Starting phenix.real_space_refine on Tue Nov 19 01:44:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sux_40779/11_2024/8sux_40779.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sux_40779/11_2024/8sux_40779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sux_40779/11_2024/8sux_40779.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sux_40779/11_2024/8sux_40779.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sux_40779/11_2024/8sux_40779.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sux_40779/11_2024/8sux_40779.cif" } resolution = 2.93 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= 0.114 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 90 5.16 5 C 11434 2.51 5 N 3200 2.21 5 O 3365 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 18101 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3032 Classifications: {'peptide': 375} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 360} Chain breaks: 1 Chain: "B" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 3010 Classifications: {'peptide': 372} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 357} Chain breaks: 2 Chain: "C" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3019 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 361} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2934 Classifications: {'peptide': 364} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 349} Chain breaks: 2 Chain: "E" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3019 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 361} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 2963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2963 Classifications: {'peptide': 368} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 353} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.94, per 1000 atoms: 0.60 Number of scatterers: 18101 At special positions: 0 Unit cell: (129.92, 116.48, 136.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 90 16.00 P 12 15.00 O 3365 8.00 N 3200 7.00 C 11434 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.47 Conformation dependent library (CDL) restraints added in 1.8 seconds 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4264 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 23 sheets defined 43.5% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'A' and resid 35 through 52 Proline residue: A 49 - end of helix Processing helix chain 'A' and resid 53 through 58 removed outlier: 6.763A pdb=" N ALA A 56 " --> pdb=" O GLY A 53 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 58 " --> pdb=" O ASP A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 66 removed outlier: 3.818A pdb=" N LEU A 65 " --> pdb=" O ASP A 62 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA A 66 " --> pdb=" O LYS A 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 66' Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 118 through 136 removed outlier: 3.810A pdb=" N ALA A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 157 removed outlier: 3.750A pdb=" N LEU A 157 " --> pdb=" O THR A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 184 removed outlier: 3.703A pdb=" N PHE A 177 " --> pdb=" O ASN A 174 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ARG A 179 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU A 180 " --> pdb=" O PHE A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 217 removed outlier: 3.733A pdb=" N PHE A 196 " --> pdb=" O ASN A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 251 removed outlier: 4.249A pdb=" N LEU A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A 246 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N GLN A 248 " --> pdb=" O CYS A 244 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N VAL A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 281 through 302 removed outlier: 3.688A pdb=" N ILE A 294 " --> pdb=" O MET A 290 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG A 297 " --> pdb=" O ASP A 293 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN A 302 " --> pdb=" O CYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 333 through 342 Processing helix chain 'A' and resid 355 through 360 removed outlier: 4.516A pdb=" N THR A 359 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'B' and resid 35 through 53 Proline residue: B 49 - end of helix Processing helix chain 'B' and resid 54 through 58 removed outlier: 3.684A pdb=" N LEU B 58 " --> pdb=" O ASP B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 72 Processing helix chain 'B' and resid 118 through 136 removed outlier: 3.728A pdb=" N LEU B 124 " --> pdb=" O MET B 120 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 157 removed outlier: 3.598A pdb=" N LEU B 157 " --> pdb=" O THR B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 184 removed outlier: 3.769A pdb=" N PHE B 177 " --> pdb=" O ASN B 174 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ARG B 179 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU B 180 " --> pdb=" O PHE B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 217 removed outlier: 3.777A pdb=" N PHE B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 217 " --> pdb=" O THR B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 247 removed outlier: 3.971A pdb=" N GLN B 229 " --> pdb=" O GLY B 225 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 280 No H-bonds generated for 'chain 'B' and resid 278 through 280' Processing helix chain 'B' and resid 281 through 302 removed outlier: 3.708A pdb=" N ILE B 294 " --> pdb=" O MET B 290 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG B 297 " --> pdb=" O ASP B 293 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN B 302 " --> pdb=" O CYS B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 332 Processing helix chain 'B' and resid 333 through 342 Processing helix chain 'B' and resid 361 through 363 No H-bonds generated for 'chain 'B' and resid 361 through 363' Processing helix chain 'C' and resid 34 through 46 removed outlier: 3.571A pdb=" N THR C 38 " --> pdb=" O ALA C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 52 removed outlier: 3.613A pdb=" N ILE C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 60 removed outlier: 6.697A pdb=" N ALA C 56 " --> pdb=" O GLY C 53 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 59 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 72 removed outlier: 3.547A pdb=" N LEU C 72 " --> pdb=" O THR C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 136 removed outlier: 3.596A pdb=" N ALA C 122 " --> pdb=" O ASP C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 184 Processing helix chain 'C' and resid 193 through 217 removed outlier: 3.734A pdb=" N TRP C 199 " --> pdb=" O GLN C 195 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 217 " --> pdb=" O THR C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 221 Processing helix chain 'C' and resid 224 through 251 removed outlier: 4.052A pdb=" N LEU C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLN C 248 " --> pdb=" O CYS C 244 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL C 249 " --> pdb=" O LEU C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 262 Processing helix chain 'C' and resid 278 through 280 No H-bonds generated for 'chain 'C' and resid 278 through 280' Processing helix chain 'C' and resid 281 through 302 removed outlier: 4.096A pdb=" N ARG C 297 " --> pdb=" O ASP C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 332 Processing helix chain 'C' and resid 333 through 342 Processing helix chain 'C' and resid 355 through 360 removed outlier: 3.915A pdb=" N VAL C 360 " --> pdb=" O LEU C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 363 No H-bonds generated for 'chain 'C' and resid 361 through 363' Processing helix chain 'D' and resid 36 through 53 Proline residue: D 49 - end of helix removed outlier: 3.836A pdb=" N GLY D 53 " --> pdb=" O PRO D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 60 removed outlier: 3.725A pdb=" N LEU D 58 " --> pdb=" O ASP D 55 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL D 60 " --> pdb=" O SER D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 72 Processing helix chain 'D' and resid 118 through 137 removed outlier: 3.549A pdb=" N ALA D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU D 137 " --> pdb=" O LYS D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 181 Processing helix chain 'D' and resid 182 through 184 No H-bonds generated for 'chain 'D' and resid 182 through 184' Processing helix chain 'D' and resid 192 through 217 removed outlier: 3.895A pdb=" N PHE D 196 " --> pdb=" O ASN D 192 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER D 217 " --> pdb=" O THR D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 247 removed outlier: 3.579A pdb=" N ARG D 230 " --> pdb=" O VAL D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 302 Processing helix chain 'D' and resid 308 through 313 Processing helix chain 'D' and resid 329 through 332 removed outlier: 3.672A pdb=" N GLN D 332 " --> pdb=" O ALA D 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 329 through 332' Processing helix chain 'D' and resid 333 through 342 Processing helix chain 'D' and resid 353 through 359 removed outlier: 4.357A pdb=" N THR D 359 " --> pdb=" O VAL D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 363 No H-bonds generated for 'chain 'D' and resid 361 through 363' Processing helix chain 'E' and resid 35 through 46 Processing helix chain 'E' and resid 47 through 53 removed outlier: 3.722A pdb=" N ILE E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY E 53 " --> pdb=" O PRO