Starting phenix.real_space_refine on Fri Dec 15 23:57:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t8b_25743/12_2023/7t8b_25743.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t8b_25743/12_2023/7t8b_25743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t8b_25743/12_2023/7t8b_25743.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t8b_25743/12_2023/7t8b_25743.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t8b_25743/12_2023/7t8b_25743.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t8b_25743/12_2023/7t8b_25743.pdb" } resolution = 3.8 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= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 21069 2.51 5 N 5801 2.21 5 O 6035 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 516": "OD1" <-> "OD2" Residue "B PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 33025 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 4143 Classifications: {'peptide': 519} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 492} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 4126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4126 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 489} Chain breaks: 7 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 4126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4126 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 489} Chain breaks: 7 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 4126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4126 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 489} Chain breaks: 7 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 4126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4126 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 489} Chain breaks: 7 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 4126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4126 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 489} Chain breaks: 7 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 4126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4126 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 489} Chain breaks: 7 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 4126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4126 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 489} Chain breaks: 7 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 15.57, per 1000 atoms: 0.47 Number of scatterers: 33025 At special positions: 0 Unit cell: (199.962, 199.962, 83.582, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 6035 8.00 N 5801 7.00 C 21069 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.51 Conformation dependent library (CDL) restraints added in 5.8 seconds 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7716 Finding SS restraints... Secondary structure from input PDB file: 191 helices and 32 sheets defined 44.1% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.41 Creating SS restraints... Processing helix chain 'A' and resid 56 through 67 Processing helix chain 'A' and resid 121 through 129 Processing helix chain 'A' and resid 154 through 160 Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 170 through 180 Processing helix chain 'A' and resid 186 through 194 removed outlier: 3.722A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 244 Processing helix chain 'A' and resid 266 through 276 removed outlier: 3.519A pdb=" N LEU A 270 " --> pdb=" O GLU A 266 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 299 Proline residue: A 296 - end of helix Processing helix chain 'A' and resid 311 through 323 Processing helix chain 'A' and resid 324 through 328 Proline residue: A 327 - end of helix No H-bonds generated for 'chain 'A' and resid 324 through 328' Processing helix chain 'A' and resid 341 through 349 Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 373 through 383 Processing helix chain 'A' and resid 384 through 388 Processing helix chain 'A' and resid 395 through 403 removed outlier: 3.681A pdb=" N ILE A 401 " --> pdb=" O ASP A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 434 removed outlier: 3.502A pdb=" N GLU A 427 " --> pdb=" O THR A 423 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 432 " --> pdb=" O TYR A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 461 removed outlier: 3.639A pdb=" N LEU A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 470 removed outlier: 3.600A pdb=" N LEU A 468 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ASP A 469 " --> pdb=" O ASP A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 479 removed outlier: 3.559A pdb=" N ASP A 476 " --> pdb=" O ASP A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 509 Processing helix chain 'A' and resid 518 through 523 removed outlier: 3.546A pdb=" N MET A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY A 523 " --> pdb=" O GLN A 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 518 through 523' Processing helix chain 'A' and resid 530 through 549 Processing helix chain 'A' and resid 576 through 583 removed outlier: 3.733A pdb=" N SER A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN A 581 " --> pdb=" O ALA A 577 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU A 582 " --> pdb=" O LYS A 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 68 removed outlier: 3.511A pdb=" N ARG B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 129 Processing helix chain 'B' and resid 154 through 160 Processing helix chain 'B' and resid 165 through 167 No H-bonds generated for 'chain 'B' and resid 165 through 167' Processing helix chain 'B' and resid 170 through 181 Processing helix chain 'B' and resid 186 through 194 removed outlier: 3.687A pdb=" N LEU B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 244 