Starting phenix.real_space_refine on Fri Oct 11 12:05:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cj8_45625/10_2024/9cj8_45625.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cj8_45625/10_2024/9cj8_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cj8_45625/10_2024/9cj8_45625.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cj8_45625/10_2024/9cj8_45625.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cj8_45625/10_2024/9cj8_45625.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cj8_45625/10_2024/9cj8_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-5477/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: 7.94, per 1000 atoms: 0.81 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 963.1 milliseconds 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2322 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 17 sheets defined 38.8% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 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: 2.57 Time building geometry restraints manager: 3.29 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: 11.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 26.220 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.710 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 341 time to evaluate : 1.251 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: 0.2462 time to fit residues: 112.5395 Evaluate side-chains 283 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 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 fitting. rotamer outliers: 18 poor density : 297 time to evaluate : 1.044 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: 0.8967 (tpp) cc_final: 0.7722 (tmm) REVERT: C 256 ARG cc_start: 0.6290 (tpt170) cc_final: 0.4471 (mmt180) REVERT: A 96 MET cc_start: 0.7016 (mmt) cc_final: 0.6759 (mmt) REVERT: B 72 GLU cc_start: 0.7152 (tp30) cc_final: 0.6931 (mm-30) REVERT: B 209 ASN cc_start: 0.8527 (t0) cc_final: 0.8293 (t0) REVERT: B 235 ARG cc_start: 0.8505 (mtm-85) cc_final: 0.6529 (mtt180) REVERT: B 256 ARG cc_start: 0.6970 (tpt-90) cc_final: 0.5469 (mtm180) REVERT: a 286 ILE cc_start: 0.7448 (tt) cc_final: 0.7135 (tt) REVERT: a 308 GLU cc_start: 0.8894 (mp0) cc_final: 0.8662 (mp0) REVERT: a 333 SER cc_start: 0.8743 (t) cc_final: 0.8258 (m) REVERT: b 355 LEU cc_start: 0.9236 (mp) cc_final: 0.9025 (mp) REVERT: b 404 GLU cc_start: 0.8168 (tp30) cc_final: 0.7881 (tp30) REVERT: c 317 ASP cc_start: 0.8102 (t70) cc_final: 0.7747 (t70) outliers start: 18 outliers final: 15 residues processed: 305 average time/residue: 0.2325 time to fit residues: 97.1056 Evaluate side-chains 293 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 278 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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 59 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 107 optimal weight: 0.3980 chunk 115 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 ASN A 185 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9914 Z= 0.254 Angle : 0.744 9.702 13453 Z= 0.348 Chirality : 0.048 0.474 1682 Planarity : 0.003 0.036 1647 Dihedral : 9.490 73.916 2268 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.10 % Allowed : 16.96 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.75 (0.28), residues: 955 helix: 0.77 (0.30), residues: 324 sheet: -1.66 (0.42), residues: 143 loop : -0.96 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP b 370 HIS 0.008 0.001 HIS C 92 PHE 0.016 0.002 PHE a 262 TYR 0.018 0.002 TYR C 66 ARG 0.004 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 326 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 298 time to evaluate : 1.027 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: 0.9031 (tpp) cc_final: 0.7978 (tmm) REVERT: C 256 ARG cc_start: 0.6272 (tpt170) cc_final: 0.4400 (mmt180) REVERT: B 63 LYS cc_start: 0.7133 (mmtm) cc_final: 