E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 66 removed outlier: 3.607A pdb=" N ALA E 66 " --> pdb=" O LYS E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 72 Processing helix chain 'E' and resid 118 through 137 removed outlier: 3.629A pdb=" N ALA E 122 " --> pdb=" O ASP E 118 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU E 137 " --> pdb=" O LYS E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 184 Processing helix chain 'E' and resid 192 through 215 removed outlier: 4.002A pdb=" N PHE E 196 " --> pdb=" O ASN E 192 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU E 215 " --> pdb=" O GLN E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 219 removed outlier: 6.262A pdb=" N SER E 219 " --> pdb=" O GLU E 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 216 through 219' Processing helix chain 'E' and resid 220 through 247 removed outlier: 5.120A pdb=" N VAL E 226 " --> pdb=" O LEU E 222 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ARG E 227 " --> pdb=" O LYS E 223 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE E 235 " --> pdb=" O MET E 231 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU E 245 " --> pdb=" O ALA E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 262 Processing helix chain 'E' and resid 278 through 280 No H-bonds generated for 'chain 'E' and resid 278 through 280' Processing helix chain 'E' and resid 281 through 302 removed outlier: 3.836A pdb=" N ARG E 297 " --> pdb=" O ASP E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 332 Processing helix chain 'E' and resid 333 through 342 removed outlier: 3.632A pdb=" N SER E 337 " --> pdb=" O GLN E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 359 Processing helix chain 'E' and resid 361 through 363 No H-bonds generated for 'chain 'E' and resid 361 through 363' Processing helix chain 'F' and resid 36 through 47 Processing helix chain 'F' and resid 47 through 53 removed outlier: 3.875A pdb=" N ILE F 51 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY F 53 " --> pdb=" O PRO F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 66 removed outlier: 3.616A pdb=" N LEU F 65 " --> pdb=" O ASP F 62 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA F 66 " --> pdb=" O LYS F 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 66' Processing helix chain 'F' and resid 68 through 72 Processing helix chain 'F' and resid 118 through 136 removed outlier: 3.782A pdb=" N ALA F 122 " --> pdb=" O ASP F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 181 Processing helix chain 'F' and resid 192 through 217 removed outlier: 3.910A pdb=" N PHE F 196 " --> pdb=" O ASN F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 247 removed outlier: 3.670A pdb=" N GLN F 229 " --> pdb=" O GLY F 225 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ARG F 230 " --> pdb=" O VAL F 226 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 280 No H-bonds generated for 'chain 'F' and resid 278 through 280' Processing helix chain 'F' and resid 281 through 302 Processing helix chain 'F' and resid 333 through 342 Processing helix chain 'F' and resid 353 through 360 removed outlier: 3.604A pdb=" N SER F 358 " --> pdb=" O GLN F 355 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR F 359 " --> pdb=" O VAL F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 363 No H-bonds generated for 'chain 'F' and resid 361 through 363' Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 20 removed outlier: 6.550A pdb=" N LYS A 15 " --> pdb=" O ASN A 10 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR A 94 " --> pdb=" O ASP A 4 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU A 6 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR A 92 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LEU A 8 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LYS A 90 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 148 through 152 removed outlier: 6.474A pdb=" N GLY A 315 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE A 348 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL A 317 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N THR A 350 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE A 319 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N THR A 26 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N THR A 351 " --> pdb=" O THR A 26 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LEU A 28 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N ARG A 366 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE A 27 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LEU A 368 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL A 29 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N GLN A 370 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 74 through 77 Processing sheet with id=AA4, first strand: chain 'A' and resid 253 through 258 removed outlier: 5.417A pdb=" N ASP A 254 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER A 268 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 20 removed outlier: 5.433A pdb=" N ILE B 3 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLU B 96 " --> pdb=" O ILE B 3 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 152 removed outlier: 6.365A pdb=" N GLY B 315 " --> pdb=" O GLN B 346 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ILE B 348 " --> pdb=" O GLY B 315 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL B 317 " --> pdb=" O ILE B 348 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N THR B 350 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ILE B 319 " --> pdb=" O THR B 350 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR B 26 " --> pdb=" O VAL B 349 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N THR B 351 " --> pdb=" O THR B 26 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N LEU B 28 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N ARG B 366 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE B 27 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU B 368 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL B 29 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 9.806A pdb=" N GLN B 370 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 74 through 77 Processing sheet with id=AA8, first strand: chain 'B' and resid 255 through 258 Processing sheet with id=AA9, first strand: chain 'C' and resid 16 through 20 removed outlier: 5.212A pdb=" N ILE C 3 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLU C 96 " --> pdb=" O ILE C 3 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 148 through 152 removed outlier: 6.285A pdb=" N GLY C 315 " --> pdb=" O GLN C 346 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE C 348 " --> pdb=" O GLY C 315 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL C 317 " --> pdb=" O ILE C 348 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N THR C 350 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE C 319 " --> pdb=" O THR C 350 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N THR C 26 " --> pdb=" O VAL C 349 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 73 through 75 removed outlier: 4.437A pdb=" N ARG C 73 " --> pdb=" O SER C 86 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU C 84 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 253 through 258 removed outlier: 5.500A pdb=" N ASP C 254 " --> pdb=" O SER C 268 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER C 268 " --> pdb=" O ASP C 254 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER C 258 " --> pdb=" O GLN C 264 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN C 264 " --> pdb=" O SER C 258 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 17 through 19 removed outlier: 3.566A pdb=" N GLY D 95 " --> pdb=" O ALA D 103 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA D 103 " --> pdb=" O GLY D 95 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N MET D 106 " --> pdb=" O GLU D 117 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N GLU D 117 " --> pdb=" O MET D 106 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASP D 108 " --> pdb=" O PRO D 115 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG D 110 " --> pdb=" O GLN D 113 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 148 through 152 removed outlier: 6.300A pdb=" N GLY D 315 " --> pdb=" O GLN D 346 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ILE D 348 " --> pdb=" O GLY D 315 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL D 317 " --> pdb=" O ILE D 348 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N THR D 350 " --> pdb=" O VAL D 317 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE D 319 " --> pdb=" O THR D 350 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N THR D 26 " --> pdb=" O VAL D 349 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ARG D 366 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE D 27 " --> pdb=" O ARG D 366 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU D 368 " --> pdb=" O ILE D 27 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 74 through 77 Processing sheet with id=AB7, first strand: chain 'D' and resid 253 through 258 removed outlier: 5.425A pdb=" N ASP D 254 " --> pdb=" O SER D 268 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER D 268 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 16 through 20 removed outlier: 7.096A pdb=" N THR E 94 " --> pdb=" O ASP E 4 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU E 6 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR E 92 " --> pdb=" O LEU E 6 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU E 8 " --> pdb=" O LYS E 90 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS E 90 " --> pdb=" O LEU E 8 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 148 through 152 removed outlier: 6.092A pdb=" N LEU E 148 " --> pdb=" O ILE E 316 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LEU E 318 " --> pdb=" O LEU E 148 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU E 150 " --> pdb=" O LEU E 318 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N ASP E 320 " --> pdb=" O LEU E 150 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU E 152 " --> pdb=" O ASP E 320 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLY E 315 " --> pdb=" O GLN E 346 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ILE E 348 " --> pdb=" O GLY E 315 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL E 317 " --> pdb=" O ILE E 348 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N THR E 350 " --> pdb=" O VAL E 317 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ILE E 319 " --> pdb=" O THR E 350 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N THR E 26 " --> pdb=" O VAL E 349 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 253 through 258 removed outlier: 5.341A pdb=" N ASP E 254 " --> pdb=" O SER E 268 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N SER E 268 " --> pdb=" O ASP E 254 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER E 258 " --> pdb=" O GLN E 264 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN E 264 " --> pdb=" O SER E 258 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY E 273 " --> pdb=" O HIS E 269 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 16 through 20 removed outlier: 6.918A pdb=" N THR F 94 " --> pdb=" O ASP F 4 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU F 6 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR F 92 " --> pdb=" O LEU F 6 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU F 8 " --> pdb=" O LYS F 90 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LYS F 90 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS F 101 " --> pdb=" O TRP F 97 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 148 through 152 removed outlier: 6.258A pdb=" N GLY F 315 " --> pdb=" O GLN F 346 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE F 348 " --> pdb=" O GLY F 315 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL F 317 " --> pdb=" O ILE F 348 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N THR F 350 " --> pdb=" O VAL F 317 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ILE F 319 " --> pdb=" O THR F 350 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N THR F 26 " --> pdb=" O VAL F 349 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N THR F 351 " --> pdb=" O THR F 26 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LEU F 28 " --> pdb=" O THR F 351 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ARG F 366 " --> pdb=" O ILE F 25 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE F 27 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU F 368 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL F 29 " --> pdb=" O LEU F 368 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 74 through 76 Processing sheet with id=AC5, first strand: chain 'F' and resid 253 through 258 removed outlier: 5.442A pdb=" N ASP F 254 " --> pdb=" O SER F 268 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER F 268 " --> pdb=" O ASP F 254 " (cutoff:3.500A) 794 hydrogen bonds defined for protein. 2139 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: 5.60 Time building geometry restraints manager: 5.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5995 1.34 - 1.46: 3260 1.46 - 1.57: 9049 1.57 - 1.69: 20 1.69 - 1.81: 156 Bond restraints: 18480 Sorted by residual: bond pdb=" CB ARG A 285 " pdb=" CG ARG A 285 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.18e+00 bond pdb=" CB VAL C 291 " pdb=" CG2 VAL C 291 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.73e-01 bond pdb=" CA GLN F 78 " pdb=" CB GLN F 78 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.69e-01 bond pdb=" CG1 ILE B 212 " pdb=" CD1 ILE B 212 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.40e-01 bond pdb=" CB PRO D 88 " pdb=" CG PRO D 88 " ideal model delta sigma weight residual 1.506 1.538 -0.032 3.90e-02 6.57e+02 6.61e-01 ... (remaining 18475 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 24900 2.54 - 5.08: 126 5.08 - 7.62: 12 7.62 - 10.16: 2 10.16 - 12.70: 1 Bond angle restraints: 25041 Sorted by residual: angle pdb=" C LEU E 305 " pdb=" N GLN E 306 " pdb=" CA GLN E 306 " ideal model delta sigma weight residual 121.54 128.97 -7.43 1.91e+00 2.74e-01 1.51e+01 angle pdb=" CA LEU A 124 " pdb=" CB LEU A 124 " pdb=" CG LEU A 124 " ideal model delta sigma weight residual 116.30 129.00 -12.70 3.50e+00 8.16e-02 1.32e+01 angle pdb=" C LEU D 305 " pdb=" N GLN D 306 " pdb=" CA GLN D 306 " ideal model delta sigma weight residual 121.54 128.22 -6.68 1.91e+00 2.74e-01 1.22e+01 angle pdb=" C ARG F 77 " pdb=" N GLN F 78 " pdb=" CA GLN F 78 " ideal model delta sigma weight residual 121.54 127.90 -6.36 1.91e+00 2.74e-01 1.11e+01 angle pdb=" C LEU F 305 " pdb=" N GLN F 306 " pdb=" CA GLN F 306 " ideal model delta sigma weight residual 121.54 127.56 -6.02 1.91e+00 2.74e-01 9.95e+00 ... (remaining 25036 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 9965 17.92 - 35.85: 1030 35.85 - 53.77: 183 53.77 - 71.69: 59 71.69 - 89.62: 26 Dihedral angle restraints: 11263 sinusoidal: 4721 harmonic: 6542 Sorted by residual: dihedral pdb=" CA LEU E 245 " pdb=" C LEU E 245 " pdb=" N THR E 246 " pdb=" CA THR E 246 " ideal model delta harmonic sigma weight residual -180.00 -159.11 -20.89 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA LEU D 305 " pdb=" C LEU D 305 " pdb=" N GLN D 306 " pdb=" CA GLN D 306 " ideal model delta harmonic sigma weight residual 180.00 159.64 20.36 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA THR C 246 " pdb=" C THR C 246 " pdb=" N GLN C 247 " pdb=" CA GLN C 247 " ideal model delta harmonic sigma weight residual -180.00 -160.15 -19.85 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 11260 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1566 0.029 - 0.057: 771 0.057 - 0.086: 276 0.086 - 0.115: 122 0.115 - 0.143: 34 Chirality restraints: 2769 Sorted by residual: chirality pdb=" CA ILE A 91 " pdb=" N ILE A 91 " pdb=" C ILE A 91 " pdb=" CB ILE A 91 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE E 91 " pdb=" N ILE E 91 " pdb=" C ILE E 91 " pdb=" CB ILE E 91 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA VAL C 266 " pdb=" N VAL C 266 " pdb=" C VAL C 266 " pdb=" CB VAL C 266 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 2766 not shown) Planarity restraints: 3195 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 327 " -0.034 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO D 328 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 328 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 328 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 48 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO E 49 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 49 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 49 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 30 " -0.032 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO C 31 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 31 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 31 " -0.028 5.00e-02 4.00e+02 ... (remaining 3192 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 438 2.71 - 3.26: 16908 3.26 - 3.81: 26793 3.81 - 4.35: 34009 4.35 - 4.90: 59820 Nonbonded interactions: 137968 Sorted by model distance: nonbonded pdb=" OG1 THR B 37 " pdb=" O3G ATP B 501 " model vdw 2.166 3.040 nonbonded pdb=" O CYS E 244 " pdb=" OG SER E 337 " model vdw 2.185 3.040 nonbonded pdb=" OG1 THR D 37 " pdb=" O3G ATP D 501 " model vdw 2.194 3.040 nonbonded pdb=" O PRO C 147 " pdb=" OH TYR C 183 " model vdw 2.195 3.040 nonbonded pdb=" O SER A 178 " pdb=" OG SER A 181 " model vdw 2.205 3.040 ... (remaining 137963 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 1 through 159 or resid 172 through 218 or resid 225 throug \ h 382)) selection = (chain 'B' and (resid 1 through 159 or resid 172 through 218 or resid 225 throug \ h 382)) selection = (chain 'C' and (resid 1 through 159 or resid 172 through 218 or resid 225 throug \ h 382)) selection = (chain 'D' and resid 1 through 382) selection = (chain 'E' and (resid 1 through 159 or resid 172 through 218 or resid 225 throug \ h 382)) selection = (chain 'F' and (resid 1 through 159 or resid 172 through 218 or resid 225 throug \ h 382)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 0.660 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 40.220 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 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 : 0.003 0.034 18480 Z= 0.211 Angle : 0.534 12.705 25041 Z= 0.292 Chirality : 0.042 0.143 2769 Planarity : 0.005 0.051 3195 Dihedral : 15.607 89.617 6999 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.31 (0.17), residues: 2201 helix: 1.08 (0.19), residues: 765 sheet: -0.27 (0.22), residues: 503 loop : -1.22 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 199 HIS 0.006 0.001 HIS E 327 PHE 0.032 0.001 PHE C 296 TYR 0.012 0.001 TYR B 200 ARG 0.003 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 1.568 Fit side-chains REVERT: A 15 LYS cc_start: 0.8214 (tttt) cc_final: 0.7928 (tttm) REVERT: A 41 ASP cc_start: 0.7138 (m-30) cc_final: 0.6861 (m-30) REVERT: A 57 SER cc_start: 0.7928 (p) cc_final: 0.7575 (m) REVERT: A 59 TYR cc_start: 0.7908 (m-80) cc_final: 0.7486 (m-80) REVERT: A 63 LYS cc_start: 0.7663 (mttm) cc_final: 0.7226 (mtpt) REVERT: A 110 ARG cc_start: 0.7179 (ttm110) cc_final: 0.6626 (ttm170) REVERT: A 129 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6998 (mt-10) REVERT: A 133 LYS cc_start: 0.7446 (ttpp) cc_final: 0.6113 (mmtt) REVERT: A 134 ARG cc_start: 0.7262 (mmm-85) cc_final: 0.6911 (mtm-85) REVERT: A 137 GLU cc_start: 0.6876 (tt0) cc_final: 0.6376 (mt-10) REVERT: A 231 MET cc_start: 0.8323 (mtm) cc_final: 0.7927 (mtp) REVERT: A 256 GLU cc_start: 0.8507 (pt0) cc_final: 0.8224 (pt0) REVERT: A 290 MET cc_start: 0.8130 (ttp) cc_final: 0.7860 (ttm) REVERT: A 334 ILE cc_start: 0.8008 (tt) cc_final: 0.7681 (pt) REVERT: A 361 LYS cc_start: 0.8340 (mttm) cc_final: 0.7501 (ptmm) REVERT: A 362 ARG cc_start: 0.8062 (ptm160) cc_final: 0.7848 (ttp80) REVERT: A 377 LYS cc_start: 0.7202 (mtpt) cc_final: 0.6429 (tptp) REVERT: B 1 MET cc_start: 0.5957 (ptp) cc_final: 0.5400 (mtm) REVERT: B 18 ASP cc_start: 0.7731 (m-30) cc_final: 0.7521 (m-30) REVERT: B 70 GLU cc_start: 0.7511 (mp0) cc_final: 0.7063 (mt-10) REVERT: B 110 ARG cc_start: 0.7278 (ttm110) cc_final: 0.6614 (ttm170) REVERT: B 129 GLU cc_start: 0.7324 (mt-10) cc_final: 0.6927 (mt-10) REVERT: B 133 LYS cc_start: 0.7408 (ttmm) cc_final: 0.6255 (mmtt) REVERT: B 154 THR cc_start: 0.8675 (m) cc_final: 0.8465 (p) REVERT: B 236 GLN cc_start: 0.7275 (tm-30) cc_final: 0.6587 (mt0) REVERT: B 256 GLU cc_start: 0.7534 (mt-10) cc_final: 0.6134 (mp0) REVERT: B 262 ASN cc_start: 0.8253 (t0) cc_final: 0.7876 (m-40) REVERT: B 290 MET cc_start: 0.8058 (ttp) cc_final: 0.7798 (ttm) REVERT: B 312 LYS cc_start: 0.7930 (mttm) cc_final: 0.7688 (mttt) REVERT: B 324 MET cc_start: 0.7373 (mtm) cc_final: 0.6366 (mmm) REVERT: B 362 ARG cc_start: 0.8429 (ptm160) cc_final: 0.8007 (ttp80) REVERT: B 373 ASN cc_start: 0.7983 (m-40) cc_final: 0.7697 (m-40) REVERT: C 5 LYS cc_start: 0.7977 (tttp) cc_final: 0.7432 (tptm) REVERT: C 16 GLN cc_start: 0.7819 (tt0) cc_final: 0.7393 (tm130) REVERT: C 23 GLU cc_start: 0.6883 (tt0) cc_final: 0.6519 (tt0) REVERT: C 77 ARG cc_start: 0.7082 (mtt-85) cc_final: 0.6404 (mtm-85) REVERT: C 78 GLN cc_start: 0.7557 (tm-30) cc_final: 0.7101 (tp-100) REVERT: C 110 ARG cc_start: 0.7126 (mtt-85) cc_final: 0.6696 (mmt180) REVERT: C 145 GLU cc_start: 0.6566 (pm20) cc_final: 0.6296 (pt0) REVERT: C 244 CYS cc_start: 0.7147 (t) cc_final: 0.6535 (m) REVERT: C 361 LYS cc_start: 0.7879 (mttm) cc_final: 0.7446 (ptpp) REVERT: C 377 LYS cc_start: 0.7643 (mtmm) cc_final: 0.6845 (tmtt) REVERT: D 214 GLN cc_start: 0.6932 (tt0) cc_final: 0.6729 (tt0) REVERT: D 233 GLU cc_start: 0.5402 (mt-10) cc_final: 0.4980 (mm-30) REVERT: D 314 GLN cc_start: 0.7924 (mt0) cc_final: 0.7600 (mt0) REVERT: E 5 LYS cc_start: 0.7494 (ptmt) cc_final: 0.6781 (ptpt) REVERT: E 16 GLN cc_start: 0.7990 (pt0) cc_final: 0.7567 (pm20) REVERT: E 75 ILE cc_start: 0.8055 (pt) cc_final: 0.7496 (mp) REVERT: E 77 ARG cc_start: 0.7277 (mtp180) cc_final: 0.6489 (mtm-85) REVERT: E 84 GLU cc_start: 0.7338 (tp30) cc_final: 0.6637 (mm-30) REVERT: E 106 MET cc_start: 0.7704 (ttm) cc_final: 0.7324 (tmm) REVERT: E 112 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6989 (mp0) REVERT: E 312 LYS cc_start: 0.7460 (mmtp) cc_final: 0.6836 (mttp) REVERT: E 324 MET cc_start: 0.8167 (ttp) cc_final: 0.7852 (ttm) REVERT: E 363 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7596 (mp0) REVERT: E 377 LYS cc_start: 0.7385 (mttp) cc_final: 0.6513 (mptt) REVERT: F 4 ASP cc_start: 0.7947 (m-30) cc_final: 0.7642 (m-30) REVERT: F 214 GLN cc_start: 0.6411 (tm-30) cc_final: 0.6105 (tt0) REVERT: F 261 HIS cc_start: 0.7727 (m90) cc_final: 0.5828 (t70) REVERT: F 262 ASN cc_start: 0.7332 (t0) cc_final: 0.6957 (t0) REVERT: F 267 MET cc_start: 0.8641 (mtt) cc_final: 0.8199 (mmt) REVERT: F 278 SER cc_start: 0.8407 (t) cc_final: 0.8054 (p) REVERT: F 323 ASP cc_start: 0.7517 (p0) cc_final: 0.7238 (p0) outliers start: 0 outliers final: 1 residues processed: 405 average time/residue: 1.5365 time to fit residues: 689.0873 Evaluate side-chains 262 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 261 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 9.9990 chunk 166 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 112 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 172 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 199 optimal weight: 8.9990 overall best weight: 6.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN A 210 HIS A 236 GLN A 253 HIS ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 HIS B 263 GLN B 307 ASN B 314 GLN C 352 HIS D 16 GLN D 130 GLN D 253 HIS D 302 ASN D 332 GLN D 344 GLN E 130 GLN F 302 ASN F 307 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.110 18480 Z= 0.796 Angle : 0.998 15.893 25041 Z= 0.505 Chirality : 0.060 0.288 2769 Planarity : 0.009 0.131 3195 Dihedral : 10.002 88.984 2549 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.59 % Favored : 95.37 % Rotamer: Outliers : 3.23 % Allowed : 11.55 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.20 (0.17), residues: 2201 helix: 0.12 (0.18), residues: 767 sheet: -0.67 (0.22), residues: 491 loop : -1.57 (0.18), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP F 158 HIS 0.018 0.003 HIS A 269 PHE 0.053 0.004 PHE A 296 TYR 0.021 0.003 TYR B 163 ARG 0.019 0.001 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 256 time to evaluate : 2.216 Fit side-chains REVERT: A 8 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7519 (mp) REVERT: A 18 ASP cc_start: 0.7848 (m-30) cc_final: 0.7638 (m-30) REVERT: A 59 TYR cc_start: 0.8028 (m-80) cc_final: 0.7327 (m-80) REVERT: A 63 LYS cc_start: 0.7856 (mttm) cc_final: 0.7367 (mtpt) REVERT: A 110 ARG cc_start: 0.7319 (ttm110) cc_final: 0.6637 (ttm170) REVERT: A 133 LYS cc_start: 0.7825 (ttpp) cc_final: 0.6273 (mmtt) REVERT: A 134 ARG cc_start: 0.7522 (mmm-85) cc_final: 0.7057 (mtm-85) REVERT: A 248 GLN cc_start: 0.8326 (tm-30) cc_final: 0.8059 (tt0) REVERT: A 256 GLU cc_start: 0.8711 (pt0) cc_final: 0.8472 (pt0) REVERT: A 308 ASP cc_start: 0.8119 (m-30) cc_final: 0.7804 (m-30) REVERT: A 334 ILE cc_start: 0.8209 (tt) cc_final: 0.7717 (pt) REVERT: B 110 ARG cc_start: 0.7592 (ttm110) cc_final: 0.6689 (ttt180) REVERT: B 120 MET cc_start: 0.7980 (mmp) cc_final: 0.7772 (mmm) REVERT: B 129 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7142 (mt-10) REVERT: B 133 LYS cc_start: 0.7577 (ttmm) cc_final: 0.6377 (mmtt) REVERT: B 236 GLN cc_start: 0.7823 (tm-30) cc_final: 0.7160 (mt0) REVERT: B 308 ASP cc_start: 0.7995 (m-30) cc_final: 0.7765 (m-30) REVERT: B 324 MET cc_start: 0.7656 (mtm) cc_final: 0.6678 (mmm) REVERT: B 336 GLN cc_start: 0.7930 (tp-100) cc_final: 0.7655 (tp40) REVERT: B 362 ARG cc_start: 0.8600 (ptm160) cc_final: 0.8384 (ptm-80) REVERT: B 373 ASN cc_start: 0.7831 (m-40) cc_final: 0.7624 (m110) REVERT: C 77 ARG cc_start: 0.7255 (mtt-85) cc_final: 0.6438 (mtp-110) REVERT: C 110 ARG cc_start: 0.7180 (mtt-85) cc_final: 0.6732 (mtp85) REVERT: C 112 GLU cc_start: 0.7346 (mm-30) cc_final: 0.6644 (mp0) REVERT: C 145 GLU cc_start: 0.6766 (pm20) cc_final: 0.5952 (mm-30) REVERT: C 190 THR cc_start: 0.7406 (m) cc_final: 0.7142 (p) REVERT: C 192 ASN cc_start: 0.7100 (p0) cc_final: 0.6767 (p0) REVERT: C 244 CYS cc_start: 0.7618 (t) cc_final: 0.6889 (m) REVERT: C 282 ASP cc_start: 0.7882 (m-30) cc_final: 0.7612 (m-30) REVERT: C 311 LEU cc_start: 0.8000 (mp) cc_final: 0.7785 (mp) REVERT: C 377 LYS cc_start: 0.7850 (mtmm) cc_final: 0.6636 (tppt) REVERT: D 106 MET cc_start: 0.6344 (OUTLIER) cc_final: 0.6074 (tpp) REVERT: D 120 MET cc_start: 0.5532 (tpp) cc_final: 0.5294 (ttt) REVERT: D 197 GLU cc_start: 0.6942 (tm-30) cc_final: 0.6708 (mt-10) REVERT: D 247 GLN cc_start: 0.7697 (tt0) cc_final: 0.7469 (tt0) REVERT: D 271 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.6985 (mt0) REVERT: D 355 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7124 (mp10) REVERT: E 77 ARG cc_start: 0.7454 (mtp180) cc_final: 0.6189 (mtm-85) REVERT: E 84 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7323 (mm-30) REVERT: E 106 MET cc_start: 0.8331 (ttm) cc_final: 0.7664 (tmm) REVERT: E 110 ARG cc_start: 0.7467 (ttm110) cc_final: 0.6693 (mtp85) REVERT: E 112 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6724 (mp0) REVERT: E 300 LYS cc_start: 0.6947 (OUTLIER) cc_final: 0.6290 (mtmt) REVERT: E 363 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7652 (mp0) REVERT: E 377 LYS cc_start: 0.7556 (mttp) cc_final: 0.7256 (mttt) REVERT: F 5 LYS cc_start: 0.8194 (pttp) cc_final: 0.7776 (ptpp) REVERT: F 195 GLN cc_start: 0.7530 (mp10) cc_final: 0.6835 (mt0) REVERT: F 197 GLU cc_start: 0.6758 (pp20) cc_final: 0.6434 (pt0) REVERT: F 214 GLN cc_start: 0.6703 (tm-30) cc_final: 0.6435 (tt0) REVERT: F 267 MET cc_start: 0.8934 (mtt) cc_final: 0.8573 (mtt) REVERT: F 271 GLN cc_start: 0.7443 (OUTLIER) cc_final: 0.6774 (mt0) REVERT: F 278 SER cc_start: 0.8695 (t) cc_final: 0.8402 (p) REVERT: F 336 GLN cc_start: 0.7789 (tp40) cc_final: 0.7051 (pt0) REVERT: F 355 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7451 (mt0) outliers start: 63 outliers final: 25 residues processed: 298 average time/residue: 1.4892 time to fit residues: 492.2995 Evaluate side-chains 270 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 237 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 380 MET Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain D residue 355 GLN Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 300 LYS Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 271 GLN Chi-restraints excluded: chain F residue 355 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 9.9990 chunk 62 optimal weight: 0.4980 chunk 166 optimal weight: 7.9990 chunk 136 optimal weight: 0.0970 chunk 55 