Processing helix chain 'B' and resid 266 through 276 Processing helix chain 'B' and resid 291 through 299 Proline residue: B 296 - end of helix Processing helix chain 'B' and resid 311 through 323 Processing helix chain 'B' and resid 324 through 328 Proline residue: B 327 - end of helix No H-bonds generated for 'chain 'B' and resid 324 through 328' Processing helix chain 'B' and resid 341 through 349 Processing helix chain 'B' and resid 351 through 356 removed outlier: 3.976A pdb=" N ILE B 355 " --> pdb=" O ASN B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 359 No H-bonds generated for 'chain 'B' and resid 357 through 359' Processing helix chain 'B' and resid 369 through 372 removed outlier: 3.787A pdb=" N GLN B 372 " --> pdb=" O SER B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 369 through 372' Processing helix chain 'B' and resid 373 through 383 Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.618A pdb=" N ALA B 388 " --> pdb=" O GLU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 403 removed outlier: 3.711A pdb=" N ILE B 401 " --> pdb=" O ASP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 434 removed outlier: 3.570A pdb=" N LEU B 432 " --> pdb=" O TYR B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 461 removed outlier: 3.565A pdb=" N LEU B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG B 453 " --> pdb=" O VAL B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 479 Processing helix chain 'B' and resid 493 through 509 Processing helix chain 'B' and resid 518 through 523 removed outlier: 3.651A pdb=" N MET B 522 " --> pdb=" O LEU B 518 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY B 523 " --> pdb=" O GLN B 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 518 through 523' Processing helix chain 'B' and resid 530 through 550 Processing helix chain 'B' and resid 576 through 583 removed outlier: 3.638A pdb=" N SER B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLN B 581 " --> pdb=" O ALA B 577 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU B 582 " --> pdb=" O LYS B 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 67 removed outlier: 3.516A pdb=" N ARG C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 129 Processing helix chain 'C' and resid 154 through 160 Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 170 through 181 Processing helix chain 'C' and resid 186 through 194 removed outlier: 3.677A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 244 Processing helix chain 'C' and resid 266 through 276 removed outlier: 3.515A pdb=" N LEU C 270 " --> pdb=" O GLU C 266 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA C 271 " --> pdb=" O LEU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 299 Proline residue: C 296 - end of helix Processing helix chain 'C' and resid 311 through 323 Processing helix chain 'C' and resid 324 through 328 Proline residue: C 327 - end of helix No H-bonds generated for 'chain 'C' and resid 324 through 328' Processing helix chain 'C' and resid 341 through 349 Processing helix chain 'C' and resid 351 through 358 removed outlier: 3.863A pdb=" N ILE C 355 " --> pdb=" O ASN C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 373 through 383 Processing helix chain 'C' and resid 395 through 403 removed outlier: 3.683A pdb=" N ILE C 401 " --> pdb=" O ASP C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 434 removed outlier: 3.599A pdb=" N LEU C 432 " --> pdb=" O TYR C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 461 removed outlier: 3.665A pdb=" N LEU C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG C 453 " --> pdb=" O VAL C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 469 No H-bonds generated for 'chain 'C' and resid 467 through 469' Processing helix chain 'C' and resid 470 through 479 removed outlier: 4.377A pdb=" N TRP C 474 " --> pdb=" O LYS C 470 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP C 476 " --> pdb=" O ASP C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 509 Processing helix chain 'C' and resid 518 through 523 removed outlier: 3.627A pdb=" N MET C 522 " --> pdb=" O LEU C 518 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY C 523 " --> pdb=" O GLN C 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 518 through 523' Processing helix chain 'C' and resid 530 through 549 Processing helix chain 'C' and resid 576 through 583 removed outlier: 3.698A pdb=" N SER C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN C 581 " --> pdb=" O ALA C 577 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU C 582 " --> pdb=" O LYS C 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 68 removed outlier: 3.501A pdb=" N ARG D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 129 Processing helix chain 'D' and resid 154 through 160 Processing helix chain 'D' and resid 165 through 167 No H-bonds generated for 'chain 'D' and resid 165 through 167' Processing helix chain 'D' and resid 170 through 180 Processing helix chain 'D' and resid 186 through 194 removed outlier: 3.634A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 276 Processing helix chain 'D' and resid 291 through 299 Proline residue: D 296 - end of helix Processing helix chain 'D' and resid 311 through 323 Processing helix chain 'D' and resid 324 through 328 Proline residue: D 327 - end of helix No H-bonds generated for 'chain 'D' and resid 324 through 328' Processing helix chain 'D' and resid 341 through 349 Processing helix chain 'D' and resid 351 through 356 removed outlier: 3.952A pdb=" N ILE D 355 " --> pdb=" O ASN D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 372 removed outlier: 3.826A pdb=" N GLN D 372 " --> pdb=" O SER D 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 369 through 372' Processing helix chain 