Starting phenix.real_space_refine on Fri Apr 12 02:42:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz8_41737/04_2024/8tz8_41737_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz8_41737/04_2024/8tz8_41737.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz8_41737/04_2024/8tz8_41737_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz8_41737/04_2024/8tz8_41737_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz8_41737/04_2024/8tz8_41737_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz8_41737/04_2024/8tz8_41737.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz8_41737/04_2024/8tz8_41737.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz8_41737/04_2024/8tz8_41737_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz8_41737/04_2024/8tz8_41737_trim_updated.pdb" } resolution = 3.19 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= 0.002 sd= 0.064 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 2 5.49 5 S 87 5.16 5 C 8179 2.51 5 N 1927 2.21 5 O 2130 1.98 5 H 12101 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 24426 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8129 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 8076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8076 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 77 Chain: "C" Number of atoms: 8076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8076 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 77 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'LBN': 1, 'XMO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'XMO': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'LBN': 1, 'XMO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 19 Time building chain proxies: 10.95, per 1000 atoms: 0.45 Number of scatterers: 24426 At special positions: 0 Unit cell: (131.76, 129.6, 76.68, 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 87 16.00 P 2 15.00 O 2130 8.00 N 1927 7.00 C 8179 6.00 H 12101 1.00 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: 19.82 Conformation dependent library (CDL) restraints added in 2.7 seconds 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2946 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 75 helices and 0 sheets defined 79.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.06 Creating SS restraints... Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 104 through 129 Processing helix chain 'A' and resid 135 through 156 Processing helix chain 'A' and resid 158 through 202 Proline residue: A 167 - end of helix removed outlier: 4.813A pdb=" N PHE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N TRP A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N TRP A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 222 Processing helix chain 'A' and resid 233 through 250 Processing helix chain 'A' and resid 253 through 281 removed outlier: 3.768A pdb=" N GLY A 271 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TYR A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N SER A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ASP A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ALA A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY A 276 " --> pdb=" O TYR A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 311 removed outlier: 4.425A pdb=" N LEU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Proline residue: A 296 - end of helix Processing helix chain 'A' and resid 313 through 329 removed outlier: 3.690A pdb=" N VAL A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 343 removed outlier: 3.786A pdb=" N ILE A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 354 Proline residue: A 351 - end of helix removed outlier: 4.756A pdb=" N VAL A 354 " --> pdb=" O SER A 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 347 through 354' Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 363 through 374 Processing helix chain 'A' and resid 382 through 388 Processing helix chain 'A' and resid 392 through 413 removed outlier: 4.222A pdb=" N ALA A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 424 through 428 Processing helix chain 'A' and resid 438 through 481 removed outlier: 3.816A pdb=" N SER A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N SER A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET A 480 " --> pdb=" O TRP A 476 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 495 Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 510 through 522 Processing helix chain 'A' and resid 525 through 541 Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.907A pdb=" N GLY A 576 " --> pdb=" O GLY A 573 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE A 577 " --> pdb=" O SER A 574 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY A 580 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N MET A 585 " --> pdb=" O LEU A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 