Starting phenix.real_space_refine on Wed Nov 20 13:46:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wj6_21690/11_2024/6wj6_21690_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wj6_21690/11_2024/6wj6_21690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wj6_21690/11_2024/6wj6_21690.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wj6_21690/11_2024/6wj6_21690.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wj6_21690/11_2024/6wj6_21690_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wj6_21690/11_2024/6wj6_21690_neut.cif" } resolution = 2.58 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= 0.008 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: 8 Type Number sf(0) Gaussians Fe 2 7.16 5 P 4 5.49 5 Mg 35 5.21 5 S 69 5.16 5 Cl 1 4.86 5 C 13000 2.51 5 N 2603 2.21 5 O 3170 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 139 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 18884 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2357 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 13, 'TRANS': 288} Chain breaks: 1 Chain: "B" Number of atoms: 3751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3751 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 26, 'TRANS': 451} Chain: "C" Number of atoms: 3259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3259 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 392} Chain breaks: 2 Chain: "D" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2734 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 16, 'TRANS': 325} Chain: "E" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 603 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 4, 'TRANS': 67} Chain: "F" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "H" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 494 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "I" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 276 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "K" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 278 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 4, 'TRANS': 30} Chain: "L" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 252 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "M" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "T" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 231 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 2, 'TRANS': 26} Chain: "X" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 262 Classifications: {'peptide': 35} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 32} Chain: "A" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 392 Unusual residues: {'BCR': 1, 'CLA': 3, 'FE2': 1, 'PHO': 1, 'PL9': 1, 'SQD': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 1301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 1301 Unusual residues: {'BCR': 3, 'CLA': 16, 'LMG': 1, 'LMT': 2, 'SQD': 1} Classifications: {'undetermined': 23} Link IDs: {None: 22} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 1102 Unusual residues: {'BCR': 3, 'CLA': 13, 'DGD': 1, 'LMG': 1, 'SQD': 1} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 554 Unusual residues: {' CL': 1, 'BCR': 1, 'BCT': 1, 'CLA': 3, 'LHG': 3, 'LMG': 1, 'PHO': 1, 'PL9': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'DGD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 103 Unusual residues: {'SQD': 2} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'BCR': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "T" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 10.93, per 1000 atoms: 0.58 Number of scatterers: 18884 At special positions: 0 Unit cell: (108.675, 133.481, 107.494, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 2 26.01 Cl 1 17.00 S 69 16.00 P 4 15.00 Mg 35 11.99 O 3170 8.00 N 2603 7.00 C 13000 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=33, symmetry=0 Number of additional bonds: simple=33, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.90 Conformation dependent library (CDL) restraints added in 2.0 seconds 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3414 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 8 sheets defined 66.7% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 removed outlier: 3.624A pdb=" N TRP A 20 " --> pdb=" O GLN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 55 Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 101 through 108 Processing helix chain 'A' and resid 109 through 137 removed outlier: 3.833A pdb=" N GLN A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TRP A 131 " --> pdb=" O MET A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 147 removed outlier: 3.884A pdb=" N ALA A 146 " --> pdb=" O TRP A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 159 removed outlier: 3.588A pdb=" N VAL A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 166 Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 176 through 191 Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 195 through 222 Processing helix chain 'A' and resid 249 through 259 removed outlier: 3.657A pdb=" N GLY A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 294 Proline residue: A 279 - end of helix Processing helix chain 'A' and resid 316 through 331 removed outlier: 3.923A pdb=" N VAL A 320 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 321 " --> pdb=" O TRP A 317 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 13 removed outlier: 3.689A pdb=" N VAL B 8 " --> pdb=" O TRP B 5 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N HIS B 9 " --> pdb=" O TYR B 6 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL B 11 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 12 " --> pdb=" O HIS B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 45 Processing helix chain 'B' and resid 54 through 59 removed outlier: 3.879A pdb=" N GLY B 59 " --> pdb=" O TRP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 69 removed outlier: 4.008A pdb=" N LEU B 69 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 117 Processing helix chain 'B' and resid 134 through 157 Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 194 through 219 removed outlier: 4.000A pdb=" N