'D' and resid 373 through 383 Processing helix chain 'D' and resid 384 through 388 removed outlier: 3.587A pdb=" N ALA D 388 " --> pdb=" O GLU D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 403 removed outlier: 3.716A pdb=" N ILE D 401 " --> pdb=" O ASP D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 434 removed outlier: 3.546A pdb=" N LEU D 432 " --> pdb=" O TYR D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 461 removed outlier: 3.531A pdb=" N LEU D 451 " --> pdb=" O SER D 447 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG D 453 " --> pdb=" O VAL D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 479 Processing helix chain 'D' and resid 493 through 509 Processing helix chain 'D' and resid 518 through 523 removed outlier: 3.594A pdb=" N MET D 522 " --> pdb=" O LEU D 518 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY D 523 " --> pdb=" O GLN D 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 518 through 523' Processing helix chain 'D' and resid 530 through 550 Processing helix chain 'D' and resid 576 through 583 removed outlier: 3.594A pdb=" N SER D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU D 582 " --> pdb=" O LYS D 578 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 67 removed outlier: 3.534A pdb=" N ARG E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 129 Processing helix chain 'E' and resid 154 through 160 Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 170 through 181 Processing helix chain 'E' and resid 186 through 194 removed outlier: 3.730A pdb=" N LEU E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 244 Processing helix chain 'E' and resid 266 through 276 removed outlier: 3.518A pdb=" N LEU E 270 " --> pdb=" O GLU E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 299 Proline residue: E 296 - end of helix Processing helix chain 'E' and resid 311 through 323 Processing helix chain 'E' and resid 324 through 328 Proline residue: E 327 - end of helix No H-bonds generated for 'chain 'E' and resid 324 through 328' Processing helix chain 'E' and resid 341 through 349 Processing helix chain 'E' and resid 351 through 358 removed outlier: 3.636A pdb=" N ILE E 355 " --> pdb=" O ASN E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 372 No H-bonds generated for 'chain 'E' and resid 370 through 372' Processing helix chain 'E' and resid 373 through 383 Processing helix chain 'E' and resid 395 through 403 removed outlier: 3.678A pdb=" N ILE E 401 " --> pdb=" O ASP E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 434 removed outlier: 3.567A pdb=" N LEU E 432 " --> pdb=" O TYR E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 461 removed outlier: 3.587A pdb=" N LEU E 451 " --> pdb=" O SER E 447 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG E 453 " --> pdb=" O VAL E 449 " (cutoff:3.500A) Processing helix chain 'E' and resid 468 through 470 No H-bonds generated for 'chain 'E' and resid 468 through 470' Processing helix chain 'E' and resid 471 through 479 Processing helix chain 'E' and resid 493 through 509 Processing helix chain 'E' and resid 518 through 523 removed outlier: 3.610A pdb=" N MET E 522 " --> pdb=" O LEU E 518 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY E 523 " --> pdb=" O GLN E 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 518 through 523' Processing helix chain 'E' and resid 530 through 549 Processing helix chain 'E' and resid 576 through 583 removed outlier: 3.780A pdb=" N SER E 580 " --> pdb=" O SER E 576 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN E 581 " --> pdb=" O ALA E 577 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU E 582 " --> pdb=" O LYS E 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 67 removed outlier: 3.541A pdb=" N ARG F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 129 Processing helix chain 'F' and resid 154 through 160 Processing helix chain 'F' and resid 165 through 167 No H-bonds generated for 'chain 'F' and resid 165 through 167' Processing helix chain 'F' and resid 170 through 181 Processing helix chain 'F' and resid 186 through 194 removed outlier: 3.697A pdb=" N LEU F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 276 Processing helix chain 'F' and resid 291 through 299 Proline residue: F 296 - end of helix Processing helix chain 'F' and resid 311 through 323 Processing helix chain 'F' and resid 324 through 328 Proline residue: F 327 - end of helix No H-bonds generated for 'chain 'F' and resid 324 through 328' Processing helix chain 'F' and resid 341 through 349 Processing helix chain 'F' and resid 369 through 372 removed outlier: 3.798A pdb=" N GLN F 372 " --> pdb=" O SER F 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 369 through 372' Processing helix chain 'F' and resid 373 through 383 Processing helix chain 'F' and resid 384 through 388 removed outlier: 3.624A pdb=" N ALA F 388 " --> pdb=" O GLU F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 403 removed outlier: 3.772A pdb=" N ILE F 401 " --> pdb=" O ASP F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 434 removed outlier: 3.555A pdb=" N LEU F 432 " --> pdb=" O TYR F 428 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 461 removed outlier: 3.600A pdb=" N LEU F 451 " --> pdb=" O SER F 447 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG F 453 " --> pdb=" O VAL F 449 " (cutoff:3.500A) Processing helix chain 'F' and resid 471 through 479 Processing helix chain 'F' and resid 493 through 509 Processing helix chain 'F' and resid 518 through 523 removed outlier: 3.651A pdb=" N MET F 522 " --> pdb=" O LEU F 518 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY F 523 " --> pdb=" O GLN F 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 518 through 523' Processing helix chain 'F' and resid 530 through 549 Processing helix chain 'F' and resid 576 through 583 removed outlier: 3.655A pdb=" N SER F 580 " --> pdb=" O SER F 576 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN F 581 " --> pdb=" O ALA F 577 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU F 582 " --> pdb=" O LYS F 578 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 67 removed outlier: 3.540A pdb=" N ARG G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 129 Processing helix chain 'G' and resid 154 through 160 Processing helix chain 'G' and resid 165 through 167 No H-bonds generated for 'chain 'G' and resid 165 through 167' Processing helix chain 'G' and resid 170 through 181 Processing helix chain 'G' and resid 186 through 194 removed outlier: 3.707A pdb=" N LEU G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 244 Processing helix chain 'G' and resid 266 through 276 removed outlier: 3.506A pdb=" N ALA G 271 " --> pdb=" O LEU G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 291 through 299 Proline residue: G 296 - end of helix Processing helix chain 'G' and resid 311 through 323 Processing helix chain 'G' and resid 324 through 328 Proline residue: G 327 - end of helix No H-bonds generated for 'chain 'G' and resid 324 through 328' Processing helix chain 'G' and resid 341 through 349 Processing helix chain 'G' and resid 351 through 358 removed outlier: 4.032A pdb=" N ILE G 355 " --> pdb=" O ASN G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 372 No H-bonds generated for 'chain 'G' and resid 370 through 372' Processing helix chain 'G' and resid 373 through 383 Processing helix chain 'G' and resid 384 through 388 removed outlier: 3.517A pdb=" N ALA G 388 " --> pdb=" O GLU G 385 " (cutoff:3.500A) Processing helix chain 'G' and resid 395 through 403 removed outlier: 3.758A pdb=" N ILE G 401 " --> pdb=" O ASP G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 420 through 434 removed outlier: 3.557A pdb=" N LEU G 432 " --> pdb=" O TYR G 428 " (cutoff:3.500A) Processing helix chain 'G' and resid 447 through 461 removed outlier: 3.616A pdb=" N LEU G 451 " --> pdb=" O SER G 447 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG G 453 " --> pdb=" O VAL G 449 " (cutoff:3.500A) Processing helix chain 'G' and resid 467 through 470 Processing helix chain 'G' and resid 471 through 479 Processing helix chain 'G' and resid 493 through 509 Processing helix chain 'G' and resid 518 through 523 removed outlier: 3.593A pdb=" N MET G 522 " --> pdb=" O LEU G 518 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY G 523 " --> pdb=" O GLN G 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 518 through 523' Processing helix chain 'G' and resid 530 through 549 Processing helix chain 'G' and resid 576 through 583 removed outlier: 3.777A pdb=" N SER G 580 " --> pdb=" O SER G 576 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN G 581 " --> pdb=" O ALA G 577 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU G 582 " --> pdb=" O LYS G 578 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 67 removed outlier: 3.515A pdb=" N ARG H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 129 Processing helix chain 'H' and resid 154 through 160 Processing helix chain 'H' and resid 165 through 167 No H-bonds generated for 'chain 'H' and resid 165 through 167' Processing helix chain 'H' and resid 170 through 181 Processing helix chain 'H' and resid 186 through 194 removed outlier: 3.694A pdb=" N LEU H 190 " --> pdb=" O THR H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 244 Processing helix chain 'H' and resid 266 through 276 removed outlier: 3.531A pdb=" N ALA H 271 " --> pdb=" O LEU H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 299 Proline residue: H 296 - end of helix Processing helix chain 'H' and resid 311 through 323 Processing helix chain 'H' and resid 324 through 328 Proline residue: H 327 - end of helix No H-bonds generated for 'chain 'H' and resid 324 through 328' Processing helix chain 'H' and resid 341 through 349 Processing helix chain 'H' and resid 351 through 356 removed outlier: 4.017A pdb=" N ILE H 355 " --> pdb=" O ASN H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 372 removed outlier: 3.801A pdb=" N GLN H 372 " --> pdb=" O SER H 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 369 through 372' Processing helix chain 'H' and resid 373 through 383 Processing helix chain 'H' and resid 384 through 388 removed outlier: 3.577A pdb=" N ALA H 388 " --> pdb=" O GLU H 385 " (cutoff:3.500A) Processing helix chain 'H' and resid 395 through 403 removed outlier: 3.744A pdb=" N ILE H 401 " --> pdb=" O ASP H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 420 through 434 removed outlier: 3.576A pdb=" N LEU H 432 " --> pdb=" O TYR H 428 " (cutoff:3.500A) Processing helix chain 'H' and resid 447 through 461 removed outlier: 3.599A pdb=" N LEU H 451 " --> pdb=" O SER H 447 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG H 453 " --> pdb=" O VAL H 449 " (cutoff:3.500A) Processing helix chain 'H' and resid 471 through 479 Processing helix chain 'H' and resid 493 through 509 Processing helix chain 'H' and resid 518 through 523 removed outlier: 3.606A pdb=" N MET H 522 " --> pdb=" O LEU H 518 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY H 523 " --> pdb=" O GLN H 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 518 through 523' Processing helix chain 'H' and resid 530 through 549 Processing helix chain 'H' and resid 576 through 583 removed outlier: 3.630A pdb=" N SER H 580 " --> pdb=" O SER H 576 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN H 581 " --> pdb=" O ALA H 577 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU H 582 " --> pdb=" O LYS H 578 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA2, first