616 removed outlier: 4.967A pdb=" N ARG A 591 " --> pdb=" O SER A 588 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR A 594 " --> pdb=" O ARG A 591 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA A 597 " --> pdb=" O THR A 594 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N MET A 598 " --> pdb=" O ALA A 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 104 through 129 Processing helix chain 'B' and resid 135 through 156 Processing helix chain 'B' and resid 158 through 202 Proline residue: B 167 - end of helix removed outlier: 4.655A pdb=" N PHE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N TRP B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N TRP B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA B 200 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 222 Processing helix chain 'B' and resid 233 through 250 Processing helix chain 'B' and resid 253 through 281 removed outlier: 4.021A pdb=" N TYR B 272 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N SER B 273 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ASP B 274 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ALA B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY B 276 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 311 removed outlier: 4.588A pdb=" N LEU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Proline residue: B 296 - end of helix Processing helix chain 'B' and resid 313 through 328 removed outlier: 3.609A pdb=" N ILE B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL B 324 " --> pdb=" O LYS B 320 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET B 325 " --> pdb=" O VAL B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 343 removed outlier: 3.895A pdb=" N ILE B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 360 Proline residue: B 351 - end of helix removed outlier: 4.845A pdb=" N VAL B 354 " --> pdb=" O SER B 350 " (cutoff:3.500A) Proline residue: B 356 - end of helix Proline residue: B 359 - end of helix Processing helix chain 'B' and resid 363 through 375 Processing helix chain 'B' and resid 379 through 387 removed outlier: 3.630A pdb=" N GLY B 383 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER B 387 " --> pdb=" O GLY B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 413 removed outlier: 4.195A pdb=" N ALA B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) Proline residue: B 404 - end of helix Processing helix chain 'B' and resid 424 through 428 Processing helix chain 'B' and resid 438 through 478 removed outlier: 4.166A pdb=" N SER B 449 " --> pdb=" O GLY B 445 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N SER B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LEU B 452 " --> pdb=" O SER B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 495 removed outlier: 3.621A pdb=" N TYR B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 503 Processing helix chain 'B' and resid 507 through 522 removed outlier: 4.125A pdb=" N PHE B 511 " --> pdb=" O TRP B 507 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N MET B 512 " --> pdb=" O GLN B 508 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 516 " --> pdb=" O MET B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 541 Processing helix chain 'B' and resid 556 through 565 Processing helix chain 'B' and resid 573 through 585 removed outlier: 3.898A pdb=" N GLY B 576 " --> pdb=" O GLY B 573 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE B 577 " --> pdb=" O SER B 574 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL B 578 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU B 582 " --> pdb=" O ILE B 579 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR B 583 " --> pdb=" O GLY B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 595 removed outlier: 4.776A pdb=" N ARG B 591 " --> pdb=" O SER B 588 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE B 593 " --> pdb=" O LYS B 590 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR B 594 " --> pdb=" O ARG B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 618 Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 104 through 129 Processing helix chain 'C' and resid 131 through 156 Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 158 through 197 Proline residue: C 167 - end of helix removed outlier: 4.430A pdb=" N PHE C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N TRP C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N TRP C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 202 No H-bonds generated for 'chain 'C' and resid 199 through 202' Processing helix chain 'C' and resid 204 through 222 Processing helix chain 'C' and resid 233 through 251 removed outlier: 3.709A pdb=" N GLY C 238 " --> pdb=" O PRO C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 277 removed outlier: 4.197A pdb=" N TYR C 272 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N SER C 273 " --> pdb=" O PHE C 269 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASP C 274 " --> pdb=" O LEU C 270 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA C 275 " --> pdb=" O GLY C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 287 No H-bonds generated for 'chain 'C' and resid 285 through 287' Processing helix chain 'C' and resid 289 through 311 removed outlier: 4.220A pdb=" N LEU C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Proline residue: C 296 - end of helix Processing helix chain 'C' and resid 313 through 329 removed outlier: 3.855A pdb=" N VAL C 324 " --> pdb=" O LYS C 320 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET C 325 " --> pdb=" O VAL C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 343 removed outlier: 3.955A pdb=" N ILE C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 353 Proline residue: C 351 - end of helix No H-bonds generated for 'chain 'C' and resid 347 through 353' Processing helix chain 'C' and resid 355 through 360 Proline residue: C 359 - end of helix Processing helix chain 'C' and resid 363 through 373 removed outlier: 3.828A pdb=" N GLY C 373 " --> pdb=" O ILE C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 387 removed outlier: 4.300A pdb=" N ALA C 384 " --> pdb=" O SER C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 413 Proline residue: C 404 - end of helix removed outlier: 3.850A pdb=" N LEU C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 428 Processing helix chain 'C' and resid 438 through 481 removed outlier: 3.908A pdb=" N SER C 449 " --> pdb=" O GLY C 445 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N SER C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU C 452 " --> pdb=" O SER C 448 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET C 480 " --> pdb=" O TRP C 476 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE C 481 " --> pdb=" O LEU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 495 removed outlier: 3.573A pdb=" N TYR C 494 " --> pdb=" O VAL C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 502 Processing helix chain 'C' and resid 507 through 522 removed outlier: 4.173A pdb=" N PHE C 511 " --> pdb=" O TRP C 507 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N MET C 512 " --> pdb=" O GLN C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 541 Processing helix chain 'C' and resid 556 through 565 Processing helix chain 'C' and resid 575 through 585 Processing helix chain 'C' and resid 587 through 595 removed outlier: 4.601A pdb=" N ARG C 591 " --> pdb=" O SER C 588 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE C 593 " --> pdb=" O LYS C 590 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR C 594 " --> pdb=" O ARG C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 617 843 hydrogen bonds defined for protein. 2403 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: 8.11 Time building geometry restraints manager: 20.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 12083 1.01 - 1.21: 28 1.21 - 1.41: 5215 1.41 - 1.61: 7272 1.61 - 1.81: 163 Bond restraints: 24761 Sorted by residual: bond pdb=" O4 LBN C 802 " pdb=" P1 LBN C 802 " ideal model delta sigma weight residual 1.497 1.645 -0.148 2.00e-02 2.50e+03 5.48e+01 bond pdb=" O4 LBN A 802 " pdb=" P1 LBN A 802 " ideal model delta sigma weight residual 1.497 1.644 -0.147 2.00e-02 2.50e+03 5.43e+01 bond pdb=" O2 LBN A 802 " pdb=" P1 LBN A 802 " ideal model delta sigma weight residual 1.650 1.509 0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" O2 LBN C 802 " pdb=" P1 LBN C 802 " ideal model delta sigma weight residual 1.650 1.509 0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" C34 LBN C 802 " pdb=" O7 LBN C 802 " ideal model delta sigma weight residual 1.331 1.430 -0.099 2.00e-02 2.50e+03 2.45e+01 ... (remaining 24756 not shown) Histogram of bond angle deviations from ideal: 99.72 - 106.58: 385 106.58 - 113.44: 28495 113.44 - 120.29: 8696 120.29 - 127.15: 6868 127.15 - 134.01: 171 Bond angle restraints: 44615 Sorted by residual: angle pdb=" O1 LBN C 802 " pdb=" P1 LBN C 802 " pdb=" O2 LBN C 802 " ideal model delta sigma weight residual 93.45 109.56 -16.11 3.00e+00 1.11e-01 2.88e+01 angle pdb=" O1 LBN A 802 " pdb=" P1 LBN A 802 " pdb=" O2 LBN A 802 " ideal model delta sigma weight residual 93.45 109.49 -16.04 3.00e+00 1.11e-01 2.86e+01 angle pdb=" O3 LBN C 802 " pdb=" P1 LBN C 802 " pdb=" O4 LBN C 802 " ideal model delta sigma weight residual 119.36 109.56 9.80 3.00e+00 1.11e-01 1.07e+01 angle pdb=" O3 LBN A 802 " pdb=" P1 LBN A 802 " pdb=" O4 LBN A 802 " ideal model delta sigma weight residual 119.36 109.64 9.72 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C35 LBN C 802 " pdb=" C34 LBN C 802 " pdb=" O7 LBN C 802 " ideal model delta sigma weight residual 111.21 119.86 -8.65 3.00e+00 1.11e-01 8.31e+00 ... (remaining 44610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.46: 11240 25.46 - 50.93: 377 50.93 - 76.39: 140 76.39 - 101.86: 4 101.86 - 127.32: 5 Dihedral angle restraints: 11766 sinusoidal: 6036 harmonic: 5730 Sorted by residual: dihedral pdb=" C01 XMO C 801 " pdb=" C02 XMO C 801 " pdb=" C04 XMO C 801 " pdb=" O06 XMO C 801 " ideal model delta sinusoidal sigma weight residual 259.35 132.03 127.32 1 3.00e+01 1.11e-03 1.71e+01 dihedral pdb=" O5 LBN A 802 " pdb=" C2 LBN A 802 " pdb=" C3 LBN A 802 " pdb=" O7 LBN A 802 " ideal model delta sinusoidal sigma weight residual 62.67 -54.55 117.22 1 3.00e+01 1.11e-03 1.55e+01 dihedral pdb=" O5 LBN C 802 " pdb=" C2 LBN C 802 " pdb=" C3 LBN C 802 " pdb=" O7 LBN C 802 " ideal model delta sinusoidal sigma weight residual 62.67 -48.82 111.49 1 3.00e+01 1.11e-03 1.46e+01 ... (remaining 11763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1393 0.035 - 0.069: 457 0.069 - 0.104: 124 0.104 - 0.138: 16 0.138 - 0.173: 1 Chirality restraints: 1991 Sorted by residual: chirality pdb=" C2 LBN A 802 " pdb=" C1 LBN A 802 " pdb=" C3 LBN A 802 " pdb=" O7 LBN A 802 " both_signs ideal model delta sigma weight residual False -2.36 -2.54 0.17 2.00e-01 2.50e+01 7.48e-01 chirality pdb=" CA PRO A 234 " pdb=" N PRO A 234 " pdb=" C PRO A 234 " pdb=" CB PRO A 234 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA PRO B 234 " pdb=" N PRO B 234 " pdb=" C PRO B 234 " pdb=" CB PRO B 234 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 1988 not shown) Planarity restraints: 3631 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 290 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C PHE C 290 " 0.033 2.00e-02 2.50e+03 pdb=" O PHE C 290 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA C 291 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 599 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.52e+00 pdb=" C ARG A 599 " 0.032 2.00e-02 2.50e+03 pdb=" O ARG A 599 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA A 600 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 608 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.16e+00 pdb=" C CYS A 608 " -0.031 2.00e-02 2.50e+03 pdb=" O CYS A 608 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE A 609 " 0.010 2.00e-02 2.50e+03 ... (remaining 3628 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 938 2.18 - 2.79: 47042 2.79 - 3.39: 67554 3.39 - 4.00: 84091 4.00 - 4.60: 134015 Nonbonded interactions: 333640 Sorted by model distance: nonbonded pdb=" OE1 GLN A 206 " pdb=" H GLN A 206 " model vdw 1.580 1.850 nonbonded pdb=" O SER A 451 " pdb="HD22 ASN A 455 " model vdw 1.588 1.850 nonbonded pdb=" H ARG A 436 " pdb=" OE1 GLU A 440 " model vdw 1.593 1.850 nonbonded pdb=" OE1 GLU A 525 " pdb=" H GLU A 525 " model vdw 1.597 1.850 nonbonded pdb=" O LEU C 248 " pdb=" HG1 THR C 252 " model vdw 1.608 1.850 ... (remaining 333635 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 'A' and (resid 90 through 104 or (resid 105 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 106 or (resid 107 thro \ ugh 110 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 111 through 113 or (resid 114 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 115 through 176 or (resid 17 \ 7 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 178 through 420 or (resid 421 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 422 through 435 or (resid 436 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 437 through 622 or resid 801)) selection = (chain 'B' and (resid 90 through 162 or (resid 163 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 164 through 433 or (re \ sid 434 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 435 through 609 or (resid 610 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 611 through 622 or resid 801 \ )) selection = (chain 'C' and (resid 90 through 162 or (resid 163 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 164 through 433 or (re \ sid 434 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 435 through 609 or (resid 610 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 611 through 622 or resid 801 \ )) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.360 Extract box with map and model: 4.930 Check model and map are aligned: 0.370 Set scattering table: 0.240 Process input model: 76.300 Find NCS groups from input model: 1.140 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.148 12660 Z= 0.343 Angle : 0.573 16.106 17229 Z= 0.290 Chirality : 0.036 0.173 1991 Planarity : 0.004 0.039 2089 Dihedral : 12.695 127.324 4288 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % 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: 2.71 (0.21), residues: 1593 helix: 2.31 (0.14), residues: 1296 sheet: None (None), residues: 0 loop : -0.55 (0.31), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 316 HIS 0.002 0.001 HIS A 288 PHE 0.018 0.001 PHE C 413 TYR 0.009 0.001 TYR A 357 ARG 0.002 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 302 