VAL B 198 " --> pdb=" O ASN B 194 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 229 Processing helix chain 'B' and resid 234 through 259 Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'B' and resid 271 through 277 removed outlier: 3.934A pdb=" N TRP B 275 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 293 removed outlier: 3.643A pdb=" N GLU B 283 " --> pdb=" O TYR B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 303 removed outlier: 3.524A pdb=" N TRP B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 313 removed outlier: 3.667A pdb=" N ASP B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 318 Processing helix chain 'B' and resid 329 through 333 Processing helix chain 'B' and resid 413 through 425 Processing helix chain 'B' and resid 446 through 475 removed outlier: 3.803A pdb=" N PHE B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 30 removed outlier: 6.015A pdb=" N ASN C 26 " --> pdb=" O TRP C 23 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE C 30 " --> pdb=" O ALA C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 61 removed outlier: 3.773A pdb=" N THR C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.696A pdb=" N GLN C 71 " --> pdb=" O MET C 68 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY C 72 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 82 removed outlier: 3.724A pdb=" N LEU C 82 " --> pdb=" O HIS C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 122 removed outlier: 3.523A pdb=" N PHE C 99 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 106 " --> pdb=" O GLY C 102 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 169 removed outlier: 3.614A pdb=" N LEU C 154 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 162 " --> pdb=" O GLY C 158 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE C 169 " --> pdb=" O LYS C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 198 through 202 Processing helix chain 'C' and resid 216 through 240 removed outlier: 3.699A pdb=" N ILE C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 251 Processing helix chain 'C' and resid 254 through 280 removed outlier: 3.672A pdb=" N TRP C 278 " --> pdb=" O SER C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 290 Processing helix chain 'C' and resid 292 through 309 removed outlier: 3.826A pdb=" N SER C 297 " --> pdb=" O GLY C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 346 removed outlier: 3.995A pdb=" N ARG C 344 " --> pdb=" O GLU C 341 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP C 346 " --> pdb=" O MET C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 372 through 382 Processing helix chain 'C' and resid 383 through 386 Processing helix chain 'C' and resid 408 through 441 Processing helix chain 'C' and resid 451 through 456 removed outlier: 3.957A pdb=" N PHE C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET C 456 " --> pdb=" O PRO C 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 451 through 456' Processing helix chain 'D' and resid 13 through 23 Processing helix chain 'D' and resid 33 through 54 Proline residue: D 39 - end of helix Processing helix chain 'D' and resid 82 through 86 Processing helix chain 'D' and resid 100 through 107 Processing helix chain 'D' and resid 109 through 137 removed outlier: 3.512A pdb=" N PHE D 113 " --> pdb=" O GLY D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 158 removed outlier: 4.403A pdb=" N GLY D 148 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Proline residue: D 149 - end of helix Processing helix chain 'D' and resid 158 through 164 Processing helix chain 'D' and resid 166 through 170 Processing helix chain 'D' and resid 175 through 188 Processing helix chain 'D' and resid 190 through 193 Processing helix chain 'D' and resid 194 through 221 Processing helix chain 'D' and resid 230 through 234 Processing helix chain 'D' and resid 245 through 257 Processing helix chain 'D' and resid 263 through 291 Proline residue: D 275 - end of helix removed outlier: 3.780A pdb=" N LEU D 291 " --> pdb=" O VAL D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 313 through 334 Proline residue: D 331 - end of helix Processing helix chain 'D' and resid 335 through 338 Processing helix chain 'D' and resid 342 through 346 Processing helix chain 'D' and resid 348 through 352 Processing helix chain 'E' and resid 10 through 15 Processing helix chain 'E' and resid 17 through 23 removed outlier: 4.041A pdb=" N ILE E 22 " --> pdb=" O ARG E 18 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS E 23 " --> pdb=" O TYR E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 40 removed outlier: 3.520A pdb=" N GLY E 34 " --> pdb=" O LEU E 30 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 48 removed outlier: 3.842A pdb=" N ASP E 45 " --> pdb=" O GLY E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 80 Processing helix chain 'F' and resid 16 through 40 removed outlier: 3.840A pdb=" N LEU F 20 " --> pdb=" O THR F 16 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU F 25 " --> pdb=" O ALA F 21 " (cutoff:3.500A) Proline residue: F 28 - end of helix Processing helix chain 'H' and resid 5 through 11 Processing helix chain 'H' and resid 12 through 16 removed outlier: 3.990A pdb=" N SER H 16 " --> pdb=" O PRO H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 50 Processing helix chain 'I' and resid 3 through 25 removed outlier: 3.688A pdb=" N SER I 17 " --> pdb=" O GLY I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 30 Processing helix chain 'K' and resid 11 through 15 removed outlier: 3.510A pdb=" N GLN K 15 " --> pdb=" O GLU K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 22 Processing helix chain 'K' and resid 23 through 25 No H-bonds generated for 'chain 'K' and resid 23 through 25' Processing helix chain 'K' and resid 26 through 31 Processing helix chain 'K' and resid 31 through 43 removed outlier: 3.908A pdb=" N PHE K 36 " --> pdb=" O LEU K 32 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N VAL K 37 " --> pdb=" O ALA K 33 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA K 40 " --> pdb=" O PHE K 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 15 through 39 removed