optimal weight: 0.7980 chunk 200 optimal weight: 8.9990 chunk 216 optimal weight: 0.9980 chunk 178 optimal weight: 0.0980 chunk 198 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN B 160 GLN B 307 ASN B 333 GLN C 130 GLN ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 ASN D 375 ASN F 302 ASN F 307 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18480 Z= 0.144 Angle : 0.521 7.509 25041 Z= 0.284 Chirality : 0.040 0.146 2769 Planarity : 0.005 0.051 3195 Dihedral : 8.503 84.908 2547 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.16 % Allowed : 14.32 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.44 (0.17), residues: 2201 helix: 1.00 (0.19), residues: 779 sheet: -0.51 (0.22), residues: 501 loop : -1.23 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 199 HIS 0.010 0.001 HIS C 269 PHE 0.020 0.001 PHE A 296 TYR 0.013 0.001 TYR B 163 ARG 0.008 0.000 ARG F 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 249 time to evaluate : 2.089 Fit side-chains revert: symmetry clash REVERT: A 18 ASP cc_start: 0.7796 (m-30) cc_final: 0.7555 (m-30) REVERT: A 59 TYR cc_start: 0.7974 (m-80) cc_final: 0.7576 (m-80) REVERT: A 63 LYS cc_start: 0.7895 (mttm) cc_final: 0.7406 (mtpt) REVERT: A 110 ARG cc_start: 0.7133 (ttm110) cc_final: 0.6534 (ttt180) REVERT: A 120 MET cc_start: 0.6820 (mmm) cc_final: 0.6587 (mmm) REVERT: A 133 LYS cc_start: 0.7419 (ttpp) cc_final: 0.5703 (mmtt) REVERT: A 134 ARG cc_start: 0.7079 (mmm-85) cc_final: 0.6709 (mtm-85) REVERT: A 231 MET cc_start: 0.8337 (mtm) cc_final: 0.7725 (mtp) REVERT: A 267 MET cc_start: 0.9067 (mtp) cc_final: 0.8698 (mtm) REVERT: A 362 ARG cc_start: 0.8642 (ptm-80) cc_final: 0.8305 (ptm-80) REVERT: B 110 ARG cc_start: 0.7481 (ttm110) cc_final: 0.6652 (ttt180) REVERT: B 129 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7052 (mt-10) REVERT: B 133 LYS cc_start: 0.7350 (ttmm) cc_final: 0.6150 (mmtt) REVERT: B 232 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7601 (ttmt) REVERT: B 236 GLN cc_start: 0.7597 (tm-30) cc_final: 0.6838 (mt0) REVERT: B 324 MET cc_start: 0.7445 (mtm) cc_final: 0.6529 (mmm) REVERT: C 5 LYS cc_start: 0.7701 (tttp) cc_final: 0.7264 (tttm) REVERT: C 16 GLN cc_start: 0.8011 (tt0) cc_final: 0.7493 (tm-30) REVERT: C 77 ARG cc_start: 0.7249 (mtt-85) cc_final: 0.6106 (mtm-85) REVERT: C 78 GLN cc_start: 0.7796 (tm-30) cc_final: 0.7161 (tp-100) REVERT: C 110 ARG cc_start: 0.7395 (mtt-85) cc_final: 0.6750 (mtp85) REVERT: C 112 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6627 (mp0) REVERT: C 145 GLU cc_start: 0.6746 (pm20) cc_final: 0.6076 (mm-30) REVERT: C 190 THR cc_start: 0.7148 (m) cc_final: 0.6941 (p) REVERT: C 244 CYS cc_start: 0.7289 (t) cc_final: 0.6657 (m) REVERT: C 344 GLN cc_start: 0.6878 (OUTLIER) cc_final: 0.6405 (mt0) REVERT: C 362 ARG cc_start: 0.7667 (ttp-110) cc_final: 0.7350 (ttp-110) REVERT: C 377 LYS cc_start: 0.7836 (mtmm) cc_final: 0.6833 (tptt) REVERT: D 106 MET cc_start: 0.6418 (OUTLIER) cc_final: 0.6213 (tpp) REVERT: D 120 MET cc_start: 0.5515 (tpp) cc_final: 0.5214 (mtt) REVERT: D 247 GLN cc_start: 0.7382 (tt0) cc_final: 0.7126 (tt0) REVERT: D 271 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.6934 (mt0) REVERT: E 77 ARG cc_start: 0.7248 (mtp180) cc_final: 0.6035 (mtm-85) REVERT: E 106 MET cc_start: 0.8126 (ttm) cc_final: 0.7467 (tmm) REVERT: E 110 ARG cc_start: 0.7443 (ttm110) cc_final: 0.6673 (mtp85) REVERT: E 112 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6682 (mp0) REVERT: E 127 TRP cc_start: 0.5000 (t60) cc_final: 0.4797 (t60) REVERT: E 363 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7563 (mp0) REVERT: E 377 LYS cc_start: 0.7573 (mttp) cc_final: 0.6675 (mtmt) REVERT: F 5 LYS cc_start: 0.8161 (pttp) cc_final: 0.7643 (ptpp) REVERT: F 68 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6836 (mtp85) REVERT: F 203 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7728 (tp) REVERT: F 214 GLN cc_start: 0.6470 (tm-30) cc_final: 0.6124 (tt0) REVERT: F 256 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7715 (pt0) REVERT: F 264 GLN cc_start: 0.8106 (mt0) cc_final: 0.7876 (mt0) REVERT: F 267 MET cc_start: 0.8851 (mtt) cc_final: 0.8559 (mtt) REVERT: F 278 SER cc_start: 0.8507 (t) cc_final: 0.8212 (p) outliers start: 42 outliers final: 9 residues processed: 278 average time/residue: 1.5092 time to fit residues: 464.6154 Evaluate side-chains 253 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 237 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain C residue 344 GLN Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain F residue 68 ARG Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 256 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 20.0000 chunk 150 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 95 optimal weight: 30.0000 chunk 134 optimal weight: 7.9990 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 190 optimal weight: 20.0000 chunk 57 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN A 263 GLN A 370 GLN B 160 GLN B 240 GLN B 253 HIS B 307 ASN D 264 GLN D 302 ASN D 375 ASN E 375 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 18480 Z= 0.551 Angle : 0.800 13.009 25041 Z= 0.408 Chirality : 0.051 0.192 2769 Planarity : 0.007 0.100 3195 Dihedral : 8.830 84.773 2547 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.23 % Favored : 95.73 % Rotamer: Outliers : 3.95 % Allowed : 15.30 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.00 (0.17), residues: 2201 helix: 0.38 (0.19), residues: 784 sheet: -0.70 (0.22), residues: 489 loop : -1.50 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP F 158 HIS 0.013 0.002 HIS B 269 PHE 0.036 0.003 PHE A 296 TYR 0.018 0.002 TYR A 159 ARG 0.010 0.001 ARG B 339 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 240 time to evaluate : 2.083 Fit side-chains REVERT: A 18 ASP cc_start: 0.7859 (m-30) cc_final: 0.7619 (m-30) REVERT: A 25 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7776 (tp) REVERT: A 59 TYR cc_start: 0.7996 (m-80) cc_final: 0.7415 (m-80) REVERT: A 63 LYS cc_start: 0.7894 (mttm) cc_final: 0.7387 (mtpt) REVERT: A 110 ARG cc_start: 0.7287 (ttm110) cc_final: 0.6661 (ttt180) REVERT: A 134 ARG cc_start: 0.7379 (mmm-85) cc_final: 0.7030 (mtp180) REVERT: A 308 ASP cc_start: 0.8018 (m-30) cc_final: 0.7786 (m-30) REVERT: A 334 ILE cc_start: 0.8298 (tt) cc_final: 0.7871 (pt) REVERT: B 110 ARG cc_start: 0.7585 (ttm110) cc_final: 0.6675 (ttt180) REVERT: B 129 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7179 (mt-10) REVERT: B 133 LYS cc_start: 0.7504 (ttmm) cc_final: 0.6326 (mmtt) REVERT: B 236 GLN cc_start: 0.7796 (tm-30) cc_final: 0.6937 (mt0) REVERT: B 324 MET cc_start: 0.7624 (mtm) cc_final: 0.6745 (mmm) REVERT: B 336 GLN cc_start: 0.7853 (tp-100) cc_final: 0.7587 (tp40) REVERT: C 16 GLN cc_start: 0.7993 (tt0) cc_final: 0.7536 (tt0) REVERT: C 77 ARG cc_start: 0.7235 (mtt-85) cc_final: 0.6349 (mtp-110) REVERT: C 110 ARG cc_start: 0.7429 (mtt-85) cc_final: 0.6719 (mtp85) REVERT: C 112 GLU cc_start: 0.7350 (mm-30) cc_final: 0.6618 (mp0) REVERT: C 145 GLU cc_start: 0.6826 (pm20) cc_final: 0.6105 (mm-30) REVERT: C 190 THR cc_start: 0.7528 (OUTLIER) cc_final: 0.7209 (p) REVERT: C 244 CYS cc_start: 0.7444 (t) cc_final: 0.6814 (m) REVERT: C 282 ASP cc_start: 0.7878 (m-30) cc_final: 0.7625 (m-30) REVERT: C 336 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7065 (mm110) REVERT: C 344 GLN cc_start: 0.7006 (OUTLIER) cc_final: 0.6320 (mt0) REVERT: C 377 LYS cc_start: 0.7914 (mtmm) cc_final: 0.6896 (tmtt) REVERT: D 106 MET cc_start: 0.6676 (OUTLIER) cc_final: 0.6441 (tpp) REVERT: D 120 MET cc_start: 0.5788 (tpp) cc_final: 0.5290 (mtt) REVERT: D 195 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.6910 (mt0) REVERT: D 247 GLN cc_start: 0.7684 (tt0) cc_final: 0.7442 (tt0) REVERT: D 267 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8603 (tpp) REVERT: D 271 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.6822 (mt0) REVERT: D 355 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7004 (mt0) REVERT: E 77 ARG cc_start: 0.7376 (mtp180) cc_final: 0.6297 (mtm-85) REVERT: E 84 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7254 (mm-30) REVERT: E 106 MET cc_start: 0.8284 (ttm) cc_final: 0.7605 (tmm) REVERT: E 110 ARG cc_start: 0.7500 (ttm110) cc_final: 0.6760 (mtp85) REVERT: E 112 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6612 (mp0) REVERT: E 324 MET cc_start: 0.8129 (ttm) cc_final: 0.7888 (ttm) REVERT: E 363 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7546 (mp0) REVERT: E 377 LYS cc_start: 0.7767 (mttp) cc_final: 0.6846 (mtmt) REVERT: F 5 LYS cc_start: 0.8180 (pttp) cc_final: 0.7677 (ptpp) REVERT: F 9 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8139 (mp) REVERT: F 120 MET cc_start: 0.5593 (tpp) cc_final: 0.5289 (ttt) REVERT: F 195 GLN cc_start: 0.7483 (mp10) cc_final: 0.6731 (mt0) REVERT: F 214 GLN cc_start: 0.6504 (tm-30) cc_final: 0.6136 (tt0) REVERT: F 256 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7897 (pt0) REVERT: F 267 MET cc_start: 0.8838 (mtt) cc_final: 0.8632 (mtt) REVERT: F 271 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.6815 (mp10) REVERT: F 278 SER cc_start: 0.8674 (t) cc_final: 0.8382 (p) REVERT: F 336 GLN cc_start: 0.7746 (tp40) cc_final: 0.6932 (pt0) REVERT: F 355 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7461 (mt0) outliers start: 77 outliers final: 33 residues processed: 298 average time/residue: 1.4270 time to fit residues: 473.1781 Evaluate side-chains 275 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 228 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain C residue 344 GLN Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 195 