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 1.938 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: A 181 TRP cc_start: 0.6533 (m100) cc_final: 0.6121 (m100) REVERT: A 264 LYS cc_start: 0.7884 (mttt) cc_final: 0.7602 (mtpt) REVERT: A 345 ILE cc_start: 0.8286 (mm) cc_final: 0.8057 (mp) REVERT: A 350 SER cc_start: 0.8346 (t) cc_final: 0.8088 (t) REVERT: A 497 MET cc_start: 0.7602 (tmm) cc_final: 0.7320 (tmm) REVERT: B 370 MET cc_start: 0.7987 (mtm) cc_final: 0.7731 (mtp) REVERT: B 458 VAL cc_start: 0.8301 (t) cc_final: 0.8020 (t) REVERT: B 585 MET cc_start: 0.8711 (mtt) cc_final: 0.8457 (mtt) REVERT: C 242 GLN cc_start: 0.8341 (mt0) cc_final: 0.8117 (mt0) REVERT: C 357 TYR cc_start: 0.8340 (m-80) cc_final: 0.8100 (m-80) REVERT: C 370 MET cc_start: 0.8805 (mtm) cc_final: 0.8569 (mtm) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.5014 time to fit residues: 221.7146 Evaluate side-chains 220 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12660 Z= 0.276 Angle : 0.497 5.237 17229 Z= 0.263 Chirality : 0.037 0.166 1991 Planarity : 0.004 0.047 2089 Dihedral : 7.947 112.594 1764 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.92 % Allowed : 8.06 % Favored : 90.02 % 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: 2.64 (0.21), residues: 1593 helix: 2.24 (0.15), residues: 1298 sheet: None (None), residues: 0 loop : -0.52 (0.32), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 184 HIS 0.002 0.001 HIS B 152 PHE 0.023 0.001 PHE B 413 TYR 0.012 0.001 TYR A 357 ARG 0.003 0.000 ARG A 436 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 239 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 215 time to evaluate : 1.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 TRP cc_start: 0.6704 (m100) cc_final: 0.6227 (m100) REVERT: A 264 LYS cc_start: 0.7958 (mttt) cc_final: 0.7670 (mtpt) REVERT: A 345 ILE cc_start: 0.8350 (mm) cc_final: 0.8141 (mt) REVERT: B 157 TYR cc_start: 0.7790 (m-10) cc_final: 0.7577 (m-80) REVERT: B 355 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7291 (ttt-90) REVERT: B 370 MET cc_start: 0.8105 (mtm) cc_final: 0.7666 (mtp) REVERT: B 503 MET cc_start: 0.9079 (mtp) cc_final: 0.8658 (mtp) REVERT: B 524 ASN cc_start: 0.9138 (p0) cc_final: 0.8873 (p0) REVERT: B 598 MET cc_start: 0.7614 (tpt) cc_final: 0.7169 (tpt) REVERT: C 219 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7839 (mp) REVERT: C 222 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7680 (tp) REVERT: C 257 MET cc_start: 0.6850 (ptt) cc_final: 0.6492 (ttm) REVERT: C 357 TYR cc_start: 0.8354 (m-80) cc_final: 0.8143 (m-80) REVERT: C 370 MET cc_start: 0.8774 (mtm) cc_final: 0.8481 (mtm) outliers start: 24 outliers final: 17 residues processed: 230 average time/residue: 0.4917 time to fit residues: 170.1488 Evaluate side-chains 225 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 205 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 506 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 444 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12660 Z= 0.259 Angle : 0.472 4.959 17229 Z= 0.250 Chirality : 0.036 0.136 1991 Planarity : 0.004 0.047 2089 Dihedral : 7.388 113.217 1764 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.60 % Allowed : 9.18 % Favored : 89.23 % 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: 2.49 (0.21), residues: 1593 helix: 2.18 (0.15), residues: 1288 sheet: None (None), residues: 0 loop : -0.67 (0.32), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 150 HIS 0.002 0.001 HIS A 288 PHE 0.020 0.001 PHE B 413 TYR 0.012 0.001 TYR A 357 ARG 0.009 0.000 ARG C 589 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 211 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.7964 (mttt) cc_final: 0.7672 (mtpt) REVERT: A 345 ILE cc_start: 0.8377 (mm) cc_final: 0.8125 (mt) REVERT: A 348 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8298 (p) REVERT: A 350 SER cc_start: 0.8318 (t) cc_final: 0.7812 (p) REVERT: B 112 TRP cc_start: 0.6238 (t60) cc_final: 0.5413 (t-100) REVERT: B 231 TYR cc_start: 0.7640 (t80) cc_final: 0.7371 (t80) REVERT: B 370 MET cc_start: 0.8060 (mtm) cc_final: 0.7636 (mtp) REVERT: B 585 MET cc_start: 0.8791 (mtt) cc_final: 0.8494 (mtt) REVERT: B 598 MET cc_start: 0.7640 (tpt) cc_final: 0.7130 (tpt) REVERT: C 219 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7819 (mp) REVERT: C 257 MET cc_start: 0.6843 (ptt) cc_final: 0.6643 (ttm) REVERT: C 370 MET cc_start: 0.8758 (mtm) cc_final: 0.8477 (mtm) REVERT: C 430 MET cc_start: 0.8073 (mpp) cc_final: 0.7795 (mtt) outliers start: 20 outliers final: 16 residues processed: 223 average time/residue: 0.4631 time to fit residues: 156.4037 Evaluate side-chains 213 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 195 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 617 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 GLN C 169 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12660 