outlier: 4.747A pdb=" N SER L 35 " --> pdb=" O ILE L 31 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N TYR L 36 " --> pdb=" O LEU L 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 28 removed outlier: 3.845A pdb=" N VAL M 15 " --> pdb=" O SER M 11 " (cutoff:3.500A) Proline residue: M 18 - end of helix Processing helix chain 'T' and resid 3 through 23 Processing helix chain 'X' and resid 2 through 16 Processing helix chain 'X' and resid 23 through 34 Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA2, first strand: chain 'B' and resid 166 through 168 Processing sheet with id=AA3, first strand: chain 'B' and resid 336 through 340 removed outlier: 6.622A pdb=" N ASP B 431 " --> pdb=" O GLN B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 377 through 380 removed outlier: 4.014A pdb=" N PHE B 346 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL B 356 " --> pdb=" O PRO B 344 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 172 through 174 Processing sheet with id=AA6, first strand: chain 'C' and resid 328 through 330 Processing sheet with id=AA7, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.548A pdb=" N GLY C 361 " --> pdb=" O GLY C 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 77 through 78 863 hydrogen bonds defined for protein. 2427 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: 6.01 Time building geometry restraints manager: 7.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.39: 7306 1.39 - 1.60: 11874 1.60 - 1.81: 150 1.81 - 2.03: 35 2.03 - 2.24: 109 Bond restraints: 19474 Sorted by residual: bond pdb=" C10 BCR C 519 " pdb=" C11 BCR C 519 " ideal model delta sigma weight residual 1.436 1.172 0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" C10 BCR X 102 " pdb=" C11 BCR X 102 " ideal model delta sigma weight residual 1.436 1.175 0.261 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C10 BCR B 618 " pdb=" C11 BCR B 618 " ideal model delta sigma weight residual 1.436 1.177 0.259 2.00e-02 2.50e+03 1.68e+02 bond pdb=" C10 BCR B 617 " pdb=" C11 BCR B 617 " ideal model delta sigma weight residual 1.436 1.178 0.258 2.00e-02 2.50e+03 1.66e+02 bond pdb=" C10 BCR C 516 " pdb=" C11 BCR C 516 " ideal model delta sigma weight residual 1.436 1.179 0.257 2.00e-02 2.50e+03 1.65e+02 ... (remaining 19469 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.46: 26716 11.46 - 22.91: 99 22.91 - 34.37: 37 34.37 - 45.83: 18 45.83 - 57.28: 9 Bond angle restraints: 26879 Sorted by residual: angle pdb=" C10 BCR X 102 " pdb=" C11 BCR X 102 " pdb=" C12 BCR X 102 " ideal model delta sigma weight residual 122.66 179.94 -57.28 3.00e+00 1.11e-01 3.65e+02 angle pdb=" C10 BCR D 407 " pdb=" C11 BCR D 407 " pdb=" C12 BCR D 407 " ideal model delta sigma weight residual 122.66 177.86 -55.20 3.00e+00 1.11e-01 3.39e+02 angle pdb=" C10 BCR B 618 " pdb=" C11 BCR B 618 " pdb=" C12 BCR B 618 " ideal model delta sigma weight residual 122.66 177.61 -54.95 3.00e+00 1.11e-01 3.35e+02 angle pdb=" C10 BCR B 619 " pdb=" C11 BCR B 619 " pdb=" C12 BCR B 619 " ideal model delta sigma weight residual 122.66 177.34 -54.68 3.00e+00 1.11e-01 3.32e+02 angle pdb=" C10 BCR C 516 " pdb=" C11 BCR C 516 " pdb=" C12 BCR C 516 " ideal model delta sigma weight residual 122.66 177.23 -54.57 3.00e+00 1.11e-01 3.31e+02 ... (remaining 26874 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.82: 9376 25.82 - 51.64: 732 51.64 - 77.45: 163 77.45 - 103.27: 19 103.27 - 129.09: 12 Dihedral angle restraints: 10302 sinusoidal: 4953 harmonic: 5349 Sorted by residual: dihedral pdb=" CA PHE A 260 " pdb=" C PHE A 260 " pdb=" N GLN A 261 " pdb=" CA GLN A 261 " ideal model delta harmonic sigma weight residual 180.00 148.02 31.98 0 5.00e+00 4.00e-02 4.09e+01 dihedral pdb=" CA ASP C 365 " pdb=" C ASP C 365 " pdb=" N LYS C 366 " pdb=" CA LYS C 366 " ideal model delta harmonic sigma weight residual 180.00 154.95 25.05 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA GLY C 209 " pdb=" C GLY C 209 " pdb=" N TRP C 210 " pdb=" CA TRP C 210 " ideal model delta harmonic sigma weight residual -180.00 -156.85 -23.15 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 10299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 2464 0.157 - 0.314: 51 0.314 - 0.471: 10 0.471 - 0.628: 19 0.628 - 0.785: 9 Chirality restraints: 2553 Sorted by residual: chirality pdb=" C3A CLA B 604 " pdb=" C2A CLA B 604 " pdb=" C4A CLA B 604 " pdb=" CMA CLA B 604 " both_signs ideal model delta sigma weight residual False -2.76 -1.98 -0.79 2.00e-01 2.50e+01 1.54e+01 chirality pdb=" C3A CLA C 512 " pdb=" C2A CLA C 512 " pdb=" C4A CLA C 512 " pdb=" CMA CLA C 512 " both_signs ideal model delta sigma weight residual False -2.76 -2.04 -0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" C3A CLA C 504 " pdb=" C2A CLA C 504 " pdb=" C4A CLA C 504 " pdb=" CMA CLA C 504 " both_signs ideal model delta sigma weight residual False -2.76 -2.04 -0.72 2.00e-01 2.50e+01 1.30e+01 ... (remaining 2550 not shown) Planarity restraints: 3320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB PHO A 404 " 0.117 2.00e-02 2.50e+03 1.31e-01 1.37e+03 pdb=" ND PHO A 404 " 0.055 2.00e-02 2.50e+03 pdb=" C1A PHO A 404 " -0.015 2.00e-02 2.50e+03 pdb=" C1B PHO A 404 " 0.063 2.00e-02 2.50e+03 pdb=" C1C PHO A 404 " 0.010 2.00e-02 2.50e+03 pdb=" C1D PHO A 404 " -0.014 2.00e-02 2.50e+03 pdb=" C2A PHO A 404 " -0.180 2.00e-02 2.50e+03 pdb=" C2B PHO A 404 " -0.114 2.00e-02 2.50e+03 pdb=" C2C PHO A 404 " 0.065 2.00e-02 2.50e+03 pdb=" C2D PHO A 404 " -0.042 2.00e-02 2.50e+03 pdb=" C3A PHO A 404 " 0.340 2.00e-02 2.50e+03 pdb=" C3B PHO A 404 " -0.150 2.00e-02 2.50e+03 pdb=" C3C PHO A 404 " 0.053 2.00e-02 2.50e+03 pdb=" C3D PHO A 404 " -0.061 2.00e-02 2.50e+03 pdb=" C4A PHO A 404 " 0.238 2.00e-02 2.50e+03 pdb=" C4B PHO A 404 " -0.001 2.00e-02 2.50e+03 pdb=" C4C PHO A 404 " -0.017 2.00e-02 2.50e+03 pdb=" C4D PHO A 404 " -0.025 2.00e-02 2.50e+03 pdb=" CAB PHO A 404 " -0.294 2.00e-02 2.50e+03 pdb=" CAC PHO A 404 " 0.098 2.00e-02 2.50e+03 pdb=" CAD PHO A 404 " -0.076 2.00e-02 2.50e+03 pdb=" CBD PHO A 404 " -0.146 2.00e-02 2.50e+03 pdb=" CHA PHO A 404 " -0.060 2.00e-02 2.50e+03 pdb=" CHB PHO A 404 " 0.155 2.00e-02 2.50e+03 pdb=" CHC PHO A 404 " 0.028 