Starting phenix.real_space_refine on Fri Mar 15 17:29:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kch_22808/03_2024/7kch_22808_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kch_22808/03_2024/7kch_22808.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kch_22808/03_2024/7kch_22808.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kch_22808/03_2024/7kch_22808.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kch_22808/03_2024/7kch_22808_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kch_22808/03_2024/7kch_22808_updated.pdb" } resolution = 4.33 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= 0.003 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 3 5.21 5 S 63 5.16 5 C 7597 2.51 5 N 2174 2.21 5 O 2405 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 4": "OE1" <-> "OE2" Residue "G PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 72": "OE1" <-> "OE2" Residue "G PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 154": "OD1" <-> "OD2" Residue "G TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4": "OE1" <-> "OE2" Residue "B PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4": "OE1" <-> "OE2" Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12248 Number of models: 1 Model: "" Number of chains: 7 Chain: "G" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "A" Number of atoms: 3365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 3365 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 592} Link IDs: {'PTRANS': 21, 'TRANS': 658} Chain breaks: 8 Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 2164 Unresolved non-hydrogen angles: 2757 Unresolved non-hydrogen dihedrals: 1796 Unresolved non-hydrogen chiralities: 187 Planarities with less than four sites: {'GLN:plan1': 34, 'HIS:plan': 19, 'TYR:plan': 20, 'ASN:plan1': 34, 'TRP:plan': 4, 'ASP:plan': 36, 'PHE:plan': 39, 'GLU:plan': 52, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 1224 Chain: "B" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "C" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.33, per 1000 atoms: 0.60 Number of scatterers: 12248 At special positions: 0 Unit cell: (123.848, 144.672, 140.288, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 6 15.00 Mg 3 11.99 O 2405 8.00 N 2174 7.00 C 7597 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.14 Conformation dependent library (CDL) restraints added in 2.5 seconds 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3372 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 78 helices and 18 sheets defined 41.0% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'G' and resid 79 through 91 Processing helix chain 'G' and resid 98 through 100 No H-bonds generated for 'chain 'G' and resid 98 through 100' Processing helix chain 'G' and resid 113 through 126 removed outlier: 3.705A pdb=" N MET G 123 " --> pdb=" O MET G 119 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE G 124 " --> pdb=" O THR G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 145 Processing helix chain 'G' and resid 182 through 196 removed outlier: 3.638A pdb=" N THR G 194 " --> pdb=" O MET G 190 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU G 195 " --> pdb=" O LYS G 191 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG G 196 " --> pdb=" O ILE G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 215 removed outlier: 3.882A pdb=" N GLU G 207 " --> pdb=" O ALA G 204 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG G 210 " --> pdb=" O GLU G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 229 Processing helix chain 'G' and resid 234 through 236 No H-bonds generated for 'chain 'G' and resid 234 through 236' Processing helix chain 'G' and resid 252 through 254 No H-bonds generated for 'chain 'G' and resid 252 through 254' Processing helix chain 'G' and resid 256 through 262 removed outlier: 3.963A pdb=" N THR G 260 " --> pdb=" O ARG G 256 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU G 261 " --> pdb=" O CYS G 257 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE G 262 " --> pdb=" O PRO G 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 256 through 262' Processing helix chain 'G' and resid 274 through 283 Processing helix chain 'G' and resid 291 through 295 removed outlier: 3.754A pdb=" N ALA G 295 " --> pdb=" O LYS G 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 291 through 295' Processing helix chain 'G' and resid 302 through 304 No H-bonds generated for 'chain 'G' and resid 302 through 304' Processing helix chain 'G' and resid 309 through 320 Processing helix chain 'G' and resid 335 through 348 removed outlier: 5.606A pdb=" N VAL G 339 " --> pdb=" O LYS G 336 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TRP G 340 " --> pdb=" O TYR G 337 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU G 346 " --> pdb=" O GLY G 343 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA G 347 " --> pdb=" O SER G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 365 Processing helix chain 'G' and resid 367 through 373 removed outlier: 4.284A pdb=" N LYS G 373 " --> pdb=" O VAL G 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 118 through 126 Processing helix chain 'A' and resid 136 through 148 Processing helix chain 'A' and resid 166 through 181 Processing helix chain 'A' and resid 191 through 206 Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 258 through 265 Processing helix chain 'A' and resid 269 through 275 removed outlier: 3.586A pdb=" N GLU A 273 " --> pdb=" O PRO A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 313 Processing helix chain 'A' and resid 317 through 334 Processing helix chain 'A' and resid 345 through 347 No H-bonds generated for 'chain 'A' and resid 345 through 347' Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 394 through 424 removed outlier: 3.597A pdb=" N ASP A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 480 Processing helix chain 'A' and resid 491 through 500 Processing helix chain 'A' and resid 507 through 516 Processing helix chain 'A' and resid 522 through 531 Processing helix chain 'A' and resid 565 through 568 No H-bonds generated for 'chain 'A' and resid 565 through 568' Processing helix chain 'A' and resid 575 through 582 Processing helix chain 'A' and resid 587 through 592 Processing helix chain 'A' and resid 616 through 633 removed outlier: 3.798A pdb=" N LEU A 633 " --> pdb=" O GLU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 664 Processing helix chain 'A' and resid 667 through 676 Processing helix chain 'A' and resid 684 through 694 Processing helix chain 'A' and resid 710 through 717 Processing helix chain 'A' and resid 736 through 747 Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 126 removed outlier: 3.705A pdb=" N MET B 123 " --> pdb=" O MET B 119 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE B 124 " --> pdb=" O THR B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 145 Processing helix chain 'B' and resid 182 through 196 removed outlier: 3.637A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 215 removed outlier: 3.882A pdb=" N GLU B 207 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG B 210 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 252 through 254 No H-bonds generated for 'chain 'B' and resid 252 through 254' Processing helix chain 'B' and resid 256 through 262 removed outlier: 3.962A pdb=" N THR B 260 " --> pdb=" O ARG B 256 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LEU B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 256 through 262' Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 291 through 295 removed outlier: 3.754A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 291 through 295' Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 335 through 348 removed outlier: 5.606A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TRP B 340 " --> pdb=" O TYR B 337 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU B 346 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 367 through 373 removed outlier: 4.284A pdb=" N LYS B 373 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.704A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE C 124 " --> pdb=" O THR C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 145 Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.638A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 215 removed outlier: 3.883A pdb=" N GLU C 207 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG C 210 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 229 Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 252 through 254 No H-bonds generated for 'chain 'C' and resid 252 through 254' Processing helix chain 'C' and resid 256 through 262 removed outlier: 3.962A pdb=" N THR C 260 " --> pdb=" O ARG C 256 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 256 through 262' Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 291 through 295 removed outlier: 3.755A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 291 through 295' Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 348 removed outlier: 5.606A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TRP C 340 " --> pdb=" O TYR C 337 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU C 346 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 373 removed outlier: 4.284A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'G' and resid 8 through 11 Processing sheet with id= B, first strand: chain 'G' and resid 35 through 38 removed outlier: 3.603A pdb=" N ARG G 37 " --> pdb=" O THR G 66 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'G' and