GLN Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 355 GLN Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 271 GLN Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 355 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 3 optimal weight: 0.8980 chunk 158 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 chunk 181 optimal weight: 7.9990 chunk 146 optimal weight: 7.9990 chunk 0 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 190 optimal weight: 20.0000 chunk 53 optimal weight: 0.7980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 GLN B 307 ASN D 302 ASN D 375 ASN E 113 GLN F 210 HIS F 262 ASN F 302 ASN F 307 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18480 Z= 0.262 Angle : 0.598 7.437 25041 Z= 0.316 Chirality : 0.043 0.153 2769 Planarity : 0.005 0.060 3195 Dihedral : 8.342 86.685 2547 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.54 % Allowed : 16.22 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.17), residues: 2201 helix: 0.70 (0.19), residues: 784 sheet: -0.71 (0.21), residues: 511 loop : -1.35 (0.18), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 199 HIS 0.011 0.001 HIS E 269 PHE 0.031 0.002 PHE A 296 TYR 0.015 0.001 TYR B 159 ARG 0.008 0.000 ARG F 362 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 233 time to evaluate : 2.215 Fit side-chains REVERT: A 18 ASP cc_start: 0.7836 (m-30) cc_final: 0.7608 (m-30) REVERT: A 59 TYR cc_start: 0.8022 (m-80) cc_final: 0.7535 (m-80) REVERT: A 63 LYS cc_start: 0.7862 (mttm) cc_final: 0.7378 (mtpt) REVERT: A 110 ARG cc_start: 0.7246 (ttm110) cc_final: 0.6617 (ttt180) REVERT: A 134 ARG cc_start: 0.7291 (mmm-85) cc_final: 0.6886 (mtp180) REVERT: A 231 MET cc_start: 0.8366 (mtm) cc_final: 0.7733 (mtp) REVERT: B 110 ARG cc_start: 0.7589 (ttm110) cc_final: 0.6700 (ttt180) REVERT: B 129 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7113 (mt-10) REVERT: B 133 LYS cc_start: 0.7459 (ttmm) cc_final: 0.6249 (mmtt) REVERT: B 236 GLN cc_start: 0.7714 (tm-30) cc_final: 0.6836 (mt0) REVERT: B 324 MET cc_start: 0.7491 (mtm) cc_final: 0.6700 (mmm) REVERT: B 336 GLN cc_start: 0.7852 (tp-100) cc_final: 0.7569 (tp40) REVERT: C 5 LYS cc_start: 0.7802 (tttp) cc_final: 0.7386 (tttm) REVERT: C 16 GLN cc_start: 0.8021 (tt0) cc_final: 0.7581 (tm-30) REVERT: C 77 ARG cc_start: 0.7081 (mtt-85) cc_final: 0.5923 (mtm-85) REVERT: C 110 ARG cc_start: 0.7425 (mtt-85) cc_final: 0.6696 (mtp85) REVERT: C 112 GLU cc_start: 0.7380 (mm-30) cc_final: 0.6635 (mp0) REVERT: C 145 GLU cc_start: 0.6797 (pm20) cc_final: 0.6134 (mm-30) REVERT: C 190 THR cc_start: 0.7474 (m) cc_final: 0.7159 (p) REVERT: C 336 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.7029 (mm110) REVERT: C 344 GLN cc_start: 0.6924 (OUTLIER) cc_final: 0.6393 (mt0) REVERT: C 377 LYS cc_start: 0.7861 (mtmm) cc_final: 0.6801 (tptt) REVERT: D 4 ASP cc_start: 0.7857 (m-30) cc_final: 0.7502 (m-30) REVERT: D 85 MET cc_start: 0.7105 (mmm) cc_final: 0.6852 (tpt) REVERT: D 120 MET cc_start: 0.5635 (tpp) cc_final: 0.5328 (mtt) REVERT: D 203 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7751 (tp) REVERT: D 247 GLN cc_start: 0.7551 (tt0) cc_final: 0.7278 (tt0) REVERT: D 271 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.6911 (mt0) REVERT: E 77 ARG cc_start: 0.7290 (mtp180) cc_final: 0.5929 (mtm-85) REVERT: E 84 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7404 (mm-30) REVERT: E 106 MET cc_start: 0.8239 (ttm) cc_final: 0.7535 (tmm) REVERT: E 110 ARG cc_start: 0.7504 (ttm110) cc_final: 0.6756 (mtp85) REVERT: E 112 GLU cc_start: 0.6964 (mm-30) cc_final: 0.6640 (mp0) REVERT: E 127 TRP cc_start: 0.5032 (t60) cc_final: 0.4824 (t60) REVERT: E 363 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7615 (mp0) REVERT: E 377 LYS cc_start: 0.7817 (mttp) cc_final: 0.6873 (mtmt) REVERT: F 5 LYS cc_start: 0.8160 (pttp) cc_final: 0.7652 (ptpp) REVERT: F 9 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8096 (mp) REVERT: F 195 GLN cc_start: 0.7232 (mp10) cc_final: 0.6564 (mt0) REVERT: F 214 GLN cc_start: 0.6573 (tm-30) cc_final: 0.6170 (tt0) REVERT: F 256 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7879 (pt0) REVERT: F 271 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.6707 (mp10) REVERT: F 278 SER cc_start: 0.8593 (t) cc_final: 0.8275 (p) REVERT: F 336 GLN cc_start: 0.7718 (tp40) cc_final: 0.6898 (pt0) REVERT: F 355 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7557 (mt0) outliers start: 69 outliers final: 30 residues processed: 287 average time/residue: 1.4275 time to fit residues: 456.4127 Evaluate side-chains 261 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 222 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain C residue 344 GLN Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 296 PHE Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 271 GLN Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 355 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 2.9990 chunk 191 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 124 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 212 optimal weight: 0.9980 chunk 176 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN B 307 ASN C 130 GLN D 375 ASN F 210 HIS F 262 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18480 Z= 0.201 Angle : 0.545 7.355 25041 Z= 0.291 Chirality : 0.042 0.151 2769 Planarity : 0.005 0.054 3195 Dihedral : 8.073 89.085 2547 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.29 % Allowed : 17.30 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.53 (0.17), residues: 2201 helix: 0.92 (0.19), residues: 789 sheet: -0.64 (0.21), residues: 501 loop : -1.25 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 199 HIS 0.011 0.001 HIS E 269 PHE 0.025 0.001 PHE A 296 TYR 0.014 0.001 TYR B 159 ARG 0.009 0.000 ARG F 362 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 231 time to evaluate : 2.212 Fit side-chains REVERT: A 18 ASP cc_start: 0.7803 (m-30) cc_final: 0.7569 (m-30) REVERT: A 59 TYR cc_start: 0.8045 (m-80) cc_final: 0.7604 (m-80) REVERT: A 63 LYS cc_start: 0.7851 (mttm) cc_final: 0.7369 (mtpt) REVERT: A 110 ARG cc_start: 0.7252 (ttm110) cc_final: 0.6627 (ttt180) REVERT: A 134 ARG cc_start: 0.7226 (mmm-85) cc_final: 0.6824 (mtp180) REVERT: A 231 MET cc_start: 0.8348 (mtm) cc_final: 0.7690 (mtp) REVERT: A 362 ARG cc_start: 0.8578 (ptm-80) cc_final: 0.8362 (ptm-80) REVERT: B 2 ARG cc_start: 0.7808 (ttm170) cc_final: 0.7593 (ttm170) REVERT: B 110 ARG cc_start: 0.7535 (ttm110) cc_final: 0.6686 (ttt180) REVERT: B 129 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7128 (mt-10) REVERT: B 133 LYS cc_start: 0.7398 (ttmm) cc_final: 0.6087 (mmtt) REVERT: B 236 GLN cc_start: 0.7727 (tm-30) cc_final: 0.6820 (mt0) REVERT: B 324 MET cc_start: 0.7303 (mtm) cc_final: 0.6559 (mmm) REVERT: C 5 LYS cc_start: 0.7707 (tttp) cc_final: 0.7208 (tttm) REVERT: C 16 GLN cc_start: 0.7999 (tt0) cc_final: 0.7594 (tm-30) REVERT: C 77 ARG cc_start: 0.7078 (mtt-85) cc_final: 0.5919 (mtm-85) REVERT: C 110 ARG cc_start: 0.7436 (mtt-85) cc_final: 0.6694 (mtp85) REVERT: C 112 GLU cc_start: 0.7338 (mm-30) cc_final: 0.6617 (mp0) REVERT: C 145 GLU cc_start: 0.6744 (pm20) cc_final: 0.6092 (mm-30) REVERT: C 190 THR cc_start: 0.7456 (m) cc_final: 0.7137 (p) REVERT: C 336 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7019 (mm110) REVERT: C 344 GLN cc_start: 0.6859 (OUTLIER) cc_final: 0.6375 (mt0) REVERT: C 377 LYS cc_start: 0.7864 (mtmm) cc_final: 0.6807 (tptt) REVERT: D 85 MET cc_start: 0.7158 (mmm) cc_final: 0.6930 (tpt) REVERT: D 120 MET cc_start: 0.5613 (tpp) cc_final: 0.5256 (mtt) REVERT: D 192 ASN cc_start: 0.8187 (p0) cc_final: 0.7976 (p0) REVERT: D 247 GLN cc_start: 0.7449 (tt0) cc_final: 0.7206 (tt0) REVERT: D 262 ASN cc_start: 0.7548 (t0) cc_final: 0.7270 (t0) REVERT: D 271 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.6884 (mt0) REVERT: D 355 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.6888 (mt0) REVERT: E 77 ARG cc_start: 0.7280 (mtp180) cc_final: 0.5886 (mtm-85) REVERT: E 106 MET cc_start: 0.8217 (ttm) cc_final: 0.7520 (tmm) REVERT: E 110 ARG cc_start: 0.7508 (ttm110) cc_final: 0.6757 (mtp85) REVERT: E 112 GLU cc_start: 0.6983 (mm-30) cc_final: 0.6654 (mp0) REVERT: E 363 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7649 (mp0) REVERT: E 377 LYS cc_start: 0.7756 (mttp) cc_final: 0.6836 (mtmt) REVERT: F 5 LYS cc_start: 0.8146 (pttp) cc_final: 0.7625 (ptpp) REVERT: F 9 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8147 (mp) REVERT: F 120 MET cc_start: 0.5768 (tpp) cc_final: 0.5285 (mtt) REVERT: F 214 GLN cc_start: 0.6525 (tm-30) cc_final: 0.6085 (tt0) REVERT: F 256 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7838 (pt0) REVERT: F 262 ASN cc_start: 0.7650 (t0) cc_final: 0.7049 (t0) REVERT: F 271 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.6554 (mp10) REVERT: F 278 SER cc_start: 0.8599 (t) cc_final: 0.8280 (p) REVERT: F 336 GLN cc_start: 0.7704 (tp40) cc_final: 0.6880 (pt0) REVERT: F 355 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7556 (mt0) outliers start: 64 outliers final: 29 residues processed: 281 average time/residue: 1.4253 time to fit residues: 446.8442 Evaluate side-chains 264 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 227 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain C residue 344 GLN Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 355 GLN Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 296 PHE Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 271 GLN Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 355 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 120 optimal weight: 0.0970 chunk 179 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 212 optimal weight: 0.4980 chunk 132 optimal weight: 9.9990 chunk 129 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 overall best weight: 2.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN B 240 GLN B 307 ASN C 130 GLN D 375 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18480 Z= 0.346 Angle : 0.652 8.297 25041 Z= 0.338 Chirality : 0.045 0.165 2769 Planarity : 0.006 0.069 3195 Dihedral : 8.308 85.706 2547 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.59 % Allowed : 18.07 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.17), residues: 2201 helix: 0.73 (0.19), residues: 784 sheet: -0.68 (0.22), residues: 498 loop : -1.26 (0.18), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 158 HIS 0.011 0.002 HIS E 269 PHE 0.033 0.002 PHE A 296 TYR 0.017 0.002 TYR B 159 ARG 0.008 0.001 ARG F 362 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 227 time to evaluate : 2.051 Fit side-chains REVERT: A 18 ASP cc_start: 0.7845 (m-30) cc_final: 0.7604 (m-30) REVERT: A 25 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7842 (tp) REVERT: A 59 TYR cc_start: 0.8041 (m-80) cc_final: 0.7563 (m-80) REVERT: A 63 LYS cc_start: 0.7865 (mttm) cc_final: 0.7380 (mtpt) REVERT: A 110 ARG cc_start: 0.7242 (ttm110) cc_final: 0.6629 (ttt180) REVERT: A 134 ARG cc_start: 0.7352 (mmm-85) cc_final: 0.6925 (mtp180) REVERT: A 231 MET cc_start: 0.8416 (mtm) cc_final: 0.7760 (mtp) REVERT: A 334 ILE cc_start: 0.8241 (tt) cc_final: 0.7868 (pt) REVERT: B 2 ARG cc_start: 0.7836 (ttm170) cc_final: 0.7622 (ttm170) REVERT: B 110 ARG cc_start: 0.7561 (ttm110) cc_final: 0.6700 (ttt180) REVERT: B 129 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7203 (mt-10) REVERT: B 133 LYS cc_start: 0.7631 (ttmm) cc_final: 0.6270 (mmtt) REVERT: B 236 GLN cc_start: 0.7783 (tm-30) cc_final: 0.6845 (mt0) REVERT: B 324 MET cc_start: 0.7444 (mtm) cc_final: 0.6728 (mmm) REVERT: B 336 GLN cc_start: 0.7868 (tp-100) cc_final: 0.7588 (tp40) REVERT: C 5 LYS cc_start: 0.7803 (tttp) cc_final: 0.7396 (tttm) REVERT: C 16 GLN cc_start: 0.7952 (tt0) cc_final: 0.7588 (tm-30) REVERT: C 77 ARG cc_start: 0.7060 (mtt-85) cc_final: 0.5894 (mtm-85) REVERT: C 110 ARG cc_start: 0.7460 (mtt-85) cc_final: 0.6707 (mtp85) REVERT: C 112 GLU cc_start: 0.7354 (mm-30) cc_final: 0.6618 (mp0) REVERT: C 145 GLU cc_start: 0.6754 (pm20) cc_final: 0.6120 (mm-30) REVERT: C 190 THR cc_start: 0.7531 (OUTLIER) cc_final: 0.7212 (p) REVERT: C 336 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.7029 (mm110) REVERT: C 377 LYS cc_start: 0.7885 (mtmm) cc_final: 0.6810 (tptt) REVERT: D 85 MET cc_start: 0.7227 (mmm) cc_final: 0.6941 (tpt) REVERT: D 120 MET cc_start: 0.5739 (tpp) cc_final: 0.5250 (mtt) REVERT: D 267 MET cc_start: 0.8964 (mmt) cc_final: 0.8660 (tpp) REVERT: D 271 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.6808 (mp10) REVERT: D 355 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.6946 (mt0) REVERT: E 77 ARG cc_start: 0.7347 (mtp180) cc_final: 0.5930 (mtm-85) REVERT: E 84 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7121 (mm-30) REVERT: E 106 MET cc_start: 0.8255 (ttm) cc_final: 0.7550 (tmm) REVERT: E 110 ARG cc_start: 0.7486 (ttm110) cc_final: 0.6737 (mtp85) REVERT: E 112 GLU cc_start: 0.6981 (mm-30) cc_final: 0.6636 (mp0) REVERT: E 363 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7640 (mp0) REVERT: E 369 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.6780 (mt-10) REVERT: E 377 LYS cc_start: 0.7737 (mttp) cc_final: 0.6831 (mtmt) REVERT: F 9 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8130 (mp) REVERT: F 214 GLN cc_start: 0.6544 (tm-30) cc_final: 0.6129 (tt0) REVERT: F 256 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7792 (pt0) REVERT: F 262 ASN cc_start: 0.7711 (t0) cc_final: 0.7218 (t0) REVERT: F 271 GLN cc_start: 0.7270 (OUTLIER) cc_final: 0.6572 (mp10) REVERT: F 336 GLN cc_start: 0.7724 (tp40) cc_final: 0.6890 (pt0) REVERT: F 355 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7582 (mt0) outliers start: 70 outliers final: 38 residues processed: 286 average time/residue: 1.5483 time to fit residues: 491.9107 Evaluate side-chains 272 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 223 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 355 GLN Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain E residue 296 PHE Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 369 GLU Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 271 GLN Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 355 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 126 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 134 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 166 optimal weight: 10.0000 chunk 192 optimal weight: 7.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN B 307 ASN C 130 GLN F 210 HIS F 307 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18480 Z= 0.277 Angle : 0.601 7.971 25041 Z= 0.315 Chirality : 0.043 0.152 2769 Planarity : 0.005 0.061 3195 Dihedral : 8.244 88.602 2547 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.49 % Allowed : 18.38 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.52 (0.17), residues: 2201 helix: 0.90 (0.19), residues: 771 sheet: -0.66 (0.22), residues: 492 loop : -1.15 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 199 HIS 0.012 0.001 HIS E 269 PHE 0.033 0.002 PHE A 296 TYR 0.015 0.001 TYR A 159 ARG 0.008 0.000 ARG F 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 221 time to evaluate : 2.062 Fit side-chains REVERT: A 18 ASP cc_start: 0.7836 (m-30) cc_final: 0.7600 (m-30) REVERT: A 25 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7833 (tp) REVERT: A 59 TYR cc_start: 0.8075 (m-80) cc_final: 0.7590 (m-80) REVERT: A 63 LYS cc_start: 0.7856 (mttm) cc_final: 0.7376 (mtpt) REVERT: A 110 ARG cc_start: 0.7254 (ttm110) cc_final: 0.6635 (ttt180) REVERT: A 134 ARG cc_start: 0.7291 (mmm-85) cc_final: 0.6879 (mtp180) REVERT: A 231 MET cc_start: 0.8384 (mtm) cc_final: 0.7788 (mtp) REVERT: B 110 ARG cc_start: 0.7528 (ttm110) cc_final: 0.6682 (ttt180) REVERT: B 129 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7173 (mt-10) REVERT: B 133 LYS cc_start: 0.7528 (ttmm) cc_final: 0.6174 (mmtt) REVERT: B 236 GLN cc_start: 0.7788 (tm-30) cc_final: 0.6867 (mt0) REVERT: B 324 MET cc_start: 0.7327 (mtm) cc_final: 0.6569 (mmm) REVERT: B 336 GLN cc_start: 0.7849 (tp-100) cc_final: 0.7574 (tp40) REVERT: C 5 LYS cc_start: 0.7685 (tttp) cc_final: 0.7294 (tttm) REVERT: C 16 GLN cc_start: 0.7940 (tt0) cc_final: 0.7583 (tm-30) REVERT: C 77 ARG cc_start: 0.7050 (mtt-85) cc_final: 0.5890 (mtm-85) REVERT: C 110 ARG cc_start: 0.7398 (mtt-85) cc_final: 0.6664 (mtp85) REVERT: C 112 GLU cc_start: 0.7366 (mm-30) cc_final: 0.6615 (mp0) REVERT: C 145 GLU cc_start: 0.6704 (pm20) cc_final: 0.6102 (mm-30) REVERT: C 190 THR cc_start: 0.7611 (OUTLIER) cc_final: 0.7276 (p) REVERT: C 336 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.7019 (mm110) REVERT: C 377 LYS cc_start: 0.7890 (mtmm) cc_final: 0.6823 (tptt) REVERT: D 120 MET cc_start: 0.5801 (tpp) cc_final: 0.5222 (mtt) REVERT: D 262 ASN cc_start: 0.7575 (t0) cc_final: 0.7297 (t0) REVERT: D 267 MET cc_start: 0.8954 (mmt) cc_final: 0.8663 (tpp) REVERT: D 271 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.6826 (mp10) REVERT: D 355 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.6901 (mt0) REVERT: E 77 ARG cc_start: 0.7284 (mtp180) cc_final: 0.5880 (mtm-85) REVERT: E 84 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7127 (mm-30) REVERT: E 102 THR cc_start: 0.7838 (m) cc_final: 0.7629 (p) REVERT: E 106 MET cc_start: 0.8249 (ttm) cc_final: 0.7541 (tmm) REVERT: E 110 ARG cc_start: 0.7481 (ttm110) cc_final: 0.6729 (mtp85) REVERT: E 112 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6648 (mp0) REVERT: E 362 ARG cc_start: 0.7758 (ttp-110) cc_final: 0.7453 (ttp-110) REVERT: E 363 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7640 (mp0) REVERT: E 377 LYS cc_start: 0.7754 (mttp) cc_final: 0.6878 (mtmt) REVERT: F 9 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8079 (mp) REVERT: F 68 ARG cc_start: 0.7001 (mtp85) cc_final: 0.5302 (mtm110) REVERT: F 120 MET cc_start: 0.5655 (tpp) cc_final: 0.5221 (mtt) REVERT: F 214 GLN cc_start: 0.6513 (tm-30) cc_final: 0.6072 (tt0) REVERT: F 256 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7765 (pt0) REVERT: F 262 ASN cc_start: 0.7829 (t0) cc_final: 0.7150 (t0) REVERT: F 267 MET cc_start: 0.8874 (mmt) cc_final: 0.8554 (tpp) REVERT: F 271 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.6534 (mp10) REVERT: F 312 LYS cc_start: 0.7766 (mtpp) cc_final: 0.7566 (mtpp) REVERT: F 336 GLN cc_start: 0.7726 (tp40) cc_final: 0.6866 (pt0) REVERT: F 355 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7565 (mt0) outliers start: 68 outliers final: 38 residues processed: 276 average time/residue: 1.4294 time to fit residues: 439.0420 Evaluate side-chains 268 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 220 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain C residue 380 MET Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 355 GLN Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 296 PHE Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 271 GLN Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 355 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 0.7980 chunk 185 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 155 optimal weight: 0.9990 chunk 60 optimal weight: 0.3980 chunk 178 optimal weight: 0.9990 chunk 186 optimal weight: 0.6980 chunk 196 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN B 307 ASN C 130 GLN F 210 HIS F 302 ASN F 307 