2.00e-02 2.50e+03 pdb=" CHD PHO A 404 " -0.049 2.00e-02 2.50e+03 pdb=" CMB PHO A 404 " -0.202 2.00e-02 2.50e+03 pdb=" CMC PHO A 404 " 0.132 2.00e-02 2.50e+03 pdb=" CMD PHO A 404 " -0.051 2.00e-02 2.50e+03 pdb=" NA PHO A 404 " 0.234 2.00e-02 2.50e+03 pdb=" NC PHO A 404 " -0.042 2.00e-02 2.50e+03 pdb=" OBD PHO A 404 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB PHO D 403 " -0.048 2.00e-02 2.50e+03 1.27e-01 1.28e+03 pdb=" ND PHO D 403 " 0.189 2.00e-02 2.50e+03 pdb=" C1A PHO D 403 " -0.045 2.00e-02 2.50e+03 pdb=" C1B PHO D 403 " -0.022 2.00e-02 2.50e+03 pdb=" C1C PHO D 403 " -0.001 2.00e-02 2.50e+03 pdb=" C1D PHO D 403 " 0.075 2.00e-02 2.50e+03 pdb=" C2A PHO D 403 " 0.089 2.00e-02 2.50e+03 pdb=" C2B PHO D 403 " 0.115 2.00e-02 2.50e+03 pdb=" C2C PHO D 403 " -0.076 2.00e-02 2.50e+03 pdb=" C2D PHO D 403 " 0.075 2.00e-02 2.50e+03 pdb=" C3A PHO D 403 " -0.311 2.00e-02 2.50e+03 pdb=" C3B PHO D 403 " 0.149 2.00e-02 2.50e+03 pdb=" C3C PHO D 403 " -0.102 2.00e-02 2.50e+03 pdb=" C3D PHO D 403 " 0.073 2.00e-02 2.50e+03 pdb=" C4A PHO D 403 " -0.203 2.00e-02 2.50e+03 pdb=" C4B PHO D 403 " 0.041 2.00e-02 2.50e+03 pdb=" C4C PHO D 403 " -0.030 2.00e-02 2.50e+03 pdb=" C4D PHO D 403 " 0.078 2.00e-02 2.50e+03 pdb=" CAB PHO D 403 " 0.240 2.00e-02 2.50e+03 pdb=" CAC PHO D 403 " -0.186 2.00e-02 2.50e+03 pdb=" CAD PHO D 403 " 0.069 2.00e-02 2.50e+03 pdb=" CBD PHO D 403 " -0.110 2.00e-02 2.50e+03 pdb=" CHA PHO D 403 " -0.024 2.00e-02 2.50e+03 pdb=" CHB PHO D 403 " -0.109 2.00e-02 2.50e+03 pdb=" CHC PHO D 403 " 0.005 2.00e-02 2.50e+03 pdb=" CHD PHO D 403 " -0.028 2.00e-02 2.50e+03 pdb=" CMB PHO D 403 " 0.163 2.00e-02 2.50e+03 pdb=" CMC PHO D 403 " -0.132 2.00e-02 2.50e+03 pdb=" CMD PHO D 403 " 0.067 2.00e-02 2.50e+03 pdb=" NA PHO D 403 " -0.214 2.00e-02 2.50e+03 pdb=" NC PHO D 403 " 0.033 2.00e-02 2.50e+03 pdb=" OBD PHO D 403 " 0.179 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BCR C 519 " -0.290 2.00e-02 2.50e+03 1.68e-01 3.51e+02 pdb=" C11 BCR C 519 " 0.200 2.00e-02 2.50e+03 pdb=" C34 BCR C 519 " 0.064 2.00e-02 2.50e+03 pdb=" C8 BCR C 519 " 0.089 2.00e-02 2.50e+03 pdb=" C9 BCR C 519 " -0.062 2.00e-02 2.50e+03 ... (remaining 3317 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 351 2.65 - 3.21: 16288 3.21 - 3.77: 31536 3.77 - 4.34: 48433 4.34 - 4.90: 74435 Nonbonded interactions: 171043 Sorted by model distance: nonbonded pdb=" OE1 GLN C 298 " pdb=" OG1 THR C 342 " model vdw 2.082 3.040 nonbonded pdb=" O TYR C 258 " pdb=" O HOH C 601 " model vdw 2.143 3.040 nonbonded pdb=" O LEU M 25 " pdb=" OG1 THR M 29 " model vdw 2.153 3.040 nonbonded pdb=" O ASN B 191 " pdb=" O HOH B 701 " model vdw 2.159 3.040 nonbonded pdb=" O HOH A 502 " pdb=" O HOH A 552 " model vdw 2.175 3.040 ... (remaining 171038 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.940 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: 0.050 Extract box with map and model: 0.790 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 43.620 Find NCS groups from input model: 0.270 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:15.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 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 : 0.025 0.264 19474 Z= 1.322 Angle : 2.549 57.283 26879 Z= 0.881 Chirality : 0.086 0.785 2553 Planarity : 0.012 0.168 3320 Dihedral : 18.877 129.089 6888 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.14 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.58 (0.16), residues: 1866 helix: -2.86 (0.11), residues: 1087 sheet: -2.78 (0.65), residues: 49 loop : -1.20 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 131 HIS 0.006 0.001 HIS C 417 PHE 0.030 0.002 PHE B 246 TYR 0.016 0.002 TYR H 49 ARG 0.006 0.001 ARG D 294 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 1.817 Fit side-chains revert: symmetry clash REVERT: A 59 ASP cc_start: 0.7123 (t0) cc_final: 0.6740 (t0) REVERT: A 86 SER cc_start: 0.8798 (t) cc_final: 0.8577 (t) REVERT: A 87 ASN cc_start: 0.8292 (t0) cc_final: 0.8076 (t0) REVERT: A 214 MET cc_start: 0.7978 (tpt) cc_final: 0.7757 (mmm) REVERT: A 293 MET cc_start: 0.7648 (mtm) cc_final: 0.7440 (mtp) REVERT: B 231 MET cc_start: 0.9135 (mtt) cc_final: 0.8777 (mtt) REVERT: B 347 LYS cc_start: 0.8174 (mttm) cc_final: 0.7946 (mttm) REVERT: B 349 LYS cc_start: 0.7357 (pttm) cc_final: 0.6802 (pttp) REVERT: B 359 MET cc_start: 0.8785 (ttm) cc_final: 0.8579 (ttp) REVERT: B 422 ARG cc_start: 0.7999 (mtt90) cc_final: 0.7755 (mtt-85) REVERT: C 65 GLU cc_start: 0.7149 (pm20) cc_final: 0.6891 (pm20) REVERT: C 91 GLU cc_start: 0.7722 (mp0) cc_final: 0.7328 (mp0) REVERT: C 169 PHE cc_start: 0.6989 (m-80) cc_final: 0.6761 (m-80) REVERT: D 317 LYS cc_start: 0.8718 (mtpp) cc_final: 0.8321 (mtpt) REVERT: D 343 GLU cc_start: 0.6856 (tp30) cc_final: 0.6583 (tp30) REVERT: D 348 ARG cc_start: 0.7605 (ptp90) cc_final: 0.6921 (ptp-110) REVERT: F 40 GLN cc_start: 0.8830 (mm-40) cc_final: 0.8611 (mm-40) REVERT: H 9 ASP cc_start: 0.7929 (m-30) cc_final: 0.7499 (m-30) REVERT: I 30 ARG cc_start: 0.7207 (mtt-85) cc_final: 0.6747 (mmt90) REVERT: L 23 LEU cc_start: 0.8320 (mt) cc_final: 0.8090 (OUTLIER) REVERT: X 32 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7457 (mm110) outliers start: 0 outliers final: 2 residues processed: 269 average time/residue: 1.3915 time to fit residues: 419.2974 Evaluate side-chains 210 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 356 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 HIS A 332 HIS B 76 ASN B 157 HIS ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 GLN B 331 ASN B 413 ASN B 438 ASN C 142 ASN C 216 ASN C 300 GLN C 309 GLN C 385 HIS D 142 ASN D 263 ASN E 67 GLN H 3 GLN M 5 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19474 Z= 0.246 Angle : 0.683 9.958 26879 Z= 0.317 Chirality : 0.045 0.201 2553 Planarity : 0.006 0.049 3320 Dihedral : 19.575 126.640 3655 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.79 % Favored : 97.16 % Rotamer: Outliers : 1.75 % Allowed : 7.91 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.85 (0.18), residues: 1866 helix: -0.27 (0.14), residues: 1106 sheet: -2.49 (0.65), residues: 49 loop : -0.66 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 131 HIS 0.007 