0.6811 (mmtt) REVERT: B 76 GLU cc_start: 0.7979 (tp30) cc_final: 0.7754 (tp30) REVERT: B 209 ASN cc_start: 0.8590 (t0) cc_final: 0.8377 (t0) REVERT: B 235 ARG cc_start: 0.8476 (mtm-85) cc_final: 0.6703 (mtt180) REVERT: B 256 ARG cc_start: 0.7059 (tpt-90) cc_final: 0.5177 (mtp85) REVERT: a 286 ILE cc_start: 0.7469 (tt) cc_final: 0.7164 (tt) REVERT: a 308 GLU cc_start: 0.8890 (mp0) cc_final: 0.8608 (mp0) REVERT: a 333 SER cc_start: 0.8695 (t) cc_final: 0.8221 (m) REVERT: a 410 MET cc_start: 0.8451 (tpp) cc_final: 0.8020 (tpt) REVERT: b 404 GLU cc_start: 0.8228 (tp30) cc_final: 0.7728 (tp30) REVERT: c 317 ASP cc_start: 0.8094 (t70) cc_final: 0.7848 (t70) outliers start: 28 outliers final: 21 residues processed: 307 average time/residue: 0.2357 time to fit residues: 98.5259 Evaluate side-chains 304 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 283 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain 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 358 ILE Chi-restraints excluded: chain b residue 367 SER Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain c residue 281 THR Chi-restraints excluded: chain c residue 296 THR Chi-restraints excluded: chain c residue 318 PHE Chi-restraints excluded: chain c residue 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 106 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 55 optimal weight: 0.0000 chunk 11 optimal weight: 10.0000 chunk 51 optimal weight: 0.4980 chunk 72 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 GLN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9914 Z= 0.251 Angle : 0.729 9.726 13453 Z= 0.343 Chirality : 0.047 0.489 1682 Planarity : 0.003 0.038 1647 Dihedral : 9.205 64.992 2268 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.44 % Allowed : 19.96 % Favored : 76.61 % 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: -0.72 (0.27), residues: 955 helix: 0.74 (0.29), residues: 332 sheet: -1.62 (0.42), residues: 145 loop : -0.92 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP b 370 HIS 0.011 0.001 HIS C 92 PHE 0.014 0.002 PHE C 140 TYR 0.018 0.002 TYR a 371 ARG 0.004 0.001 ARG b 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 289 time to evaluate : 1.090 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 76 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7964 (mm-30) REVERT: C 194 MET cc_start: 0.9047 (tpp) cc_final: 0.8000 (tmm) REVERT: C 223 GLN cc_start: 0.8561 (pm20) cc_final: 0.8163 (pm20) REVERT: C 256 ARG cc_start: 0.6244 (tpt170) cc_final: 0.4407 (mmt180) REVERT: A 217 TYR cc_start: 0.8183 (m-80) cc_final: 0.7963 (m-80) REVERT: B 76 GLU cc_start: 0.8147 (tp30) cc_final: 0.7889 (tp30) REVERT: B 209 ASN cc_start: 0.8517 (t0) cc_final: 0.8204 (t0) REVERT: B 235 ARG cc_start: 0.8574 (mtm-85) cc_final: 0.6894 (mtt180) REVERT: B 256 ARG cc_start: 0.7068 (tpt-90) cc_final: 0.5167 (mtp85) REVERT: B 258 LEU cc_start: 0.8905 (tp) cc_final: 0.8658 (tp) REVERT: a 286 ILE cc_start: 0.7465 (tt) cc_final: 0.7186 (tt) REVERT: a 308 GLU cc_start: 0.8904 (mp0) cc_final: 0.8576 (mp0) REVERT: a 333 SER cc_start: 0.8669 (t) cc_final: 0.7578 (m) REVERT: a 363 TYR cc_start: 0.7714 (p90) cc_final: 0.7408 (p90) REVERT: b 404 GLU cc_start: 0.8252 (tp30) cc_final: 0.7866 (tp30) REVERT: c 324 GLN cc_start: 0.8591 (pt0) cc_final: 0.8361 (pt0) outliers start: 31 outliers final: 26 residues processed: 300 average time/residue: 0.2368 time to fit residues: 97.1412 Evaluate side-chains 306 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 280 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 137 ILE Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain 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 367 SER Chi-restraints excluded: chain b residue 375 THR Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain c residue 281 THR Chi-restraints excluded: chain c residue 296 THR Chi-restraints