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18480 Z= 0.158 Angle : 0.516 8.086 25041 Z= 0.277 Chirality : 0.041 0.147 2769 Planarity : 0.005 0.053 3195 Dihedral : 7.907 89.401 2547 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.62 % Allowed : 19.56 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.23 (0.17), residues: 2201 helix: 1.27 (0.19), residues: 764 sheet: -0.56 (0.22), residues: 487 loop : -1.06 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 199 HIS 0.011 0.001 HIS E 269 PHE 0.022 0.001 PHE A 296 TYR 0.011 0.001 TYR A 159 ARG 0.007 0.000 ARG D 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 235 time to evaluate : 2.234 Fit side-chains REVERT: A 18 ASP cc_start: 0.7789 (m-30) cc_final: 0.7557 (m-30) REVERT: A 59 TYR cc_start: 0.8051 (m-80) cc_final: 0.7581 (m-80) REVERT: A 63 LYS cc_start: 0.7759 (mttm) cc_final: 0.7305 (mtpt) REVERT: A 110 ARG cc_start: 0.7210 (ttm110) cc_final: 0.6612 (ttt180) REVERT: A 134 ARG cc_start: 0.7144 (mmm-85) cc_final: 0.6748 (mtp180) REVERT: A 231 MET cc_start: 0.8298 (mtm) cc_final: 0.7822 (mtp) REVERT: A 267 MET cc_start: 0.9141 (mtp) cc_final: 0.8765 (mtm) REVERT: A 362 ARG cc_start: 0.8585 (ptm-80) cc_final: 0.8362 (ptm-80) REVERT: B 110 ARG cc_start: 0.7502 (ttm110) cc_final: 0.6661 (ttt180) REVERT: B 129 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7207 (mt-10) REVERT: B 133 LYS cc_start: 0.7406 (ttmm) cc_final: 0.5967 (mmtt) REVERT: B 236 GLN cc_start: 0.7767 (tm-30) cc_final: 0.6821 (mt0) REVERT: B 324 MET cc_start: 0.7246 (mtm) cc_final: 0.6560 (mmm) REVERT: C 5 LYS cc_start: 0.7496 (tttp) cc_final: 0.6981 (tttm) REVERT: C 16 GLN cc_start: 0.7974 (tt0) cc_final: 0.7579 (tm-30) REVERT: C 77 ARG cc_start: 0.7056 (mtt-85) cc_final: 0.5902 (mtm-85) REVERT: C 110 ARG cc_start: 0.7393 (mtt-85) cc_final: 0.6660 (mtp85) REVERT: C 112 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6600 (mp0) REVERT: C 145 GLU cc_start: 0.6630 (pm20) cc_final: 0.6054 (mm-30) REVERT: C 190 THR cc_start: 0.7517 (OUTLIER) cc_final: 0.7009 (p) REVERT: C 336 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7019 (mm110) REVERT: C 377 LYS cc_start: 0.7871 (mtmm) cc_final: 0.6812 (tptt) REVERT: D 4 ASP cc_start: 0.7817 (m-30) cc_final: 0.7457 (m-30) REVERT: D 120 MET cc_start: 0.5920 (tpp) cc_final: 0.5209 (mtt) REVERT: D 262 ASN cc_start: 0.7433 (t0) cc_final: 0.7164 (t0) REVERT: D 267 MET cc_start: 0.8917 (mmt) cc_final: 0.8603 (tpp) REVERT: D 271 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.6836 (mp10) REVERT: E 77 ARG cc_start: 0.7345 (mtp180) cc_final: 0.6258 (mtp-110) REVERT: E 84 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7072 (mm-30) REVERT: E 106 MET cc_start: 0.8207 (ttm) cc_final: 0.7503 (tmm) REVERT: E 110 ARG cc_start: 0.7507 (ttm110) cc_final: 0.6747 (mtp85) REVERT: E 112 GLU cc_start: 0.6861 (mm-30) cc_final: 0.6614 (mp0) REVERT: E 272 TYR cc_start: 0.8069 (m-80) cc_final: 0.7833 (m-80) REVERT: E 362 ARG cc_start: 0.7690 (ttp-110) cc_final: 0.7368 (ttp-110) REVERT: E 363 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7786 (mp0) REVERT: E 377 LYS cc_start: 0.7781 (mttp) cc_final: 0.6686 (mmmt) REVERT: F 9 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8075 (mp) REVERT: F 68 ARG cc_start: 0.6954 (mtp85) cc_final: 0.5336 (mtm110) REVERT: F 214 GLN cc_start: 0.6561 (tm-30) cc_final: 0.6122 (tt0) REVERT: F 256 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7687 (pt0) REVERT: F 262 ASN cc_start: 0.7838 (t0) cc_final: 0.7214 (t0) REVERT: F 333 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.7127 (mm-40) REVERT: F 336 GLN cc_start: 0.7707 (tp40) cc_final: 0.6860 (pt0) outliers start: 51 outliers final: 25 residues processed: 272 average time/residue: 1.4436 time to fit residues: 436.7210 Evaluate side-chains 258 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 226 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 296 PHE Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 333 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 4.9990 chunk 127 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 219 optimal weight: 5.9990 chunk 201 optimal weight: 10.0000 chunk 174 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 GLN B 307 ASN C 130 GLN D 192 ASN ** D 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 ASN F 307 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.083 18480 Z= 0.568 Angle : 0.808 11.924 25041 Z= 0.410 Chirality : 0.051 0.182 2769 Planarity : 0.007 0.092 3195 Dihedral : 8.468 89.983 2547 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.59 % Favored : 95.37 % Rotamer: Outliers : 2.87 % Allowed : 19.71 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.17), residues: 2201 helix: 0.61 (0.19), residues: 760 sheet: -0.76 (0.22), residues: 506 loop : -1.29 (0.18), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP F 158 HIS 0.013 0.002 HIS B 269 PHE 0.046 0.003 PHE A 296 TYR 0.017 0.003 TYR B 272 ARG 0.015 0.001 ARG C 2 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 233 time to evaluate : 2.222 Fit side-chains REVERT: A 18 ASP cc_start: 0.7860 (m-30) cc_final: 0.7615 (m-30) REVERT: A 25 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7777 (tp) REVERT: A 59 TYR cc_start: 0.8035 (m-80) cc_final: 0.7470 (m-80) REVERT: A 63 LYS cc_start: 0.7878 (mttm) cc_final: 0.7391 (mtpt) REVERT: A 106 MET cc_start: 0.8121 (ttp) cc_final: 0.7827 (ttp) REVERT: A 110 ARG cc_start: 0.7262 (ttm110) cc_final: 0.6656 (ttt180) REVERT: A 134 ARG cc_start: 0.7423 (mmm-85) cc_final: 0.6999 (mtp180) REVERT: A 231 MET cc_start: 0.8481 (mtm) cc_final: 0.7772 (mtp) REVERT: A 334 ILE cc_start: 0.8399 (tt) cc_final: 0.7968 (pt) REVERT: B 110 ARG cc_start: 0.7578 (ttm110) cc_final: 0.6714 (ttt180) REVERT: B 133 LYS cc_start: 0.7573 (ttmm) cc_final: 0.6197 (mmtt) REVERT: B 236 GLN cc_start: 0.7803 (tm-30) cc_final: 0.6923 (mt0) REVERT: B 324 MET cc_start: 0.7484 (mtm) cc_final: 0.6679 (mmm) REVERT: B 336 GLN cc_start: 0.7865 (tp-100) cc_final: 0.7576 (tp40) REVERT: C 5 LYS cc_start: 0.7801 (tttp) cc_final: 0.7297 (tttm) REVERT: C 77 ARG cc_start: 0.7103 (mtt-85) cc_final: 0.6142 (mtp-110) REVERT: C 110 ARG cc_start: 0.7319 (mtt-85) cc_final: 0.6615 (mtp85) REVERT: C 145 GLU cc_start: 0.6734 (pm20) cc_final: 0.6131 (mm-30) REVERT: C 190 THR cc_start: 0.7725 (OUTLIER) cc_final: 0.7232 (p) REVERT: C 336 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.6982 (mm110) REVERT: C 377 LYS cc_start: 0.7931 (mtmm) cc_final: 0.6855 (tptt) REVERT: D 120 MET cc_start: 0.5940 (tpp) cc_final: 0.5313 (mtt) REVERT: D 267 MET cc_start: 0.9009 (mmt) cc_final: 0.8680 (tpp) REVERT: D 271 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.6874 (mp10) REVERT: E 77 ARG cc_start: 0.7378 (mtp180) cc_final: 0.5923 (mtm-85) REVERT: E 84 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7092 (mm-30) REVERT: E 106 MET cc_start: 0.8311 (ttm) cc_final: 0.7570 (tmm) REVERT: E 110 ARG cc_start: 0.7517 (ttm110) cc_final: 0.6764 (mtp85) REVERT: E 112 GLU cc_start: 0.6985 (mm-30) cc_final: 0.6628 (mp0) REVERT: E 336 GLN cc_start: 0.7676 (tp40) cc_final: 0.7427 (tp-100) REVERT: E 362 ARG cc_start: 0.7749 (ttp-110) cc_final: 0.7413 (ttp-110) REVERT: E 363 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7741 (mp0) REVERT: E 377 LYS cc_start: 0.7760 (mttp) cc_final: 0.6855 (mtmt) REVERT: F 9 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8089 (mp) REVERT: F 68 ARG cc_start: 0.7002 (mtp85) cc_final: 0.5359 (mtm110) REVERT: F 214 GLN cc_start: 0.6627 (tm-30) cc_final: 0.6204 (tt0) REVERT: F 256 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7774 (pt0) REVERT: F 262 ASN cc_start: 0.8077 (t0) cc_final: 0.7362 (t0) REVERT: F 267 MET cc_start: 0.8965 (mmt) cc_final: 0.8595 (tpp) REVERT: F 333 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.7302 (mm-40) REVERT: F 336 GLN cc_start: 0.7773 (tp40) cc_final: 0.6911 (pt0) REVERT: F 355 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7651 (mt0) outliers start: 56 outliers final: 29 residues processed: 274 average time/residue: 1.4713 time to fit residues: 447.4519 Evaluate side-chains 259 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 221 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 336 GLN Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 271 GLN Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain E residue 296 PHE Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 333 GLN Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 355 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 174 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 179 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 153 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 GLN B 307 ASN C 130 GLN D 304 HIS F 210 HIS F 302 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.207269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.133293 restraints weight = 17204.525| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.88 r_work: 0.3207 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18480 Z= 0.186 Angle : 0.559 8.763 25041 Z= 0.297 Chirality : 0.041 0.148 2769 Planarity : 0.005 0.070 3195 Dihedral : 8.064 87.063 2547 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.16 % Allowed : 20.43 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.41 (0.17), residues: 2201 helix: 1.05 (0.19), residues: 766 sheet: -0.69 (0.22), residues: 501 loop : -1.09 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 199 HIS 0.013 0.001 HIS E 269 PHE 0.030 0.001 PHE A 296 TYR 0.014 0.001 TYR B 159 ARG 0.016 0.000 ARG C 2 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7464.43 seconds wall clock time: 135 minutes 1.38 seconds (8101.38 seconds total)