0.002 HIS C 417 PHE 0.031 0.002 PHE B 246 TYR 0.013 0.002 TYR B 172 ARG 0.006 0.001 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 217 time to evaluate : 1.906 Fit side-chains REVERT: A 59 ASP cc_start: 0.7212 (t0) cc_final: 0.6808 (t0) REVERT: A 86 SER cc_start: 0.8768 (t) cc_final: 0.8539 (t) REVERT: A 87 ASN cc_start: 0.8333 (t0) cc_final: 0.8113 (t0) REVERT: A 322 ASN cc_start: 0.8137 (t0) cc_final: 0.7904 (t0) REVERT: B 22 VAL cc_start: 0.9104 (OUTLIER) cc_final: 0.8794 (m) REVERT: B 231 MET cc_start: 0.9167 (mtt) cc_final: 0.8804 (mtt) REVERT: B 347 LYS cc_start: 0.8232 (mttm) cc_final: 0.7963 (mttm) REVERT: B 349 LYS cc_start: 0.7634 (pttm) cc_final: 0.7207 (pttp) REVERT: B 350 GLU cc_start: 0.7112 (mp0) cc_final: 0.6845 (mp0) REVERT: B 359 MET cc_start: 0.8848 (ttm) cc_final: 0.8620 (ttp) REVERT: B 387 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6238 (mm-30) REVERT: C 65 GLU cc_start: 0.7144 (pm20) cc_final: 0.6926 (pm20) REVERT: C 169 PHE cc_start: 0.7090 (m-80) cc_final: 0.6825 (m-80) REVERT: C 229 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8245 (mm) REVERT: C 330 ARG cc_start: 0.7007 (mtt-85) cc_final: 0.6789 (mtt-85) REVERT: C 366 LYS cc_start: 0.7943 (mtpt) cc_final: 0.7655 (mttp) REVERT: C 372 GLN cc_start: 0.7212 (mm-40) cc_final: 0.6658 (mm110) REVERT: D 348 ARG cc_start: 0.7396 (ptp90) cc_final: 0.7153 (ptp-110) REVERT: H 9 ASP cc_start: 0.7759 (m-30) cc_final: 0.7520 (m-30) REVERT: H 12 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.6643 (tpm170) REVERT: H 31 MET cc_start: 0.8683 (ttp) cc_final: 0.8320 (ttp) REVERT: I 30 ARG cc_start: 0.6886 (mtt-85) cc_final: 0.6546 (mmt90) REVERT: L 23 LEU cc_start: 0.8295 (mt) cc_final: 0.8051 (mp) outliers start: 27 outliers final: 10 residues processed: 228 average time/residue: 1.4001 time to fit residues: 358.2468 Evaluate side-chains 216 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 202 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain X residue 2 THR Chi-restraints excluded: chain X residue 19 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 167 optimal weight: 1.9990 chunk 180 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 chunk 165 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN B 438 ASN C 300 GLN C 375 GLN D 142 ASN D 263 ASN D 336 HIS E 67 GLN H 3 GLN M 5 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19474 Z= 0.177 Angle : 0.596 8.595 26879 Z= 0.275 Chirality : 0.043 0.192 2553 Planarity : 0.005 0.047 3320 Dihedral : 18.650 123.104 3653 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.98 % Favored : 97.96 % Rotamer: Outliers : 1.69 % Allowed : 9.40 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: 0.39 (0.19), residues: 1866 helix: 0.84 (0.15), residues: 1108 sheet: -2.05 (0.66), residues: 49 loop : -0.35 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 131 HIS 0.005 0.001 HIS C 417 PHE 0.026 0.001 PHE B 246 TYR 0.010 0.001 TYR B 172 ARG 0.007 0.000 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 216 time to evaluate : 1.645 Fit side-chains REVERT: A 59 ASP cc_start: 0.7214 (t0) cc_final: 0.6874 (t0) REVERT: A 86 SER cc_start: 0.8751 (t) cc_final: 0.8534 (t) REVERT: A 107 TYR cc_start: 0.8953 (t80) cc_final: 0.8618 (t80) REVERT: B 22 VAL cc_start: 0.9079 (OUTLIER) cc_final: 0.8749 (m) REVERT: B 231 MET cc_start: 0.9160 (mtt) cc_final: 0.8839 (mtt) REVERT: B 347 LYS cc_start: 0.8007 (mttm) cc_final: 0.7734 (mttm) REVERT: B 349 LYS cc_start: 0.7789 (pttm) cc_final: 0.7421 (pttp) REVERT: B 350 GLU cc_start: 0.6994 (mp0) cc_final: 0.6720 (mp0) REVERT: B 359 MET cc_start: 0.8844 (ttm) cc_final: 0.8536 (ttp) REVERT: C 169 PHE cc_start: 0.7041 (m-80) cc_final: 0.6769 (m-80) REVERT: C 366 LYS cc_start: 0.7935 (mtpt) cc_final: 0.7655 (mttp) REVERT: C 368 ARG cc_start: 0.6473 (mmt-90) cc_final: 0.5880 (mmp80) REVERT: C 377 ARG cc_start: 0.7691 (ttp-170) cc_final: 0.7437 (mtp180) REVERT: D 348 ARG cc_start: 0.7373 (ptp90) cc_final: 0.7144 (ptp-110) REVERT: E 20 TRP cc_start: 0.6387 (OUTLIER) cc_final: 0.6117 (m-90) REVERT: F 39 MET cc_start: 0.9071 (mtt) cc_final: 0.8641 (mtm) REVERT: H 9 ASP cc_start: 0.7752 (m-30) cc_final: 0.7405 (m-30) REVERT: H 12 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7294 (tpm170) REVERT: H 31 MET cc_start: 0.8612 (ttp) cc_final: 0.8225 (ttp) REVERT: I 30 ARG cc_start: 0.7011 (mtt-85) cc_final: 0.6735 (mmt90) REVERT: K 22 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7746 (m-30) REVERT: L 23 LEU cc_start: 0.8253 (mt) cc_final: 0.8018 (mp) REVERT: M 6 LEU cc_start: 0.8729 (mp) cc_final: 0.8491 (mm) REVERT: M 8 PHE cc_start: 0.8528 (t80) cc_final: 0.8250 (t80) outliers start: 26 outliers final: 10 residues processed: 230 average time/residue: 1.3967 time to fit residues: 361.0073 Evaluate side-chains 219 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 205 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain D residue 12 ARG Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain E residue 20 TRP Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain K residue 22 ASP Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain X residue 2 THR Chi-restraints excluded: chain X residue 4 SER Chi-restraints excluded: chain X residue 19 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 159 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN B 438 ASN C 298 GLN D 263 ASN E 67 GLN H 3 GLN M 5 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19474 Z= 0.227 Angle : 0.602 8.893 26879 Z= 0.279 Chirality : 0.044 0.204 2553 Planarity : 0.005 0.049 3320 Dihedral : 18.216 124.854 3653 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.09 % Favored : 97.86 % Rotamer: Outliers : 1.88 % Allowed : 10.24 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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 (0.19), residues: 1866 helix: 1.19 (0.16), residues: 1112 sheet: -1.72 (0.68), residues: 49 loop : -0.23 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 131 HIS 0.008 0.001 HIS C 417 PHE 0.029 0.002 PHE B 246 TYR 0.014 0.002 TYR B 172 ARG 0.009 0.001 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 1.737 Fit side-chains revert: symmetry clash REVERT: A 59 ASP