excluded: chain c residue 318 PHE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 376 THR Chi-restraints excluded: chain c residue 388 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 GLN 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9914 Z= 0.267 Angle : 0.737 9.719 13453 Z= 0.350 Chirality : 0.047 0.489 1682 Planarity : 0.003 0.039 1647 Dihedral : 9.171 59.992 2268 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.55 % Allowed : 21.29 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.64 (0.28), residues: 955 helix: 0.91 (0.30), residues: 332 sheet: -1.78 (0.41), residues: 152 loop : -0.87 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP b 370 HIS 0.010 0.001 HIS C 92 PHE 0.012 0.002 PHE b 318 TYR 0.024 0.002 TYR a 371 ARG 0.004 0.001 ARG a 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 320 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 288 time to evaluate : 1.057 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 76 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7956 (mm-30) REVERT: C 104 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7599 (tp30) REVERT: C 146 ASN cc_start: 0.8431 (m-40) cc_final: 0.8201 (m110) REVERT: C 194 MET cc_start: 0.9060 (tpp) cc_final: 0.8029 (tmm) REVERT: C 223 GLN cc_start: 0.8611 (pm20) cc_final: 0.8146 (pm20) REVERT: C 256 ARG cc_start: 0.6285 (tpt170) cc_final: 0.4416 (mmt180) REVERT: B 76 GLU cc_start: 0.8186 (tp30) cc_final: 0.7895 (tp30) REVERT: B 209 ASN cc_start: 0.8612 (t0) cc_final: 0.8409 (t0) REVERT: B 235 ARG cc_start: 0.8579 (mtm-85) cc_final: 0.6956 (mtt180) REVERT: B 256 ARG cc_start: 0.7064 (tpt-90) cc_final: 0.5158 (mtp85) REVERT: B 258 LEU cc_start: 0.8902 (tp) cc_final: 0.8683 (tp) REVERT: a 286 ILE cc_start: 0.7542 (tt) cc_final: 0.7304 (tt) REVERT: a 308 GLU cc_start: 0.8917 (mp0) cc_final: 0.8559 (mp0) REVERT: a 333 SER cc_start: 0.8504 (t) cc_final: 0.8166 (m) REVERT: a 363 TYR cc_start: 0.7765 (p90) cc_final: 0.7445 (p90) REVERT: a 410 MET cc_start: 0.8476 (tpp) cc_final: 0.8117 (tpt) REVERT: b 351 MET cc_start: 0.8497 (tmm) cc_final: 0.8285 (tpp) REVERT: b 404 GLU cc_start: 0.8245 (tp30) cc_final: 0.7722 (tp30) REVERT: c 261 THR cc_start: 0.8918 (t) cc_final: 0.8642 (p) REVERT: c 308 GLU cc_start: 0.7962 (mp0) cc_final: 0.7439 (pm20) outliers start: 32 outliers final: 24 residues processed: 298 average time/residue: 0.2312 time to fit residues: 93.8744 Evaluate side-chains 301 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 276 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 ASN Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain A residue 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 a residue 349 LEU Chi-restraints excluded: chain a residue 353 ASN Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain b residue 281 THR Chi-restraints excluded: chain b residue 318 PHE Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 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 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 38 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 114 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 52 optimal weight: 0.0070 chunk 9 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9914 Z= 0.191 Angle : 0.706 10.170 13453 Z= 0.333 Chirality : 0.046 0.476 1682 Planarity : 0.003 0.039 1647 Dihedral : 8.818 58.348 2268 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.10 % Allowed : 21.29 % Favored : 75.61 % 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: -0.48 (0.28), residues: 955 helix: 1.03 (0.30), residues: 332 sheet: -1.63 (0.41), residues: 147 loop : -0.80 (0.29), residues: 476 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 0.011 0.001 PHE b 318 TYR 0.023 0.002 TYR a 371 ARG 0.004 0.001 ARG a 282 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 300 time to evaluate : 1.069 