resid 103 through 105 Processing sheet with id= D, first strand: chain 'G' and resid 298 through 300 removed outlier: 3.548A pdb=" N SER G 155 " --> pdb=" O SER G 300 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL G 163 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP G 154 " --> pdb=" O HIS G 161 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'G' and resid 238 through 241 removed outlier: 3.693A pdb=" N LYS G 238 " --> pdb=" O ILE G 250 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 103 through 107 removed outlier: 4.100A pdb=" N GLN A 154 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 156 " --> pdb=" O GLY A 435 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU A 437 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL A 158 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL A 432 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ASN A 228 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ILE A 232 " --> pdb=" O ASN A 228 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 539 through 541 Processing sheet with id= H, first strand: chain 'A' and resid 680 through 683 Processing sheet with id= I, first strand: chain 'B' and resid 8 through 11 Processing sheet with id= J, first strand: chain 'B' and resid 35 through 38 removed outlier: 3.603A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 103 through 105 Processing sheet with id= L, first strand: chain 'B' and resid 298 through 300 removed outlier: 3.547A pdb=" N SER B 155 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 163 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP B 154 " --> pdb=" O HIS B 161 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 238 through 241 removed outlier: 3.692A pdb=" N LYS B 238 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 8 through 11 Processing sheet with id= O, first strand: chain 'C' and resid 35 through 38 removed outlier: 3.603A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 103 through 105 Processing sheet with id= Q, first strand: chain 'C' and resid 298 through 300 removed outlier: 3.548A pdb=" N SER C 155 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 163 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP C 154 " --> pdb=" O HIS C 161 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 238 through 241 removed outlier: 3.693A pdb=" N LYS C 238 " --> pdb=" O ILE C 250 " (cutoff:3.500A) 507 hydrogen bonds defined for protein. 1299 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: 3.89 Time building geometry restraints manager: 5.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3964 1.33 - 1.45: 1731 1.45 - 1.57: 6616 1.57 - 1.68: 9 1.68 - 1.80: 111 Bond restraints: 12431 Sorted by residual: bond pdb=" C GLY C 150 " pdb=" N ILE C 151 " ideal model delta sigma weight residual 1.333 1.292 0.040 1.20e-02 6.94e+03 1.13e+01 bond pdb=" C GLY G 150 " pdb=" N ILE G 151 " ideal model delta sigma weight residual 1.333 1.293 0.040 1.20e-02 6.94e+03 1.12e+01 bond pdb=" C GLY B 150 " pdb=" N ILE B 151 " ideal model delta sigma weight residual 1.333 1.293 0.039 1.20e-02 6.94e+03 1.08e+01 bond pdb=" C VAL B 163 " pdb=" N PRO B 164 " ideal model delta sigma weight residual 1.331 1.293 0.038 1.28e-02 6.10e+03 9.01e+00 bond pdb=" C VAL G 163 " pdb=" N PRO G 164 " ideal model delta sigma weight residual 1.331 1.293 0.038 1.28e-02 6.10e+03 8.80e+00 ... (remaining 12426 not shown) Histogram of bond angle deviations from ideal: 98.83 - 106.18: 324 106.18 - 113.53: 7083 113.53 - 120.88: 5826 120.88 - 128.23: 3662 128.23 - 135.58: 83 Bond angle restraints: 16978 Sorted by residual: angle pdb=" C LEU C 94 " pdb=" N ARG C 95 " pdb=" CA ARG C 95 " ideal model delta sigma weight residual 121.54 129.47 -7.93 1.91e+00 2.74e-01 1.72e+01 angle pdb=" C LEU B 94 " pdb=" N ARG B 95 " pdb=" CA ARG B 95 " ideal model delta sigma weight residual 121.54 129.45 -7.91 1.91e+00 2.74e-01 1.72e+01 angle pdb=" C LEU G 94 " pdb=" N ARG G 95 " pdb=" CA ARG G 95 " ideal model delta sigma weight residual 121.54 129.45 -7.91 1.91e+00 2.74e-01 1.71e+01 angle pdb=" C ASN C 162 " pdb=" N VAL C 163 " pdb=" CA VAL C 163 " ideal model delta sigma weight residual 123.33 119.79 3.54 8.70e-01 1.32e+00 1.65e+01 angle pdb=" C ASN B 162 " pdb=" N VAL B 163 " pdb=" CA VAL B 163 " ideal model delta sigma weight residual 123.33 119.82 3.51 8.70e-01 1.32e+00 1.63e+01 ... (remaining 16973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.14: 7241 34.14 - 68.29: 168 68.29 - 102.43: 3 102.43 - 136.57: 9 136.57 - 170.72: 6 Dihedral angle restraints: 7427 sinusoidal: 2214 harmonic: 5213 Sorted by residual: dihedral pdb=" C2' ADP C 401 " pdb=" C1' ADP C 401 " pdb=" N9 ADP C 401 " pdb=" C4 ADP C 401 " ideal model delta sinusoidal sigma weight residual 91.55 -97.73 -170.72 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C2' ADP G 401 " pdb=" C1' ADP G 401 " pdb=" N9 ADP G 401 " pdb=" C4 ADP G 401 " ideal model delta sinusoidal sigma weight residual 91.55 -97.75 -170.70 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C2' ADP B 401 " pdb=" C1' ADP B 401 " pdb=" N9 ADP B 401 " pdb=" C4 ADP B 401 " ideal model delta sinusoidal sigma weight residual 91.55 -97.79 -170.66 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 7424 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1243 0.048 - 0.095: 571 0.095 - 0.143: 161 0.143 - 0.191: 26 0.191 - 0.238: 9 Chirality restraints: 2010 Sorted by residual: chirality pdb=" CB ILE B 34 " pdb=" CA ILE B 34 " pdb=" CG1 ILE B 34 " pdb=" CG2 ILE B 34 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB ILE G 34 " pdb=" CA ILE G 34 " pdb=" CG1 ILE G 34 " pdb=" CG2 ILE G 34 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB ILE C 34 " pdb=" CA ILE C 34 " pdb=" CG1 ILE C 34 " pdb=" CG2 ILE C 34 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 2007 not shown) Planarity restraints: 2252 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 257 " -0.053 5.00e-02 4.00e+02 7.91e-02 1.00e+01 pdb=" N PRO B 258 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 258 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 258 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS G 257 " 0.053 5.00e-02 4.00e+02 7.90e-02 9.99e+00 pdb=" N PRO G 258 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO G 258 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO G 258 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 257 " 0.053 5.00e-02 4.00e+02 7.90e-02 9.98e+00 pdb=" N PRO C 258 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO C 258 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 258 " 0.045 5.00e-02 4.00e+02 ... (remaining 2249 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1352 2.72 - 3.26: 12257 3.26 - 3.81: 20477 3.81 - 4.35: 21794 4.35 - 4.90: 36928 Nonbonded interactions: 92808 Sorted by model distance: nonbonded pdb=" O ASN B 297 " pdb=" OD1 ASN B 297 " model vdw 2.175 3.040 nonbonded pdb=" O ASN G 297 " pdb=" OD1 ASN G 297 " model vdw 2.176 3.040 nonbonded pdb=" O ASN C 297 " pdb=" OD1 ASN C 297 " model vdw 2.176 3.040 nonbonded pdb=" CB MET G 47 " pdb=" NH2 ARG C 147 " model vdw 2.215 3.520 nonbonded pdb=" O SER C 155 " pdb=" OG1 THR C 303 " model vdw 2.241 2.440 ... (remaining 92803 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'G' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 27.120 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 36.730 Find NCS groups from input model: 0.670 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5244 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 : 0.011 0.063 12431 Z= 0.770 Angle : 1.074 12.124 16978 Z= 0.619 Chirality : 0.057 0.238 2010 Planarity : 0.008 0.079 2252 Dihedral : 16.548 170.718 4055 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 4.72 % Allowed : 16.35 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.19 (0.16), residues: 1781 helix: -2.75 (0.12), residues: 761 sheet: -1.81 (0.31), residues: 257 loop : -3.06 (0.20), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP G 79 HIS 0.016 0.004 HIS C 275 PHE 0.029 0.003 PHE B 255 TYR 0.008 0.002 TYR B 279 ARG 0.005 0.001 ARG B 196 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 351 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 41 GLN cc_start: 0.6624 (tt0) cc_final: 0.5894 (pm20) REVERT: G 122 ILE cc_start: 0.7662 (mt) cc_final: 0.7175 (mt) REVERT: G 167 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.6909 (tp30) REVERT: G 179 ASP cc_start: 0.6417 (m-30) cc_final: 0.6031 (p0) REVERT: B 176 MET cc_start: 0.4989 (mmm) cc_final: 0.4678 (tpp) REVERT: C 10 CYS cc_start: 0.6038 (p) cc_final: 0.5737 (p) REVERT: C 81 ASP cc_start: 0.7331 (m-30) cc_final: 0.6862 (m-30) REVERT: C 121 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7903 (tm-30) REVERT: C 140 LEU cc_start: 0.7725 (mp) cc_final: 0.7410 (mp) outliers start: 45 outliers final: 12 residues processed: 380 average time/residue: 0.2299 time to fit residues: 125.7396 Evaluate side-chains 233 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 220 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 151 optimal weight: 0.9980 chunk 135 optimal weight: 0.0570 chunk 75 optimal weight: 5.9990 chunk 46 optimal weight: 40.0000 chunk 91 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 140 optimal weight: 0.7980 chunk 54 optimal weight: 30.0000 chunk 85 optimal weight: 8.9990 chunk 104 optimal weight: 40.0000 chunk 162 optimal weight: 0.6980 overall best weight: 1.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 HIS ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 353 GLN B 78 ASN B 101 HIS ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 GLN C 73 HIS ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN C 173 HIS C 246 GLN C 353 GLN C 371 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.5959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 12431 Z= 0.326 Angle : 0.849 15.710 16978 Z= 0.428 Chirality : 0.049 0.265 2010 Planarity : 0.007 0.066 2252 Dihedral : 12.571 175.283 1931 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.10 % Allowed : 5.35 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.18), residues: 1781 helix: -0.76 (0.16), residues: 797 sheet: -1.66 (0.30), residues: 276 loop : -2.39 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 79 HIS 0.015 0.002 HIS G 161 PHE 0.025 0.003 PHE G 31 TYR 0.034 0.003 TYR B 198 ARG 0.015 0.002 ARG C 335 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 240 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 209 VAL cc_start: 0.8791 (t) cc_final: 0.8580 (t) REVERT: G 227 MET cc_start: 0.7532 (mmt) cc_final: 0.7120 (mmt) REVERT: G 283 MET cc_start: 0.7391 (mmm) cc_final: 0.6465 (tpt) REVERT: G 305 MET cc_start: 0.6374 (mmp) cc_final: 0.6072 (mmm) REVERT: B 82 MET cc_start: 0.6138 (ppp) cc_final: 0.5891 (ppp) REVERT: B 123 MET cc_start: 0.8573 (pmm) cc_final: 0.7330 (mmt) REVERT: B 132 MET cc_start: 0.7248 (ppp) cc_final: 0.6972 (ppp) REVERT: C 83 GLU cc_start: 0.8036 (tt0) cc_final: 0.7696 (tp30) REVERT: C 118 LYS cc_start: 0.8968 (mmmt) cc_final: 0.8711 (mmmm) REVERT: C 186 THR cc_start: 0.7876 (p) cc_final: 0.7584 (p) REVERT: C 203 THR cc_start: 0.7395 (m) cc_final: 0.6994 (p) REVERT: C 227 MET cc_start: 0.7708 (tpp) cc_final: 0.7498 (tpt) REVERT: C 313 MET cc_start: 0.8221 (tpt) cc_final: 0.7869 (tpp) REVERT: C 352 PHE cc_start: 0.8038 (m-10) cc_final: 0.7828 (m-10) REVERT: C 359 LYS cc_start: 0.8675 (tptm) cc_final: 0.8424 (tptt) outliers start: 1 outliers final: 0 residues processed: 240 average time/residue: 0.2279 time to fit residues: 80.5533 Evaluate side-chains 173 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 90 optimal weight: 0.2980 chunk 50 optimal weight: 50.0000 chunk 135 optimal weight: 2.9990 chunk 110 optimal weight: 0.4980 chunk 44 optimal weight: 50.0000 chunk 162 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 55 optimal weight: 20.0000 chunk 130 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS B 280 ASN ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.7928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12431 Z= 0.229 Angle : 0.656 9.701 16978 Z= 0.328 Chirality : 0.045 0.188 2010 Planarity : 0.005 0.055 2252 Dihedral : 12.125 179.648 1931 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.20), residues: 1781 helix: 0.28 (0.19), residues: 781 sheet: -1.41 (0.31), residues: 280 loop : -1.95 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 79 HIS 0.006 0.001 HIS G 371 PHE 0.020 0.002 PHE G 21 TYR 0.029 0.002 TYR B 279 ARG 0.007 0.001 ARG G 147 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 72 GLU cc_start: 0.6644 (tt0) cc_final: 0.6149 (pt0) REVERT: G 176 MET cc_start: 0.7563 (mtm) cc_final: 0.7077 (mtp) REVERT: G 227 MET cc_start: 0.7698 (mmt) cc_final: 0.7155 (mmm) REVERT: G 299 MET cc_start: 0.8673 (mpp) cc_final: 0.8281 (mpp) REVERT: B 30 VAL cc_start: 0.7848 (t) cc_final: 0.7549 (p) REVERT: B 119 MET cc_start: 0.8149 (ptp) cc_final: 0.7576 (ptp) REVERT: B 167 GLU cc_start: 0.7762 (pt0) cc_final: 0.7480 (pt0) REVERT: B 173 HIS cc_start: 0.7166 (p-80) cc_final: 0.6789 (p-80) REVERT: B 278 THR cc_start: 0.9070 (m) cc_final: 0.8789 (p) REVERT: C 47 MET cc_start: 0.4953 (mpp) cc_final: 0.4508 (tmm) REVERT: C 105 LEU cc_start: 0.9236 (mm) cc_final: 0.9006 (mm) REVERT: C 227 MET cc_start: 0.7751 (tpp) cc_final: 0.7532 (tpt) REVERT: C 253 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7003 (mp0) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.1983 time to fit residues: 59.8651 Evaluate side-chains 151 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 160 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 109 optimal weight: 0.0770 chunk 163 optimal weight: 4.9990 chunk 173 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 154 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 overall best weight: 2.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 1.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12431 Z= 0.329 Angle : 0.754 13.927 16978 Z= 0.376 Chirality : 0.047 0.276 2010 Planarity : 0.005 0.047 2252 Dihedral : 12.002 176.407 1931 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.20), residues: 1781 helix: 0.65 (0.20), residues: 773 sheet: -1.05 (0.31), residues: 272 loop : -1.93 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 356 HIS 0.010 0.002 HIS C 275 PHE 0.019 0.002 PHE B 124 TYR 0.033 0.002 TYR B 279 ARG 0.010 0.001 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 72 GLU cc_start: 0.7733 (tt0) cc_final: 0.7140 (pt0) REVERT: G 187 ASP cc_start: 0.8935 (m-30) cc_final: 0.8724 (t0) REVERT: G 227 MET cc_start: 0.8198 (mmt) cc_final: 0.7694 (mmm) REVERT: G 305 MET cc_start: 0.8578 (mmm) cc_final: 0.8263 (mmm) REVERT: B 81 ASP cc_start: 0.8373 (m-30) cc_final: 0.7857 (p0) REVERT: B 119 MET cc_start: 0.8597 (ptp) cc_final: 0.8282 (ptp) REVERT: B 167 GLU cc_start: 0.8329 (pt0) cc_final: 0.7788 (tm-30) REVERT: C 8 LEU cc_start: 0.9149 (mm) cc_final: 0.8919 (mm) REVERT: C 47 MET cc_start: 0.5896 (mpp) cc_final: 0.4755 (tmm) REVERT: C 80 ASP cc_start: 0.8600 (m-30) cc_final: 0.8386 (m-30) REVERT: C 83 GLU cc_start: 0.8610 (pt0) cc_final: 0.8365 (mp0) REVERT: C 227 MET cc_start: 0.8222 (tpp) cc_final: 0.8014 (tpt) REVERT: C 269 MET cc_start: 0.7830 (ttp) cc_final: 0.7456 (ttm) REVERT: C 299 MET cc_start: 0.7867 (ppp) cc_final: 0.7607 (ppp) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2129 time to fit residues: 44.5621 Evaluate side-chains 112 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 144 optimal weight: 1.9990 chunk 98 optimal weight: 50.0000 chunk 2 optimal weight: 0.5980 chunk 128 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 147 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 155 optimal weight: 0.5980 chunk 43 optimal weight: 30.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 12 ASN G 40 HIS G 49 GLN ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 1.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12431 Z= 0.220 Angle : 0.587 9.361 16978 Z= 0.291 Chirality : 0.045 0.173 2010 Planarity : 0.004 0.052 2252 Dihedral : 11.834 179.900 1931 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.21), residues: 1781 helix: 1.01 (0.20), residues: 784 sheet: -0.82 (0.32), residues: 257 loop : -1.77 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 86 HIS 0.007 0.001 HIS G 371 PHE 0.016 0.001 PHE C 223 TYR 0.016 0.001 TYR B 279 ARG 0.008 0.001 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.510 Fit side-chains REVERT: G 47 MET cc_start: 0.6751 (tpp) cc_final: 0.6282 (tmm) REVERT: G 51 ASP cc_start: 0.6964 (p0) cc_final: 0.6711 (p0) REVERT: G 72 GLU cc_start: 0.7617 (tt0) cc_final: 0.7098 (pt0) REVERT: G 132 MET cc_start: 0.8708 (tmm) cc_final: 0.8474 (tmm) REVERT: G 176 MET cc_start: 0.8301 (mpp) cc_final: 0.7969 (mtp) REVERT: G 187 ASP cc_start: 0.9022 (m-30) cc_final: 0.8814 (t0) REVERT: G 227 MET cc_start: 0.8541 (mmt) cc_final: 0.7881 (mmm) REVERT: G 299 MET cc_start: 0.8692 (mpp) cc_final: 0.8091 (mpp) REVERT: G 305 MET cc_start: 0.8665 (mmm) cc_final: 0.8388 (mmm) REVERT: B 85 ILE cc_start: 0.9142 (pt) cc_final: 0.8887 (pt) REVERT: B 86 TRP cc_start: 0.8055 (m100) cc_final: 0.7841 (m-90) REVERT: B 119 MET cc_start: 0.8554 (ptp) cc_final: 0.8351 (ptp) REVERT: B 167 GLU cc_start: 0.8303 (pt0) cc_final: 0.7734 (tm-30) REVERT: B 224 GLU cc_start: 0.8279 (mp0) cc_final: 0.7537 (mm-30) REVERT: B 305 MET cc_start: 0.8253 (mmp) cc_final: 0.7984 (mmm) REVERT: C 47 MET cc_start: 0.5826 (mpp) cc_final: 0.5187 (tmm) REVERT: C 57 GLU cc_start: 0.7562 (pt0) cc_final: 0.7288 (tm-30) REVERT: C 179 ASP cc_start: 0.8421 (p0) cc_final: 0.8204 (p0) REVERT: C 227 MET cc_start: 0.8484 (tpp) cc_final: 0.8137 (tpt) REVERT: C 305 MET cc_start: 0.8370 (mmm) cc_final: 0.8055 (mmm) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.2122 time to fit residues: 42.4821 Evaluate side-chains 105 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 58 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 34 optimal weight: 0.0050 chunk 101 optimal weight: 50.0000 chunk 42 optimal weight: 40.0000 chunk 173 optimal weight: 0.7980 chunk 143 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 57 optimal weight: 40.0000 chunk 90 optimal weight: 0.0770 overall best weight: 1.5554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 12 ASN G 49 GLN G 121 GLN ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 1.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12431 Z= 0.211 Angle : 0.598 12.226 16978 Z= 0.290 Chirality : 0.044 0.141 2010 Planarity : 0.004 0.039 2252 Dihedral : 11.640 178.060 1931 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.21), residues: 1781 helix: 1.38 (0.20), residues: 761 sheet: -0.61 (0.33), residues: 257 loop : -1.55 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 86 HIS 0.005 0.001 HIS C 275 PHE 0.013 0.001 PHE B 223 TYR 0.013 0.001 TYR G 188 ARG 0.005 0.000 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.561 Fit side-chains REVERT: G 51 ASP cc_start: 0.6980 (p0) cc_final: 0.6709 (p0) REVERT: G 227 MET cc_start: 0.8632 (mmt) cc_final: 0.8261 (mmm) REVERT: G 299 MET cc_start: 0.8530 (mpp) cc_final: 0.7880 (mpp) REVERT: G 374 CYS cc_start: 0.7135 (m) cc_final: 0.6908 (m) REVERT: B 81 ASP cc_start: 0.8587 (m-30) cc_final: 0.8323 (m-30) REVERT: B 132 MET cc_start: 0.9194 (ppp) cc_final: 0.8591 (ppp) REVERT: B 167 GLU cc_start: 0.8284 (pt0) cc_final: 0.7689 (tm-30) REVERT: C 47 MET cc_start: 0.5792 (mpp) cc_final: 0.5319 (tmm) REVERT: C 57 GLU cc_start: 0.7788 (pt0) cc_final: 0.7464 (tm-30) REVERT: C 179 ASP cc_start: 0.8686 (p0) cc_final: 0.8293 (p0) REVERT: C 227 MET cc_start: 0.8574 (tpp) cc_final: 0.8316 (tpt) REVERT: C 299 MET cc_start: 0.7774 (ppp) cc_final: 0.7503 (ppp) REVERT: C 305 MET cc_start: 0.8529 (mmm) cc_final: 0.8209 (mmm) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1810 time to fit residues: 34.4704 Evaluate side-chains 98 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 166 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 98 optimal weight: 40.0000 chunk 126 optimal weight: 0.7980 chunk 97 optimal weight: 30.0000 chunk 145 optimal weight: 4.9990 chunk 96 optimal weight: 50.0000 chunk 172 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS B 314 GLN C 49 GLN C 73 HIS ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 1.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 12431 Z= 0.462 Angle : 0.820 19.608 16978 Z= 0.401 Chirality : 0.049 0.321 2010 Planarity : 0.005 0.050 2252 Dihedral : 12.301 177.138 1931 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.21), residues: 1781 helix: 0.80 (0.20), residues: 797 sheet: -0.85 (0.32), residues: 260 loop : -1.87 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 86 HIS 0.013 0.002 HIS B 161 PHE 0.023 0.002 PHE C 223 TYR 0.025 0.002 TYR B 198 ARG 0.008 0.001 ARG G 177 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.532 Fit side-chains REVERT: G 51 ASP cc_start: 0.7065 (p0) cc_final: 0.6809 (p0) REVERT: G 227 MET cc_start: 0.9063 (mmt) cc_final: 0.8699 (mmm) REVERT: G 305 MET cc_start: 0.8645 (mmp) cc_final: 0.8343 (mmm) REVERT: G 355 MET cc_start: 0.8663 (pmm) cc_final: 0.8432 (pmm) REVERT: B 81 ASP cc_start: 0.8684 (m-30) cc_final: 0.8484 (m-30) REVERT: B 132 MET cc_start: 0.9376 (ppp) cc_final: 0.8608 (ppp) REVERT: B 167 GLU cc_start: 0.8338 (pt0) cc_final: 0.7862 (tm-30) REVERT: C 44 MET cc_start: 0.6293 (pmm) cc_final: 0.4394 (ptt) REVERT: C 47 MET cc_start: 0.5806 (mpp) cc_final: 0.5506 (tmm) REVERT: C 305 MET cc_start: 0.8441 (mmm) cc_final: 0.8129 (mmm) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1803 time to fit residues: 31.1715 Evaluate side-chains 87 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 106 optimal weight: 0.0570 chunk 68 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 51 optimal weight: 40.0000 chunk 33 optimal weight: 0.9990 chunk 109 optimal weight: 0.0010 chunk 117 optimal weight: 0.9980 chunk 85 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 135 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 overall best weight: 0.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 HIS ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 1.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12431 Z= 0.150 Angle : 0.588 9.137 16978 Z= 0.285 Chirality : 0.044 0.137 2010 Planarity : 0.004 0.036 2252 Dihedral : 11.643 177.530 1931 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.21), residues: 1781 helix: 1.33 (0.20), residues: 761 sheet: -0.69 (0.33), residues: 257 loop : -1.51 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 340 HIS 0.010 0.001 HIS B 87 PHE 0.014 0.001 PHE G 223 TYR 0.018 0.001 TYR G 69 ARG 0.005 0.001 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.514 Fit side-chains REVERT: G 51 ASP cc_start: 0.7068 (p0) cc_final: 0.6746 (p0) REVERT: G 227 MET cc_start: 0.9003 (mmt) cc_final: 0.8446 (mmm) REVERT: G 299 MET cc_start: 0.8686 (mpp) cc_final: 0.7781 (mpp) REVERT: B 81 ASP cc_start: 0.8690 (m-30) cc_final: 0.8434 (m-30) REVERT: B 113 LYS cc_start: 0.8745 (pttt) cc_final: 0.8518 (ptmt) REVERT: B 167 GLU cc_start: 0.8189 (pt0) cc_final: 0.7866 (tp30) REVERT: B 305 MET cc_start: 0.8653 (mmp) cc_final: 0.8169 (mmm) REVERT: B 313 MET cc_start: 0.8878 (tpp) cc_final: 0.8672 (tpt) REVERT: C 43 VAL cc_start: 0.9057 (m) cc_final: 0.8414 (p) REVERT: C 44 MET cc_start: 0.5867 (pmm) cc_final: 0.4341 (ptt) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2103 time to fit residues: 41.7726 Evaluate side-chains 92 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 165 optimal weight: 10.0000 chunk 150 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 96 optimal weight: 0.4980 chunk 70 optimal weight: 30.0000 chunk 126 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 chunk 145 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 170 optimal weight: 3.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 1.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 12431 Z= 0.360 Angle : 0.735 17.696 16978 Z= 0.353 Chirality : 0.046 0.238 2010 Planarity : 0.004 0.044 2252 Dihedral : 11.891 179.846 1931 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.21), residues: 1781 helix: 1.25 (0.20), residues: 763 sheet: -0.74 (0.32), residues: 275 loop : -1.64 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 79 HIS 0.008 0.002 HIS B 161 PHE 0.016 0.002 PHE G 223 TYR 0.020 0.002 TYR B 198 ARG 0.008 0.001 ARG C 312 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.474 Fit side-chains REVERT: G 51 ASP cc_start: 0.7143 (p0) cc_final: 0.6877 (p0) REVERT: G 227 MET cc_start: 0.9153 (mmt) cc_final: 0.8758 (mmm) REVERT: G 355 MET cc_start: 0.8930 (pmm) cc_final: 0.8715 (pmm) REVERT: G 374 CYS cc_start: 0.7884 (m) cc_final: 0.7624 (m) REVERT: B 113 LYS cc_start: 0.8740 (pttt) cc_final: 0.8476 (ptmt) REVERT: B 123 MET cc_start: 0.8948 (mpp) cc_final: 0.8639 (mpp) REVERT: B 132 MET cc_start: 0.9243 (ppp) cc_final: 0.8794 (ppp) REVERT: B 167 GLU cc_start: 0.8368 (pt0) cc_final: 0.7833 (tm-30) REVERT: B 305 MET cc_start: 0.8661 (mmp) cc_final: 0.8408 (mmm) REVERT: B 313 MET cc_start: 0.9032 (tpp) cc_final: 0.8825 (tpt) REVERT: C 43 VAL cc_start: 0.9100 (m) cc_final: 0.8560 (p) REVERT: C 44 MET cc_start: 0.4832 (pmm) cc_final: 0.3960 (ptt) REVERT: C 227 MET cc_start: 0.8196 (mmm) cc_final: 0.7939 (tpp) REVERT: C 305 MET cc_start: 0.8486 (mmm) cc_final: 0.8248 (mmm) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1950 time to fit residues: 33.5324 Evaluate side-chains 88 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 103 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 142 optimal weight: 10.0000 chunk 14 optimal weight: 0.1980 chunk 109 optimal weight: 0.9980 chunk 87 optimal weight: 0.4980 chunk 112 optimal weight: 0.6980 chunk 151 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 GLN ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 1.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12431 Z= 0.143 Angle : 0.587 10.113 16978 Z= 0.281 Chirality : 0.044 0.137 2010 Planarity : 0.003 0.032 2252 Dihedral : 11.434 175.416 1931 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.21), residues: 1781 helix: 1.48 (0.21), residues: 752 sheet: -0.68 (0.33), residues: 257 loop : -1.36 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 86 HIS 0.004 0.001 HIS G 371 PHE 0.014 0.001 PHE C 375 TYR 0.015 0.001 TYR G 69 ARG 0.004 0.000 ARG G 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.492 Fit side-chains REVERT: G 51 ASP cc_start: 0.7181 (p0) cc_final: 0.6917 (p0) REVERT: G 227 MET cc_start: 0.9042 (mmt) cc_final: 0.8626 (mmm) REVERT: G 299 MET cc_start: 0.8645 (mpp) cc_final: 0.8074 (mpp) REVERT: B 47 MET cc_start: 0.0624 (ttp) cc_final: 0.0373 (ttp) REVERT: B 113 LYS cc_start: 0.8762 (pttt) cc_final: 0.8523 (ptmt) REVERT: B 167 GLU cc_start: 0.8248 (pt0) cc_final: 0.7911 (tp30) REVERT: B 305 MET cc_start: 0.8590 (mmp) cc_final: 0.7893 (mmm) REVERT: B 313 MET cc_start: 0.8813 (tpp) cc_final: 0.8609 (mmt) REVERT: C 43 VAL cc_start: 0.9015 (m) cc_final: 0.8462 (p) REVERT: C 44 MET cc_start: 0.4766 (pmm) cc_final: 0.3708 (ptt) REVERT: C 119 MET cc_start: 0.9149 (ttm) cc_final: 0.8935 (tpp) REVERT: C 227 MET cc_start: 0.8215 (mmm) cc_final: 0.7851 (tpp) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1950 time to fit residues: 37.1551 Evaluate side-chains 90 residues out of total 1546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 43 optimal weight: 40.0000 chunk 130 optimal weight: 3.9990 chunk 20 optimal weight: 0.0470 chunk 39 optimal weight: 50.0000 chunk 142 optimal weight: 10.0000 chunk 59 optimal weight: 50.0000 chunk 146 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.065651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.050032 restraints weight = 66298.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.051339 restraints weight = 39508.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.052246 restraints weight = 26759.953| |-----------------------------------------------------------------------------| r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 1.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12431 Z= 0.141 Angle : 0.569 8.647 16978 Z= 0.272 Chirality : 0.043 0.131 2010 Planarity : 0.003 0.035 2252 Dihedral : 11.154 172.447 1931 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.21), residues: 1781 helix: 1.61 (0.21), residues: 735 sheet: -0.54 (0.33), residues: 255 loop : -1.23 (0.23), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 86 HIS 0.003 0.001 HIS C 275 PHE 0.009 0.001 PHE C 223 TYR 0.013 0.001 TYR G 69 ARG 0.003 0.000 ARG G 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2492.94 seconds wall clock time: 47 minutes 48.69 seconds (2868.69 seconds total)