cc_start: 0.7270 (t0) cc_final: 0.6909 (t0) REVERT: A 86 SER cc_start: 0.8761 (t) cc_final: 0.8543 (t) REVERT: A 107 TYR cc_start: 0.8963 (t80) cc_final: 0.8650 (t80) REVERT: B 22 VAL cc_start: 0.9075 (OUTLIER) cc_final: 0.8730 (m) REVERT: B 231 MET cc_start: 0.9146 (mtt) cc_final: 0.8797 (mtt) REVERT: B 347 LYS cc_start: 0.7984 (mttm) cc_final: 0.7721 (mttm) REVERT: B 349 LYS cc_start: 0.7713 (pttm) cc_final: 0.7171 (pttp) REVERT: B 350 GLU cc_start: 0.7041 (mp0) cc_final: 0.6750 (mp0) REVERT: B 359 MET cc_start: 0.8867 (ttm) cc_final: 0.8577 (ttp) REVERT: B 387 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6198 (mm-30) REVERT: C 91 GLU cc_start: 0.7626 (mp0) cc_final: 0.7344 (mp0) REVERT: C 169 PHE cc_start: 0.7038 (m-80) cc_final: 0.6761 (m-80) REVERT: C 366 LYS cc_start: 0.7913 (mtpt) cc_final: 0.7648 (mttp) REVERT: C 368 ARG cc_start: 0.6545 (mmt-90) cc_final: 0.5950 (mmp80) REVERT: C 372 GLN cc_start: 0.7139 (mm-40) cc_final: 0.6704 (mm110) REVERT: C 377 ARG cc_start: 0.7703 (ttp-170) cc_final: 0.7492 (mtp180) REVERT: D 348 ARG cc_start: 0.7369 (ptp90) cc_final: 0.7130 (ptp-110) REVERT: E 20 TRP cc_start: 0.6357 (OUTLIER) cc_final: 0.6134 (m-90) REVERT: H 9 ASP cc_start: 0.7788 (m-30) cc_final: 0.7533 (m-30) REVERT: H 31 MET cc_start: 0.8602 (ttp) cc_final: 0.8238 (ttp) REVERT: I 30 ARG cc_start: 0.7110 (mtt-85) cc_final: 0.6726 (mmt90) REVERT: K 22 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7776 (m-30) REVERT: L 23 LEU cc_start: 0.8257 (mt) cc_final: 0.8023 (mp) REVERT: M 6 LEU cc_start: 0.8759 (mp) cc_final: 0.8516 (mm) outliers start: 29 outliers final: 17 residues processed: 224 average time/residue: 1.4391 time to fit residues: 361.0790 Evaluate side-chains 224 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 203 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain E residue 20 TRP Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain K residue 22 ASP Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain X residue 2 THR Chi-restraints excluded: chain X residue 4 SER Chi-restraints excluded: chain X residue 19 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 0.5980 chunk 100 optimal weight: 5.9990 chunk 2 optimal weight: 0.0970 chunk 132 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 151 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN B 438 ASN ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 375 GLN D 263 ASN E 67 GLN H 3 GLN M 5 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19474 Z= 0.215 Angle : 0.582 9.033 26879 Z= 0.271 Chirality : 0.043 0.198 2553 Planarity : 0.005 0.049 3320 Dihedral : 17.874 124.539 3653 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.93 % Favored : 98.02 % Rotamer: Outliers : 2.07 % Allowed : 10.95 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: 1.05 (0.20), residues: 1866 helix: 1.37 (0.16), residues: 1112 sheet: -1.56 (0.69), residues: 49 loop : -0.11 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 131 HIS 0.007 0.001 HIS C 417 PHE 0.028 0.001 PHE B 246 TYR 0.012 0.001 TYR B 172 ARG 0.009 0.000 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 209 time to evaluate : 1.840 Fit side-chains revert: symmetry clash REVERT: A 59 ASP cc_start: 0.7236 (t0) cc_final: 0.6867 (t0) REVERT: A 86 SER cc_start: 0.8753 (t) cc_final: 0.8540 (t) REVERT: A 107 TYR cc_start: 0.8963 (t80) cc_final: 0.8646 (t80) REVERT: B 231 MET cc_start: 0.9142 (mtt) cc_final: 0.8802 (mtt) REVERT: B 347 LYS cc_start: 0.7953 (mttm) cc_final: 0.7696 (mttm) REVERT: B 349 LYS cc_start: 0.7736 (pttm) cc_final: 0.7192 (pttp) REVERT: B 350 GLU cc_start: 0.7062 (mp0) cc_final: 0.6743 (mp0) REVERT: B 359 MET cc_start: 0.8869 (ttm) cc_final: 0.8584 (ttp) REVERT: B 387 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6192 (mm-30) REVERT: C 169 PHE cc_start: 0.6992 (m-80) cc_final: 0.6758 (m-80) REVERT: C 366 LYS cc_start: 0.7906 (mtpt) cc_final: 0.7632 (mttp) REVERT: C 372 GLN cc_start: 0.7224 (mm-40) cc_final: 0.6843 (mm110) REVERT: F 39 MET cc_start: 0.9062 (mtt) cc_final: 0.8691 (mtm) REVERT: H 9 ASP cc_start: 0.7801 (m-30) cc_final: 0.7554 (m-30) REVERT: H 31 MET cc_start: 0.8593 (ttp) cc_final: 0.8241 (ttp) REVERT: I 30 ARG cc_start: 0.7138 (mtt-85) cc_final: 0.6759 (mmt90) REVERT: K 22 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7740 (m-30) REVERT: L 23 LEU cc_start: 0.8251 (mt) cc_final: 0.8011 (mp) REVERT: M 6 LEU cc_start: 0.8749 (mp) cc_final: 0.8518 (mm) REVERT: T 16 VAL cc_start: 0.7994 (t) cc_final: 0.7470 (p) outliers start: 32 outliers final: 20 residues processed: 224 average time/residue: 1.4321 time to fit residues: 359.9238 Evaluate side-chains 223 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 201 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain K residue 22 ASP Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain X residue 2 THR Chi-restraints excluded: chain X residue 4 SER Chi-restraints excluded: chain X residue 19 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 178 optimal weight: 0.0570 chunk 147 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN B 438 ASN H 3 GLN M 5 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19474 Z= 0.156 Angle : 0.540 8.560 26879 Z= 0.251 Chirality : 0.041 0.210 2553 Planarity : 0.004 0.048 3320 Dihedral : 17.253 122.660 3653 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.94 % Allowed : 11.54 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.20), residues: 1866 helix: 1.62 (0.16), residues: 1112 sheet: -1.47 (0.68), residues: 49 loop : -0.01 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 131 HIS 0.005 0.001 HIS C 417 PHE 0.027 0.001 PHE B 246 TYR 0.010 0.001 TYR B 273 ARG 0.007 0.000 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 213 time to evaluate : 1.864 Fit side-chains REVERT: A 59 ASP cc_start: 0.7202 (t0) cc_final: 0.6837 (t0) REVERT: A 86 SER cc_start: 0.8730 (t) cc_final: 0.8520 (t) REVERT: A 107 TYR cc_start: 0.8958 (t80) cc_final: 0.8662 (t80) REVERT: B 22 VAL cc_start: 0.8985 (OUTLIER) cc_final: 0.8617 (m) REVERT: B 231 MET cc_start: 0.9103 (mtt) cc_final: 0.8778 (mtt) REVERT: B 347 LYS cc_start: 0.7937 (mttm) cc_final: 0.7680 (mttm) REVERT: B 359 MET cc_start: 