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 76 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7963 (mm-30) REVERT: C 94 TYR cc_start: 0.7339 (m-80) cc_final: 0.6879 (m-10) REVERT: C 156 ASP cc_start: 0.7599 (t0) cc_final: 0.7394 (t0) REVERT: C 194 MET cc_start: 0.9068 (tpp) cc_final: 0.8045 (tmm) REVERT: C 223 GLN cc_start: 0.8518 (pm20) cc_final: 0.8042 (pm20) REVERT: C 250 ARG cc_start: 0.8130 (mtp85) cc_final: 0.7929 (mtp85) REVERT: C 256 ARG cc_start: 0.6195 (tpt170) cc_final: 0.4385 (mmt180) REVERT: A 193 ARG cc_start: 0.8848 (mtp180) cc_final: 0.8384 (mtp180) REVERT: A 245 LEU cc_start: 0.8949 (mt) cc_final: 0.8730 (mt) REVERT: A 248 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.7357 (ttp-110) REVERT: B 76 GLU cc_start: 0.8173 (tp30) cc_final: 0.7896 (tp30) REVERT: B 134 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8678 (mtp) REVERT: B 209 ASN cc_start: 0.8548 (t0) cc_final: 0.8246 (t0) REVERT: B 235 ARG cc_start: 0.8519 (mtm-85) cc_final: 0.6914 (mtt180) REVERT: B 256 ARG cc_start: 0.7010 (tpt-90) cc_final: 0.5100 (mtp85) REVERT: B 258 LEU cc_start: 0.8854 (tp) cc_final: 0.8591 (tp) REVERT: a 308 GLU cc_start: 0.8863 (mp0) cc_final: 0.8484 (mp0) REVERT: a 333 SER cc_start: 0.8477 (t) cc_final: 0.8147 (m) REVERT: a 363 TYR cc_start: 0.7738 (p90) cc_final: 0.7507 (p90) REVERT: a 410 MET cc_start: 0.8418 (tpp) cc_final: 0.8006 (tpt) REVERT: b 351 MET cc_start: 0.8541 (tmm) cc_final: 0.8336 (tpp) REVERT: b 368 LYS cc_start: 0.8476 (ttpt) cc_final: 0.8232 (ttpt) REVERT: c 261 THR cc_start: 0.8902 (t) cc_final: 0.8656 (p) REVERT: c 308 GLU cc_start: 0.7973 (mp0) cc_final: 0.7433 (pm20) outliers start: 28 outliers final: 19 residues processed: 306 average time/residue: 0.2439 time to fit residues: 100.3623 Evaluate side-chains 304 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 283 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 188 LEU Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 353 ASN Chi-restraints excluded: chain b residue 266 LEU 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 318 PHE Chi-restraints excluded: chain c residue 361 ILE Chi-restraints excluded: chain c residue 388 VAL Chi-restraints excluded: chain c residue 403 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 65 optimal weight: 0.0070 chunk 83 optimal weight: 6.9990 chunk 64 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN B 232 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9914 Z= 0.194 Angle : 0.710 15.252 13453 Z= 0.336 Chirality : 0.046 0.467 1682 Planarity : 0.003 0.038 1647 Dihedral : 8.595 58.354 2268 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.22 % Allowed : 22.95 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.28 (0.28), residues: 955 helix: 1.09 (0.30), residues: 332 sheet: -1.28 (0.46), residues: 120 loop : -0.74 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP b 370 HIS 0.009 0.001 HIS C 92 PHE 0.011 0.001 PHE b 318 TYR 0.036 0.002 TYR C 129 ARG 0.004 0.001 ARG a 282 *********************** 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 325 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 296 time to evaluate : 1.143 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 76 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7958 (mm-30) REVERT: C 94 TYR cc_start: 0.7232 (m-80) cc_final: 0.6986 (m-10) REVERT: C 194 MET cc_start: 0.9029 (tpp) cc_final: 0.8055 (tmm) REVERT: C 223 GLN cc_start: 0.8531 (pm20) cc_final: 0.8152 (pm20) REVERT: C 256 ARG cc_start: 0.6180 (tpt170) cc_final: 0.4395 (mmt180) REVERT: A 153 MET cc_start: 0.8482 (tpt) cc_final: 0.8263 (tpt) REVERT: A 185 ASN cc_start: 0.7827 (OUTLIER) cc_final: 0.7537 (t0) REVERT: A 217 TYR cc_start: 0.8377 (m-80) cc_final: 0.8118 (m-80) REVERT: A 248 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.7376 (ttp-110) REVERT: B 76 GLU cc_start: 0.8180 (tp30) cc_final: 0.7900 (tp30) REVERT: B 134 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8755 (mtp) REVERT: B 148 ASN cc_start: 0.8697 (p0) cc_final: 0.8489 (p0) REVERT: B 209 ASN cc_start: 0.8530 (t0) cc_final: 0.8310 (t0) REVERT: B 212 CYS cc_start: 0.6225 (m) cc_final: 0.5941 (m) REVERT: B 235 ARG cc_start: 0.8517 (mtm-85) cc_final: 0.6880 (mtt180) REVERT: B 256 ARG cc_start: 0.7011 (tpt-90) cc_final: 0.5078 (mtp85) REVERT: B 258 LEU cc_start: 0.8857 (tp) cc_final: 0.8610 (tp) REVERT: a 308 GLU cc_start: 0.8851 (mp0) cc_final: 0.8428 (mp0) REVERT: a 333 SER cc_start: 0.8480 (t) cc_final: 0.8141 (m) REVERT: a 363 TYR cc_start: 0.7693 (p90) cc_final: 0.7454 (p90) REVERT: b 351 MET cc_start: 0.8539 (tmm) cc_final: 0.8331 (tpp) REVERT: b 404 GLU cc_start: 0.8420 (tp30) cc_final: 0.8027 (tp30) REVERT: c 261 THR cc_start: 0.8888 (t) cc_final: 0.8647 (p) REVERT: c 286 ILE cc_start: 0.6559 (OUTLIER) cc_final: 0.6173 (tt) REVERT: c 308 GLU cc_start: 0.8008 (mp0) cc_final: 0.7431 (pm20) outliers start: 29 outliers final: 20 residues processed: 304 average time/residue: 0.2362 time to fit residues: 97.7266 Evaluate side-chains 307 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 283 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 248 ARG Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 353 ASN Chi-restraints excluded: chain b residue 266 LEU Chi-restraints excluded: chain b residue 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 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 Chi-restraints excluded: chain c residue 403 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.4980 chunk 45 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 ASN A 185 ASN B 131 HIS B 232 GLN ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 409 ASN ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 342 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9914 Z= 0.212 Angle : 0.718 15.277 13453 Z= 0.341 Chirality : 0.046 0.462 1682 Planarity : 0.003 0.045 1647 Dihedral : 8.530 59.723 2268 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.22 % Allowed : 24.50 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.32 (0.28), residues: 955 helix: 1.14 (0.30), residues: 331 sheet: -1.51 (0.42), residues: 147 loop : -0.68 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP b 370 HIS 0.008 0.001 HIS C 92 PHE 0.009 0.001 PHE B 157 TYR 0.027 0.002 TYR C 129 ARG 0.004 0.001 ARG a 282 *********************** 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 fitting. rotamer outliers: 29 poor density : 292 time to evaluate : 1.005 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: 0.9012 (tpp) cc_final: 0.8051 (tmm) REVERT: C 223 GLN cc_start: 0.8553 (pm20) cc_final: 0.8246 (pm20) REVERT: C 230 HIS cc_start: 0.6478 (m-70) cc_final: 0.6258 (m-70) REVERT: C 250 ARG cc_start: 0.8211 (mtp85) cc_final: 0.7820 (mtp85) REVERT: C 256 ARG cc_start: 0.6165 (tpt170) cc_final: 0.4382 (mmt180) REVERT: A 153 MET cc_start: 0.8496 (tpt) cc_final: 0.8264 (tpt) REVERT: A 217 TYR cc_start: 0.8399 (m-80) cc_final: 0.8135 (m-80) REVERT: A 248 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7344 (ttp-110) REVERT: B 76 GLU cc_start: 0.8202 (tp30) cc_final: 0.7903 (tp30) REVERT: B 134 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8773 (mtp) REVERT: B 235 ARG cc_start: 0.8533 (mtm-85) cc_final: 0.6938 (mtt-85) REVERT: B 256 ARG cc_start: 0.7030 (tpt-90) cc_final: 0.5065 (mtp85) REVERT: B 258 LEU cc_start: 0.8874 (tp) cc_final: 0.8624 (tp) REVERT: a 308 GLU cc_start: 0.8828 (mp0) cc_final: 0.8439 (mp0) REVERT: a 333 SER cc_start: 0.8487 (t) cc_final: 0.8146 (m) REVERT: a 410 MET cc_start: 0.8517 (tpp) cc_final: 0.8255 (tpt) REVERT: b 404 GLU cc_start: 0.8532 (tp30) cc_final: 0.8176 (tp30) REVERT: c 261 THR cc_start: 0.8895 (t) cc_final: 0.8663 (p) REVERT: c 286 ILE cc_start: 0.6754 (OUTLIER) cc_final: 0.6199 (tp) REVERT: c 308 GLU cc_start: 0.8019 (mp0) cc_final: 0.7488 (pm20) outliers start: 29 outliers final: 19 residues processed: 302 average time/residue: 0.2269 time to fit residues: 93.6972 Evaluate side-chains 306 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 284 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain a residue 353 ASN Chi-restraints excluded: chain b residue 266 LEU 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 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 108 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 105 optimal weight: 0.4980 chunk 63 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 ASN B 232 GLN ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 338 ASN c 342 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9914 Z= 0.263 Angle : 0.761 16.331 13453 Z= 0.363 Chirality : 0.048 0.471 1682 Planarity : 0.003 0.044 1647 Dihedral : 8.648 58.902 2268 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.33 % Allowed : 25.17 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.28), residues: 955 helix: 1.11 (0.30), residues: 332 sheet: -1.28 (0.46), residues: 120 loop : -0.72 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP b 370 HIS 0.007 0.001 HIS C 92 PHE 0.010 0.002 PHE a 262 TYR 0.026 0.002 TYR a 363 ARG 0.003 0.001 ARG b 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 318 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 288 time to evaluate : 1.049 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: 0.9037 (tpp) cc_final: 0.8069 (tmm) REVERT: C 223 GLN cc_start: 0.8624 (pm20) cc_final: 0.8302 (pm20) REVERT: C 250 ARG cc_start: 0.8117 (mtp85) cc_final: 0.7842 (mtp85) REVERT: C 256 ARG cc_start: 0.6217 (tpt170) cc_final: 0.4405 (mmt180) REVERT: A 153 MET cc_start: 0.8560 (tpt) cc_final: 0.8304 (tpt) REVERT: A 217 TYR cc_start: 0.8481 (m-80) cc_final: 0.8214 (m-80) REVERT: A 248 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7381 (ttp-110) REVERT: B 106 THR cc_start: 0.8752 (OUTLIER) cc_final: 0.8525 (m) REVERT: B 134 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8760 (mtp) REVERT: B 207 CYS cc_start: 0.6689 (t) cc_final: 0.6446 (t) REVERT: B 209 ASN cc_start: 0.8603 (t0) cc_final: 0.8300 (t0) REVERT: B 235 ARG cc_start: 0.8498 (mtm-85) cc_final: 0.7018 (mtt-85) REVERT: B 256 ARG cc_start: 0.7148 (tpt-90) cc_final: 0.5087 (mtp85) REVERT: B 258 LEU cc_start: 0.8932 (tp) cc_final: 0.8703 (tp) REVERT: a 308 GLU cc_start: 0.8880 (mp0) cc_final: 0.8496 (mp0) REVERT: a 333 SER cc_start: 0.8517 (t) cc_final: 0.8181 (m) REVERT: a 405 GLN cc_start: 0.9021 (tp40) cc_final: 0.8813 (tp-100) REVERT: a 410 MET cc_start: 0.8547 (tpp) cc_final: 0.8253 (tpt) REVERT: b 351 MET cc_start: 0.8526 (tmm) cc_final: 0.8307 (tmm) REVERT: b 404 GLU cc_start: 0.8564 (tp30) cc_final: 0.8256 (tp30) REVERT: c 261 THR cc_start: 0.8926 (t) cc_final: 0.8717 (p) REVERT: c 286 ILE cc_start: 0.6972 (OUTLIER) cc_final: 0.6306 (tp) REVERT: c 308 GLU cc_start: 0.8103 (mp0) cc_final: 0.7527 (pm20) REVERT: c 351 MET cc_start: 0.8514 (mmp) cc_final: 0.8246 (tpp) outliers start: 30 outliers final: 19 residues processed: 296 average time/residue: 0.2337 time to fit residues: 94.5368 Evaluate side-chains 307 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 284 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain a residue 353 ASN Chi-restraints excluded: chain b residue 266 LEU 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 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 68 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 0.0970 chunk 74 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 ASN B 232 GLN ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 342 ASN ** c 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9914 Z= 0.250 Angle : 0.765 16.149 13453 Z= 0.366 Chirality : 0.048 0.476 1682 Planarity : 0.003 0.040 1647 Dihedral : 8.637 59.187 2268 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.66 % Allowed : 25.94 % Favored : 71.40 % 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: -0.29 (0.28), residues: 955 helix: 1.05 (0.30), residues: 332 sheet: -1.24 (0.46), residues: 120 loop : -0.73 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP b 370 HIS 0.008 0.001 HIS C 92 PHE 0.010 0.001 PHE a 293 TYR 0.024 0.002 TYR a 371 ARG 0.003 0.001 ARG a 282 ********************** 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 311 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 287 time to evaluate : 1.025 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: 0.8989 (tpp) cc_final: 0.8051 (tmm) REVERT: C 223 GLN cc_start: 0.8584 (pm20) cc_final: 0.8243 (pm20) REVERT: C 250 ARG cc_start: 0.8110 (mtp85) cc_final: 0.7910 (mtp85) REVERT: C 256 ARG cc_start: 0.6186 (tpt170) cc_final: 0.4398 (mmt180) REVERT: A 153 MET cc_start: 0.8546 (tpt) cc_final: 0.8292 (tpt) REVERT: A 217 TYR cc_start: 0.8479 (m-80) cc_final: 0.8205 (m-80) REVERT: A 248 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.7345 (ttp-110) REVERT: B 106 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8512 (m) REVERT: B 134 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8756 (mtp) REVERT: B 207 CYS cc_start: 0.6639 (t) cc_final: 0.6393 (t) REVERT: B 235 ARG cc_start: 0.8519 (mtm-85) cc_final: 0.7028 (mtt-85) REVERT: B 256 ARG cc_start: 0.7118 (tpt-90) cc_final: 0.5057 (mtp85) REVERT: a 308 GLU cc_start: 0.8854 (mp0) cc_final: 0.8461 (mp0) REVERT: a 333 SER cc_start: 0.8512 (t) cc_final: 0.8157 (m) REVERT: a 405 GLN cc_start: 0.9028 (tp40) cc_final: 0.8826 (tp-100) REVERT: a 410 MET cc_start: 0.8556 (tpp) cc_final: 0.8264 (tpt) REVERT: c 286 ILE cc_start: 0.7314 (OUTLIER) cc_final: 0.6581 (tp) REVERT: c 308 GLU cc_start: 0.8109 (mp0) cc_final: 0.7512 (pm20) REVERT: c 351 MET cc_start: 0.8508 (mmp) cc_final: 0.8215 (tpp) REVERT: c 414 MET cc_start: 0.6240 (tmm) cc_final: 0.5968 (tmm) outliers start: 24 outliers final: 18 residues processed: 293 average time/residue: 0.2370 time to fit residues: 94.3771 Evaluate side-chains 304 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 282 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 155 CYS Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain b residue 266 LEU 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 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 28 optimal weight: 0.9980 chunk 86 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 96 optimal weight: 0.2980 chunk 11 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN A 185 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.131552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.112720 restraints weight = 21513.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.115776 restraints weight = 11491.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.117869 restraints weight = 7616.163| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3594 r_free = 0.3594 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3594 r_free = 0.3594 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 9914 Z= 0.295 Angle : 0.795 16.108 13453 Z= 0.380 Chirality : 0.049 0.481 1682 Planarity : 0.004 0.039 1647 Dihedral : 8.759 58.681 2268 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.88 % Allowed : 26.61 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (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: -0.37 (0.28), residues: 955 helix: 0.97 (0.30), residues: 332 sheet: -1.24 (0.47), residues: 120 loop : -0.78 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP b 370 HIS 0.008 0.001 HIS C 92 PHE 0.009 0.002 PHE a 262 TYR 0.025 0.002 TYR C 66 ARG 0.006 0.001 ARG b 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2546.69 seconds wall clock time: 47 minutes 20.20 seconds (2840.20 seconds total)