Z= 0.178 Angle : 0.430 4.900 17229 Z= 0.225 Chirality : 0.034 0.132 1991 Planarity : 0.003 0.047 2089 Dihedral : 7.014 113.150 1764 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.68 % Allowed : 10.53 % Favored : 87.79 % 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: 2.72 (0.22), residues: 1593 helix: 2.30 (0.15), residues: 1302 sheet: None (None), residues: 0 loop : -0.50 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 316 HIS 0.002 0.000 HIS A 288 PHE 0.013 0.001 PHE B 413 TYR 0.010 0.001 TYR A 357 ARG 0.002 0.000 ARG C 589 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 221 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 200 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.7957 (mttt) cc_final: 0.7672 (mtpt) REVERT: A 345 ILE cc_start: 0.8364 (mm) cc_final: 0.8113 (mt) REVERT: A 350 SER cc_start: 0.8363 (t) cc_final: 0.7819 (p) REVERT: B 112 TRP cc_start: 0.6211 (t60) cc_final: 0.5443 (t-100) REVERT: B 158 GLU cc_start: 0.6898 (pm20) cc_final: 0.6461 (pm20) REVERT: B 231 TYR cc_start: 0.7614 (t80) cc_final: 0.7275 (t80) REVERT: B 370 MET cc_start: 0.8035 (mtm) cc_final: 0.7776 (mtp) REVERT: B 585 MET cc_start: 0.8804 (mtt) cc_final: 0.8529 (mtt) REVERT: B 598 MET cc_start: 0.7567 (tpt) cc_final: 0.7014 (tpt) REVERT: C 219 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7883 (mp) REVERT: C 257 MET cc_start: 0.6826 (ptt) cc_final: 0.6616 (ttm) REVERT: C 370 MET cc_start: 0.8723 (mtm) cc_final: 0.8415 (mtm) REVERT: C 430 MET cc_start: 0.8058 (mpp) cc_final: 0.7842 (mtt) outliers start: 21 outliers final: 16 residues processed: 214 average time/residue: 0.4411 time to fit residues: 144.5680 Evaluate side-chains 210 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 193 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 506 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 63 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 78 optimal weight: 3.9990 chunk 137 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 GLN B 444 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12660 Z= 0.281 Angle : 0.472 5.143 17229 Z= 0.252 Chirality : 0.036 0.151 1991 Planarity : 0.004 0.049 2089 Dihedral : 7.155 114.998 1764 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.76 % Allowed : 11.33 % Favored : 86.91 % 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: 2.52 (0.21), residues: 1593 helix: 2.15 (0.15), residues: 1290 sheet: None (None), residues: 0 loop : -0.46 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 181 HIS 0.002 0.001 HIS A 288 PHE 0.019 0.001 PHE B 413 TYR 0.011 0.001 TYR A 357 ARG 0.003 0.000 ARG C 589 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 218 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 196 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.8054 (mttt) cc_final: 0.7763 (mtpt) REVERT: A 345 ILE cc_start: 0.8411 (mm) cc_final: 0.8147 (mt) REVERT: A 350 SER cc_start: 0.8372 (t) cc_final: 0.7854 (p) REVERT: B 112 TRP cc_start: 0.6188 (t60) cc_final: 0.5507 (t-100) REVERT: B 158 GLU cc_start: 0.7034 (pm20) cc_final: 0.6421 (pm20) REVERT: B 231 TYR cc_start: 0.7733 (t80) cc_final: 0.7394 (t80) REVERT: B 370 MET cc_start: 0.8106 (mtm) cc_final: 0.7677 (mtp) REVERT: B 503 MET cc_start: 0.9030 (mtp) cc_final: 0.8657 (mtp) REVERT: B 585 MET cc_start: 0.8845 (mtt) cc_final: 0.8577 (mtt) REVERT: B 598 MET cc_start: 0.7703 (tpt) cc_final: 0.7168 (tpt) REVERT: C 219 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7977 (mp) REVERT: C 370 MET cc_start: 0.8739 (mtm) cc_final: 0.8445 (mtm) outliers start: 22 outliers final: 19 residues processed: 211 average time/residue: 0.4470 time to fit residues: 145.2831 Evaluate side-chains 213 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 193 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 506 ASP Chi-restraints excluded: chain C residue 617 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12660 Z= 0.231 Angle : 0.449 4.920 17229 Z= 0.237 Chirality : 0.035 0.139 1991 Planarity : 0.004 0.048 2089 Dihedral : 6.960 114.654 1764 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.76 % Allowed : 11.89 % Favored : 86.35 % 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: 2.56 (0.22), residues: 1593 helix: 2.18 (0.15), residues: 1295 sheet: None (None), residues: 0 loop : -0.45 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 316 HIS 0.002 0.001 HIS A 288 PHE 0.014 0.001 PHE C 413 TYR 0.011 0.001 TYR A 357 ARG 0.003 0.000 ARG C 589 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 195 time to evaluate : 1.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.8044 (mttt) cc_final: 0.7756 (mtpt) REVERT: A 345 ILE cc_start: 0.8408 (mm) cc_final: 0.8143 (mt) REVERT: A 350 SER cc_start: 0.8337 (t) cc_final: 0.7784 (p) REVERT: B 112 TRP cc_start: 0.6226 (t60) cc_final: 0.5626 (t-100) REVERT: B 158 GLU cc_start: 0.7090 (pm20) cc_final: 0.6415 (pm20) REVERT: B 370 MET cc_start: 0.8076 (mtm) cc_final: 0.7637 (mtp) REVERT: B 503 MET cc_start: 0.8980 (mtp) cc_final: 0.8588 (mtp) REVERT: B 585 MET cc_start: 0.8833 (mtt) cc_final: 0.8587 (mtt) REVERT: B 598 MET cc_start: 0.7663 (tpt) cc_final: 0.7109 (tpt) REVERT: C 219 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7994 (mp) REVERT: C 370 MET cc_start: 0.8689 (mtm) cc_final: 0.8417 (mtm) REVERT: C 413 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.8355 (t80) outliers start: 22 outliers final: 18 residues processed: 213 average time/residue: 0.4772 time to fit residues: 157.7853 Evaluate side-chains 208 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 188 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 571 ASN Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 506 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 129 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 61 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12660 Z= 0.172 Angle : 0.423 4.835 17229 Z= 0.222 Chirality : 0.034 0.132 1991 Planarity : 0.003 0.047 2089 Dihedral : 6.737 114.402 1764 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.68 % Allowed : 12.29 % Favored : 86.03 % 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: 2.83 (0.22), residues: 1593 helix: 2.35 (0.15), residues: 1297 sheet: None (None), residues: 0 loop : -0.28 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 184 HIS 0.002 0.000 HIS B 394 PHE 0.011 0.001 PHE C 413 TYR 0.010 0.001 TYR A 357 ARG 0.002 0.000 ARG C 589 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 189 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.7973 (mttt) cc_final: 0.7677 (mtpt) REVERT: A 345 ILE cc_start: 0.8412 (mm) cc_final: 0.8149 (mt) REVERT: A 350 SER cc_start: 0.8330 (t) cc_final: 0.7767 (p) REVERT: A 428 MET cc_start: 0.8439 (mmt) cc_final: 0.8065 (mmp) REVERT: B 112 TRP cc_start: 0.6217 (t60) cc_final: 0.5692 (t-100) REVERT: B 370 MET cc_start: 0.8032 (mtm) cc_final: 0.7761 (mtp) REVERT: B 585 MET cc_start: 0.8795 (mtt) cc_final: 0.8570 (mtt) REVERT: B 598 MET cc_start: 0.7590 (tpt) cc_final: 0.7041 (tpt) REVERT: C 157 TYR cc_start: 0.7552 (m-10) cc_final: 0.7346 (m-80) REVERT: C 219 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8028 (mp) REVERT: C 370 MET cc_start: 0.8650 (mtm) cc_final: 0.8377 (mtm) REVERT: C 413 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.8395 (t80) outliers start: 21 outliers final: 18 residues processed: 207 average time/residue: 0.4634 time to fit residues: 146.6304 Evaluate side-chains 206 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 186 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 571 ASN Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 506 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12660 Z= 0.255 Angle : 0.458 5.185 17229 Z= 0.243 Chirality : 0.036 0.144 1991 Planarity : 0.004 0.048 2089 Dihedral : 6.938 115.158 1764 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.76 % Allowed : 12.53 % Favored : 85.71 % 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: 2.59 (0.22), residues: 1593 helix: 2.18 (0.15), residues: 1297 sheet: None (None), residues: 0 loop : -0.40 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 184 HIS 0.002 0.001 HIS A 288 PHE 0.017 0.001 PHE C 413 TYR 0.011 0.001 TYR A 357 ARG 0.002 0.000 ARG A 436 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 215 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 193 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 TYR cc_start: 0.7953 (m-80) cc_final: 0.7752 (m-80) REVERT: A 264 LYS cc_start: 0.8060 (mttt) cc_final: 0.7765 (mtpt) REVERT: A 345 ILE cc_start: 0.8428 (mm) cc_final: 0.8160 (mt) REVERT: A 350 SER cc_start: 0.8296 (t) cc_final: 0.7753 (p) REVERT: A 428 MET cc_start: 0.8418 (mmt) cc_final: 0.7987 (mmp) REVERT: B 112 TRP cc_start: 0.6286 (t60) cc_final: 0.5803 (t-100) REVERT: B 370 MET cc_start: 0.8092 (mtm) cc_final: 0.7656 (mtp) REVERT: B 503 MET cc_start: 0.8983 (mtp) cc_final: 0.8610 (mtp) REVERT: B 585 MET cc_start: 0.8818 (mtt) cc_final: 0.8565 (mtt) REVERT: B 598 MET cc_start: 0.7690 (tpt) cc_final: 0.7150 (tpt) REVERT: C 219 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8072 (mp) REVERT: C 370 MET cc_start: 0.8699 (mtm) cc_final: 0.8415 (mtm) REVERT: C 413 PHE cc_start: 0.8914 (OUTLIER) cc_final: 0.8427 (t80) outliers start: 22 outliers final: 20 residues processed: 210 average time/residue: 0.4675 time to fit residues: 149.9104 Evaluate side-chains 210 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 188 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 571 ASN Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 506 ASP Chi-restraints excluded: chain C residue 617 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 1.9990 chunk 142 optimal weight: 0.4980 chunk 146 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12660 Z= 0.189 Angle : 0.433 5.263 17229 Z= 0.227 Chirality : 0.034 0.134 1991 Planarity : 0.003 0.050 2089 Dihedral : 6.758 117.573 1764 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.76 % Allowed : 12.77 % Favored : 85.47 % 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: 2.78 (0.22), residues: 1593 helix: 2.33 (0.15), residues: 1293 sheet: None (None), residues: 0 loop : -0.35 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 184 HIS 0.002 0.000 HIS B 394 PHE 0.012 0.001 PHE C 413 TYR 0.010 0.001 TYR A 357 ARG 0.002 0.000 ARG C 589 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 190 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.7980 (mttt) cc_final: 0.7682 (mtpt) REVERT: A 345 ILE cc_start: 0.8432 (mm) cc_final: 0.8160 (mt) REVERT: A 350 SER cc_start: 0.8270 (t) cc_final: 0.7708 (p) REVERT: A 428 MET cc_start: 0.8426 (mmt) cc_final: 0.8007 (mmp) REVERT: A 503 MET cc_start: 0.9035 (mtp) cc_final: 0.8762 (mtp) REVERT: B 112 TRP cc_start: 0.6367 (t60) cc_final: 0.5913 (t-100) REVERT: B 370 MET cc_start: 0.8043 (mtm) cc_final: 0.7584 (mtp) REVERT: B 503 MET cc_start: 0.8953 (mtp) cc_final: 0.8575 (mtp) REVERT: B 585 MET cc_start: 0.8771 (mtt) cc_final: 0.8539 (mtt) REVERT: B 598 MET cc_start: 0.7573 (tpt) cc_final: 0.7042 (tpt) REVERT: C 219 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8101 (mp) REVERT: C 370 MET cc_start: 0.8640 (mtm) cc_final: 0.8367 (mtm) REVERT: C 413 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8441 (t80) outliers start: 22 outliers final: 19 residues processed: 208 average time/residue: 0.4731 time to fit residues: 149.4939 Evaluate side-chains 210 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 189 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 571 ASN Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 506 ASP Chi-restraints excluded: chain C residue 617 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12660 Z= 0.253 Angle : 0.462 5.965 17229 Z= 0.245 Chirality : 0.036 0.145 1991 Planarity : 0.004 0.049 2089 Dihedral : 6.891 114.569 1764 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.76 % Allowed : 12.93 % Favored : 85.32 % 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: 2.55 (0.22), residues: 1593 helix: 2.16 (0.15), residues: 1298 sheet: None (None), residues: 0 loop : -0.41 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 184 HIS 0.002 0.001 HIS C 288 PHE 0.017 0.001 PHE B 413 TYR 0.011 0.001 TYR A 357 ARG 0.002 0.000 ARG C 589 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue THR 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue ILE 110 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 190 time to evaluate : 1.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LYS cc_start: 0.8058 (mttt) cc_final: 0.7764 (mtpt) REVERT: A 345 ILE cc_start: 0.8445 (mm) cc_final: 0.8168 (mt) REVERT: A 350 SER cc_start: 0.8350 (t) cc_final: 0.7799 (p) REVERT: A 428 MET cc_start: 0.8418 (mmt) cc_final: 0.8008 (mmp) REVERT: A 503 MET cc_start: 0.9061 (mtp) cc_final: 0.8783 (mtp) REVERT: B 112 TRP cc_start: 0.6389 (t60) cc_final: 0.5968 (t-100) REVERT: B 370 MET cc_start: 0.8096 (mtm) cc_final: 0.7662 (mtp) REVERT: B 503 MET cc_start: 0.8995 (mtp) cc_final: 0.8622 (mtp) REVERT: B 585 MET cc_start: 0.8793 (mtt) cc_final: 0.8538 (mtt) REVERT: B 598 MET cc_start: 0.7670 (tpt) cc_final: 0.7122 (tpt) REVERT: C 219 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8106 (mp) REVERT: C 370 MET cc_start: 0.8675 (mtm) cc_final: 0.8398 (mtm) REVERT: C 413 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.8487 (t80) outliers start: 22 outliers final: 19 residues processed: 208 average time/residue: 0.4829 time to fit residues: 152.7427 Evaluate side-chains 210 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 189 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 571 ASN Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 506 ASP Chi-restraints excluded: chain C residue 617 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.139141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.105485 restraints weight = 42075.002| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.91 r_work: 0.3095 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12660 Z= 0.232 Angle : 0.450 5.796 17229 Z= 0.237 Chirality : 0.035 0.139 1991 Planarity : 0.004 0.050 2089 Dihedral : 6.817 115.112 1764 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.68 % Allowed : 13.01 % Favored : 85.32 % 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: 2.58 (0.22), residues: 1593 helix: 2.19 (0.15), residues: 1295 sheet: None (None), residues: 0 loop : -0.43 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 184 HIS 0.002 0.001 HIS A 288 PHE 0.014 0.001 PHE C 413 TYR 0.011 0.001 TYR A 357 ARG 0.002 0.000 ARG C 589 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5208.07 seconds wall clock time: 93 minutes 40.62 seconds (5620.62 seconds total)