0.8855 (ttm) cc_final: 0.8508 (ttp) REVERT: C 169 PHE cc_start: 0.6930 (m-80) cc_final: 0.6646 (m-80) REVERT: C 366 LYS cc_start: 0.7848 (mtpt) cc_final: 0.7586 (mttp) REVERT: C 368 ARG cc_start: 0.6541 (mmt-90) cc_final: 0.5947 (mmp80) REVERT: C 372 GLN cc_start: 0.7123 (mm-40) cc_final: 0.6776 (mm110) REVERT: F 39 MET cc_start: 0.9058 (mtt) cc_final: 0.8645 (mtm) REVERT: H 9 ASP cc_start: 0.7821 (m-30) cc_final: 0.7496 (m-30) REVERT: H 12 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.5679 (tpm170) REVERT: H 31 MET cc_start: 0.8583 (ttp) cc_final: 0.8230 (ttp) REVERT: I 30 ARG cc_start: 0.7174 (mtt-85) cc_final: 0.6784 (mmt90) REVERT: K 22 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7957 (m-30) REVERT: L 23 LEU cc_start: 0.8256 (mt) cc_final: 0.8016 (mp) REVERT: M 6 LEU cc_start: 0.8747 (mp) cc_final: 0.8536 (mm) REVERT: T 16 VAL cc_start: 0.7956 (t) cc_final: 0.7445 (p) outliers start: 30 outliers final: 13 residues processed: 231 average time/residue: 1.4080 time to fit residues: 365.1299 Evaluate side-chains 219 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 203 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain K residue 22 ASP Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain X residue 2 THR Chi-restraints excluded: chain X residue 4 SER Chi-restraints excluded: chain X residue 19 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 110 optimal weight: 0.0770 chunk 108 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.2940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN B 438 ASN C 105 HIS D 263 ASN H 3 GLN M 5 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19474 Z= 0.186 Angle : 0.562 8.771 26879 Z= 0.261 Chirality : 0.042 0.189 2553 Planarity : 0.004 0.048 3320 Dihedral : 17.162 123.866 3653 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.62 % Allowed : 12.18 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: 1.41 (0.20), residues: 1866 helix: 1.66 (0.16), residues: 1111 sheet: -1.39 (0.69), residues: 49 loop : 0.05 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 131 HIS 0.006 0.001 HIS C 417 PHE 0.028 0.001 PHE B 246 TYR 0.012 0.001 TYR B 273 ARG 0.008 0.000 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 1.824 Fit side-chains REVERT: A 59 ASP cc_start: 0.7242 (t0) cc_final: 0.6864 (t0) REVERT: A 86 SER cc_start: 0.8730 (t) cc_final: 0.8469 (t) REVERT: A 107 TYR cc_start: 0.8931 (t80) cc_final: 0.8517 (t80) REVERT: B 22 VAL cc_start: 0.9049 (OUTLIER) cc_final: 0.8729 (m) REVERT: B 231 MET cc_start: 0.9111 (mtt) cc_final: 0.8764 (mtt) REVERT: B 347 LYS cc_start: 0.7930 (mttm) cc_final: 0.7669 (mttm) REVERT: B 359 MET cc_start: 0.8867 (ttm) cc_final: 0.8530 (ttp) REVERT: B 387 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6249 (mm-30) REVERT: C 366 LYS cc_start: 0.7871 (mtpt) cc_final: 0.7600 (mttp) REVERT: C 372 GLN cc_start: 0.7133 (mm-40) cc_final: 0.6811 (mm110) REVERT: F 39 MET cc_start: 0.9065 (mtt) cc_final: 0.8653 (mtm) REVERT: H 9 ASP cc_start: 0.7778 (m-30) cc_final: 0.7527 (m-30) REVERT: H 31 MET cc_start: 0.8594 (ttp) cc_final: 0.8234 (ttp) REVERT: I 30 ARG cc_start: 0.7188 (mtt-85) cc_final: 0.6805 (mmt90) REVERT: K 15 GLN cc_start: 0.7760 (mt0) cc_final: 0.7494 (mt0) REVERT: K 22 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7729 (m-30) REVERT: L 23 LEU cc_start: 0.8248 (mt) cc_final: 0.8006 (mp) REVERT: M 6 LEU cc_start: 0.8754 (mp) cc_final: 0.8547 (mm) REVERT: T 16 VAL cc_start: 0.7989 (t) cc_final: 0.7478 (p) outliers start: 25 outliers final: 15 residues processed: 212 average time/residue: 1.4845 time to fit residues: 354.9228 Evaluate side-chains 213 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 195 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain K residue 22 ASP Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain X residue 2 THR Chi-restraints excluded: chain X residue 4 SER Chi-restraints excluded: chain X residue 19 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 139 optimal weight: 8.9990 chunk 161 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN H 3 GLN M 5 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19474 Z= 0.300 Angle : 0.638 9.038 26879 Z= 0.295 Chirality : 0.046 0.216 2553 Planarity : 0.005 0.049 3320 Dihedral : 17.534 126.032 3653 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.07 % Allowed : 11.92 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: 1.18 (0.20), residues: 1866 helix: 1.44 (0.16), residues: 1118 sheet: -1.29 (0.70), residues: 47 loop : -0.02 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 131 HIS 0.008 0.002 HIS C 417 PHE 0.029 0.002 PHE B 246 TYR 0.016 0.002 TYR B 172 ARG 0.008 0.001 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 205 time to evaluate : 1.704 Fit side-chains REVERT: A 59 ASP cc_start: 0.7263 (t0) cc_final: 0.6833 (t0) REVERT: A 86 SER cc_start: 0.8778 (t) cc_final: 0.8501 (t) REVERT: A 107 TYR cc_start: 0.8954 (t80) cc_final: 0.8533 (t80) REVERT: B 149 LEU cc_start: 0.8783 (tp) cc_final: 0.8552 (tp) REVERT: B 231 MET cc_start: 0.9141 (mtt) cc_final: 0.8798 (mtt) REVERT: B 347 LYS cc_start: 0.7982 (mttm) cc_final: 0.7714 (mttm) REVERT: B 359 MET cc_start: 0.8882 (ttm) cc_final: 0.8637 (ttp) REVERT: B 387 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6348 (mm-30) REVERT: C 91 GLU cc_start: 0.7491 (mp0) cc_final: 0.7229 (mp0) REVERT: C 169 PHE cc_start: 0.7007 (m-80) cc_final: 0.6796 (m-10) REVERT: C 366 LYS cc_start: 0.7904 (mtpt) cc_final: 0.7659 (mttp) REVERT: C 368 ARG cc_start: 0.6486 (mmt-90) cc_final: 0.6028 (mmp80) REVERT: C 372 GLN cc_start: 0.7124 (mm-40) cc_final: 0.6794 (mm110) REVERT: F 39 MET cc_start: 0.9084 (mtt) cc_final: 0.8664 (mtm) REVERT: F 40 GLN cc_start: 0.8850 (mm-40) cc_final: 0.8629 (mm-40) REVERT: H 9 ASP cc_start: 0.7789 (m-30) cc_final: 0.7531 (m-30) REVERT: H 31 MET cc_start: 0.8609 (ttp) cc_final: 0.8265 (ttp) REVERT: I 30 ARG cc_start: 0.7097 (mtt-85) cc_final: 0.6707 (mmt90) REVERT: K 22 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7727 (m-30) REVERT: L 23 LEU cc_start: 0.8271 (mt) cc_final: 0.8032 (mp) REVERT: M 6 LEU cc_start: 0.8763 (mp) cc_final: 0.8551 (mm) REVERT: T 16 VAL cc_start: 0.8045 (t) cc_final: 0.7520 (p) outliers start: 32 outliers final: 20 residues processed: 222 average time/residue: 1.4573 time to fit residues: 362.3864 Evaluate side-chains 221 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 199 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain K residue 22 ASP Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain X residue 2 THR Chi-restraints excluded: chain X residue 4 SER Chi-restraints excluded: chain X residue 19 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 129 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 chunk 156 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN H 3 GLN M 5 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19474 Z= 0.155 Angle : 0.544 9.061 26879 Z= 0.254 Chirality : 0.041 0.191 2553 Planarity : 0.004 0.049 3320 Dihedral : 16.887 123.061 3653 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.36 % Allowed : 12.96 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: 1.51 (0.20), residues: 1866 helix: 1.72 (0.16), residues: 1114 sheet: -1.32 (0.69), residues: 49 loop : 0.12 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 131 HIS 0.008 0.001 HIS D 214 PHE 0.028 0.001 PHE B 246 TYR 0.010 0.001 TYR B 273 ARG 0.009 0.000 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 1.906 Fit side-chains REVERT: A 59 ASP cc_start: 0.7193 (t0) cc_final: 0.6815 (t0) REVERT: A 86 SER cc_start: 0.8683 (t) cc_final: 0.8443 (t) REVERT: A 107 TYR cc_start: 0.8958 (t80) cc_final: 0.8668 (t80) REVERT: B 22 VAL cc_start: 0.8964 (OUTLIER) cc_final: 0.8603 (m) REVERT: B 231 MET cc_start: 0.9106 (mtt) cc_final: 0.8769 (mtt) REVERT: B 347 LYS cc_start: 0.7929 (mttm) cc_final: 0.7673 (mttm) REVERT: B 359 MET cc_start: 0.8867 (ttm) cc_final: 0.8535 (ttp) REVERT: C 366 LYS cc_start: 0.7853 (mtpt) cc_final: 0.7600 (mttp) REVERT: C 368 ARG cc_start: 0.6559 (mmt-90) cc_final: 0.6091 (mmp80) REVERT: C 372 GLN cc_start: 0.7093 (mm-40) cc_final: 0.6724 (mm110) REVERT: E 20 TRP cc_start: 0.6037 (m-90) cc_final: 0.5799 (m100) REVERT: F 39 MET cc_start: 0.9063 (mtt) cc_final: 0.8641 (mtm) REVERT: H 9 ASP cc_start: 0.7757 (m-30) cc_final: 0.7520 (m-30) REVERT: H 31 MET cc_start: 0.8584 (ttp) cc_final: 0.8254 (ttp) REVERT: I 30 ARG cc_start: 0.7006 (mtt-85) cc_final: 0.6640 (mmt90) REVERT: K 15 GLN cc_start: 0.7749 (mt0) cc_final: 0.7489 (mt0) REVERT: K 22 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7925 (m-30) REVERT: L 23 LEU cc_start: 0.8252 (mt) cc_final: 0.8012 (mp) REVERT: T 16 VAL cc_start: 0.7968 (t) cc_final: 0.7456 (p) outliers start: 21 outliers final: 15 residues processed: 208 average time/residue: 1.4443 time to fit residues: 336.9596 Evaluate side-chains 215 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 2.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain K residue 22 ASP Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain X residue 2 THR Chi-restraints excluded: chain X residue 4 SER Chi-restraints excluded: chain X residue 19 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 0.0040 chunk 106 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 168 optimal weight: 0.2980 chunk 145 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 112 optimal weight: 0.0270 chunk 89 optimal weight: 0.8980 chunk 115 optimal weight: 9.9990 overall best weight: 0.4452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 375 GLN H 3 GLN M 5 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19474 Z= 0.131 Angle : 0.515 8.503 26879 Z= 0.241 Chirality : 0.040 0.211 2553 Planarity : 0.004 0.049 3320 Dihedral : 16.066 121.690 3653 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.17 % Allowed : 13.22 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % 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: 1.81 (0.20), residues: 1866 helix: 1.96 (0.16), residues: 1115 sheet: -1.03 (0.77), residues: 37 loop : 0.19 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 131 HIS 0.007 0.001 HIS D 214 PHE 0.027 0.001 PHE B 246 TYR 0.009 0.001 TYR A 147 ARG 0.009 0.000 ARG C 122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 1.981 Fit side-chains REVERT: A 59 ASP cc_start: 0.7180 (t0) cc_final: 0.6820 (t0) REVERT: A 107 TYR cc_start: 0.8933 (t80) cc_final: 0.8561 (t80) REVERT: A 312 ARG cc_start: 0.7142 (mtm180) cc_final: 0.6873 (mtt180) REVERT: B 22 VAL cc_start: 0.8893 (OUTLIER) cc_final: 0.8643 (m) REVERT: B 231 MET cc_start: 0.9057 (mtt) cc_final: 0.8734 (mtt) REVERT: B 347 LYS cc_start: 0.7845 (mttm) cc_final: 0.7586 (mttm) REVERT: B 359 MET cc_start: 0.8816 (ttm) cc_final: 0.8431 (ttp) REVERT: C 366 LYS cc_start: 0.7808 (mtpt) cc_final: 0.7526 (mttp) REVERT: C 368 ARG cc_start: 0.6490 (mmt-90) cc_final: 0.6038 (mmp80) REVERT: E 20 TRP cc_start: 0.6119 (m-90) cc_final: 0.5895 (m100) REVERT: F 39 MET cc_start: 0.9042 (mtt) cc_final: 0.8629 (mtm) REVERT: H 9 ASP cc_start: 0.7817 (m-30) cc_final: 0.7586 (m-30) REVERT: H 31 MET cc_start: 0.8627 (ttp) cc_final: 0.8236 (ttp) REVERT: I 30 ARG cc_start: 0.7135 (mtt-85) cc_final: 0.6795 (mmt90) REVERT: K 15 GLN cc_start: 0.7745 (mt0) cc_final: 0.7497 (mt0) REVERT: K 22 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.7997 (m-30) REVERT: L 23 LEU cc_start: 0.8242 (mt) cc_final: 0.8000 (mp) REVERT: T 16 VAL cc_start: 0.7980 (t) cc_final: 0.7475 (p) REVERT: T 21 ILE cc_start: 0.8526 (mt) cc_final: 0.8242 (mm) outliers start: 18 outliers final: 11 residues processed: 218 average time/residue: 1.4416 time to fit residues: 353.2502 Evaluate side-chains 214 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 201 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain K residue 22 ASP Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain X residue 2 THR Chi-restraints excluded: chain X residue 4 SER Chi-restraints excluded: chain X residue 19 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN K 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.129316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.103036 restraints weight = 22078.115| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.46 r_work: 0.3011 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2500 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: