 155 CYS Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain a residue 296 THR 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 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 281 THR Chi-restraints excluded: chain c residue 286 ILE Chi-restraints excluded: chain c residue 296 THR Chi-restraints excluded: chain c residue 318 PHE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 388 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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** c 354 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.123081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.103884 restraints weight = 21698.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.106811 restraints weight = 11993.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.108701 restraints weight = 8033.791| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3384 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3384 r_free = 0.3384 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3384 r_free = 0.3384 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3384 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 9914 Z= 0.430 Angle : 0.882 9.865 13453 Z= 0.421 Chirality : 0.052 0.482 1682 Planarity : 0.004 0.036 1647 Dihedral : 9.908 59.365 2268 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.77 % Allowed : 25.28 % 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: -1.03 (0.27), residues: 955 helix: 0.42 (0.29), residues: 329 sheet: -1.72 (0.46), residues: 120 loop : -1.14 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP b 370 HIS 0.009 0.002 HIS C 92 PHE 0.014 0.002 PHE a 262 TYR 0.024 0.003 TYR b 393 ARG 0.005 0.001 ARG a 314 *********************** 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 321 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 278 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 194 MET cc_start: 0.9126 (tpp) cc_final: 0.8124 (tmm) REVERT: C 256 ARG cc_start: 0.6380 (tpt170) cc_final: 0.4588 (mmt180) REVERT: A 82 MET cc_start: 0.9008 (pmm) cc_final: 0.8721 (pmm) REVERT: A 122 ASP cc_start: 0.7453 (t0) cc_final: 0.7174 (t0) REVERT: A 248 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.7571 (ttp-110) REVERT: B 209 ASN cc_start: 0.8927 (t0) cc_final: 0.8420 (t0) REVERT: B 235 ARG cc_start: 0.8664 (mtm-85) cc_final: 0.7189 (mtt180) REVERT: B 256 ARG cc_start: 0.7413 (tpt-90) cc_final: 0.5355 (mtp85) REVERT: a 333 SER cc_start: 0.8741 (t) cc_final: 0.8446 (m) REVERT: a 363 TYR cc_start: 0.7913 (p90) cc_final: 0.7691 (p90) REVERT: a 405 GLN cc_start: 0.9038 (tp40) cc_final: 0.8828 (tp-100) REVERT: b 404 GLU cc_start: 0.8666 (tp30) cc_final: 0.8378 (tp30) REVERT: c 261 THR cc_start: 0.8840 (t) cc_final: 0.8636 (p) REVERT: c 286 ILE cc_start: 0.7521 (OUTLIER) cc_final: 0.6647 (tp) REVERT: c 308 GLU cc_start: 0.7952 (mp0) cc_final: 0.7468 (pm20) REVERT: c 332 MET cc_start: 0.6423 (mmm) cc_final: 0.6045 (mmm) REVERT: c 386 TRP cc_start: 0.9019 (t-100) cc_final: 0.8052 (m-90) REVERT: c 410 MET cc_start: 0.7694 (ptm) cc_final: 0.7018 (ptm) outliers start: 43 outliers final: 32 residues processed: 296 average time/residue: 0.2368 time to fit residues: 95.2975 Evaluate side-chains 302 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 268 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 230 HIS Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 358 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 347 ASP 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 396 GLU Chi-restraints excluded: chain c residue 286 ILE Chi-restraints excluded: chain c residue 296 THR Chi-restraints excluded: chain c residue 318 PHE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 388 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 17 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3641 r_free = 0.3641 target = 0.125551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.107540 restraints weight = 21387.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.110144 restraints weight = 12495.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.112014 restraints weight = 8705.199| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3426 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3426 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9914 Z= 0.285 Angle : 0.830 16.604 13453 Z= 0.394 Chirality : 0.050 0.477 1682 Planarity : 0.004 0.037 1647 Dihedral : 9.578 58.881 2268 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.99 % Allowed : 25.83 % Favored : 70.18 % 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: -0.93 (0.27), residues: 955 helix: 0.49 (0.29), residues: 330 sheet: -1.74 (0.45), residues: 120 loop : -1.05 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP b 370 HIS 0.010 0.001 HIS C 92 PHE 0.014 0.002 PHE b 318 TYR 0.021 0.002 TYR a 393 ARG 0.009 0.001 ARG c 314 *********************** 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 316 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 280 time to evaluate : 0.903 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 194 MET cc_start: 0.9099 (tpp) cc_final: 0.8528 (tmm) REVERT: C 250 ARG cc_start: 0.8251 (mtp85) cc_final: 0.7955 (mtp85) REVERT: C 256 ARG cc_start: 0.6299 (tpt170) cc_final: 0.4582 (mmt180) REVERT: A 122 ASP cc_start: 0.7385 (t0) cc_final: 0.7102 (t0) REVERT: A 248 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.7507 (ttp-110) REVERT: B 209 ASN cc_start: 0.8925 (t0) cc_final: 0.8456 (t0) REVERT: B 235 ARG cc_start: 0.8587 (mtm-85) cc_final: 0.7153 (mtt180) REVERT: B 256 ARG cc_start: 0.7389 (tpt-90) cc_final: 0.5338 (mtp85) REVERT: a 333 SER cc_start: 0.8699 (t) cc_final: 0.8391 (m) REVERT: a 363 TYR cc_start: 0.7778 (p90) cc_final: 0.7552 (p90) REVERT: a 410 MET cc_start: 0.8591 (tpp) cc_final: 0.8277 (tpt) REVERT: b 404 GLU cc_start: 0.8555 (tp30) cc_final: 0.8269 (tp30) REVERT: c 286 ILE cc_start: 0.7464 (OUTLIER) cc_final: 0.6686 (tp) REVERT: c 308 GLU cc_start: 0.7887 (mp0) cc_final: 0.7418 (pm20) REVERT: c 332 MET cc_start: 0.6438 (mmm) cc_final: 0.6093 (mmm) REVERT: c 410 MET cc_start: 0.7717 (ptm) cc_final: 0.7019 (ptm) outliers start: 36 outliers final: 30 residues processed: 294 average time/residue: 0.2340 time to fit residues: 93.9680 Evaluate side-chains 304 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 272 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 230 HIS Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain b residue 281 THR Chi-restraints excluded: chain b residue 318 PHE Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 347 ASP 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 385 CYS Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain c residue 286 ILE Chi-restraints excluded: chain c residue 318 PHE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 388 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 36 optimal weight: 0.0770 overall best weight: 2.0144 ------------------------------------------------------------------------------- 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** ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 = 0.3633 r_free = 0.3633 target = 0.124860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.106344 restraints weight = 21503.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.109071 restraints weight = 12224.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.110869 restraints weight = 8363.159| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 9914 Z= 0.337 Angle : 0.862 16.552 13453 Z= 0.412 Chirality : 0.051 0.480 1682 Planarity : 0.004 0.037 1647 Dihedral : 9.460 58.624 2268 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.21 % Allowed : 25.83 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.27), residues: 955 helix: 0.50 (0.29), residues: 330 sheet: -1.73 (0.45), residues: 120 loop : -1.12 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP b 370 HIS 0.009 0.001 HIS C 92 PHE 0.015 0.002 PHE a 262 TYR 0.022 0.002 TYR a 393 ARG 0.009 0.001 ARG c 314 ********************** 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 308 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 270 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 194 MET cc_start: 0.9105 (tpp) cc_final: 0.8555 (tmm) REVERT: C 227 TRP cc_start: 0.7724 (t60) cc_final: 0.7073 (t60) REVERT: C 250 ARG cc_start: 0.8238 (mtp85) cc_final: 0.8001 (mtp85) REVERT: C 256 ARG cc_start: 0.6349 (tpt170) cc_final: 0.4634 (mmt180) REVERT: A 122 ASP cc_start: 0.7392 (t0) cc_final: 0.7112 (t0) REVERT: A 248 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7469 (ttp-110) REVERT: B 76 GLU cc_start: 0.8314 (tp30) cc_final: 0.8087 (tp30) REVERT: B 209 ASN cc_start: 0.8924 (t0) cc_final: 0.8440 (t0) REVERT: B 235 ARG cc_start: 0.8619 (mtm-85) cc_final: 0.7171 (mtt180) REVERT: B 256 ARG cc_start: 0.7446 (tpt-90) cc_final: 0.5391 (mtp85) REVERT: a 333 SER cc_start: 0.8680 (t) cc_final: 0.8362 (m) REVERT: a 363 TYR cc_start: 0.7790 (p90) cc_final: 0.7586 (p90) REVERT: a 410 MET cc_start: 0.8602 (tpp) cc_final: 0.8289 (tpt) REVERT: b 404 GLU cc_start: 0.8616 (tp30) cc_final: 0.8317 (tp30) REVERT: c 286 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.6621 (tp) REVERT: c 308 GLU cc_start: 0.7902 (mp0) cc_final: 0.7449 (pm20) REVERT: c 332 MET cc_start: 0.6396 (mmm) cc_final: 0.6035 (mmm) REVERT: c 386 TRP cc_start: 0.8921 (t-100) cc_final: 0.8097 (m-90) REVERT: c 410 MET cc_start: 0.7744 (ptm) cc_final: 0.7067 (ptm) outliers start: 38 outliers final: 33 residues processed: 284 average time/residue: 0.2371 time to fit residues: 91.6108 Evaluate side-chains 297 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 262 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 230 HIS Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 212 CYS Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain b residue 281 THR Chi-restraints excluded: chain b residue 318 PHE Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 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 385 CYS Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain c residue 286 ILE Chi-restraints excluded: chain c residue 296 THR Chi-restraints excluded: chain c residue 318 PHE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 388 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 113 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 97 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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** B 69 GLN ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.127625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.109681 restraints weight = 21462.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.112430 restraints weight = 11959.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.114328 restraints weight = 8054.180| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9914 Z= 0.228 Angle : 0.801 16.846 13453 Z= 0.382 Chirality : 0.049 0.472 1682 Planarity : 0.003 0.039 1647 Dihedral : 8.970 58.388 2268 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.55 % Allowed : 26.83 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.27), residues: 955 helix: 0.60 (0.29), residues: 332 sheet: -1.58 (0.45), residues: 119 loop : -1.16 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP b 370 HIS 0.010 0.001 HIS C 92 PHE 0.013 0.002 PHE a 262 TYR 0.027 0.002 TYR B 129 ARG 0.009 0.001 ARG c 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3438.23 seconds wall clock time: 63 minutes 8.13 seconds (3788.13 seconds total)