strand: chain 'A' and resid 162 through 163 removed outlier: 6.544A pdb=" N LEU A 204 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU A 221 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE A 206 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LEU A 219 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TRP A 208 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 280 through 282 removed outlier: 6.718A pdb=" N VAL A 260 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N TRP A 307 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LEU A 262 " --> pdb=" O TRP A 307 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 367 through 368 removed outlier: 4.046A pdb=" N ILE H 515 " --> pdb=" O THR H 554 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU H 410 " --> pdb=" O ASN H 585 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N LEU H 587 " --> pdb=" O LEU H 410 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL H 412 " --> pdb=" O LEU H 587 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N LEU H 589 " --> pdb=" O VAL H 412 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N THR H 414 " --> pdb=" O LEU H 589 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N ASP H 591 " --> pdb=" O THR H 414 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY H 615 " --> pdb=" O VAL H 605 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN H 622 " --> pdb=" O THR H 627 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR H 627 " --> pdb=" O ASN H 622 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 627 through 629 removed outlier: 3.643A pdb=" N THR A 627 " --> pdb=" O ASN A 622 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN A 622 " --> pdb=" O THR A 627 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER A 606 " --> pdb=" O VAL A 586 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL A 586 " --> pdb=" O SER A 606 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR A 411 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE A 557 " --> pdb=" O THR A 411 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE A 413 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE A 515 " --> pdb=" O THR A 554 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU A 440 " --> pdb=" O ILE A 514 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA7, first strand: chain 'B' and resid 162 through 163 removed outlier: 6.484A pdb=" N LEU B 204 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU B 221 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N PHE B 206 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LEU B 219 " --> pdb=" O PHE B 206 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TRP B 208 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 280 through 282 removed outlier: 6.876A pdb=" N VAL B 260 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N TRP B 307 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU B 262 " --> pdb=" O TRP B 307 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 627 through 629 removed outlier: 3.669A pdb=" N THR B 627 " --> pdb=" O ASN B 622 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN B 622 " --> pdb=" O THR B 627 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY B 615 " --> pdb=" O VAL B 605 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER B 606 " --> pdb=" O VAL B 586 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL B 586 " --> pdb=" O SER B 606 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU B 410 " --> pdb=" O ASN B 585 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N LEU B 587 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL B 412 " --> pdb=" O LEU B 587 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LEU B 589 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR B 414 " --> pdb=" O LEU B 589 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N ASP B 591 " --> pdb=" O THR B 414 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N THR B 411 " --> pdb=" O LEU B 555 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE B 557 " --> pdb=" O THR B 411 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N PHE B 413 " --> pdb=" O ILE B 557 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE B 515 " --> pdb=" O THR B 554 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB2, first strand: chain 'C' and resid 162 through 163 removed outlier: 6.519A pdb=" N LEU C 204 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU C 221 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N PHE C 206 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU C 219 " --> pdb=" O PHE C 206 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TRP C 208 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 280 through 282 removed outlier: 6.835A pdb=" N VAL C 260 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N TRP C 307 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LEU C 262 " --> pdb=" O TRP C 307 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 627 through 629 removed outlier: 3.634A pdb=" N THR C 627 " --> pdb=" O ASN C 622 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN C 622 " --> pdb=" O THR C 627 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER C 606 " --> pdb=" O VAL C 586 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL C 586 " --> pdb=" O SER C 606 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE C 515 " --> pdb=" O THR C 554 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AB6, first strand: chain 'D' and resid 162 through 163 removed outlier: 6.442A pdb=" N LEU D 204 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU D 221 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE D 206 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LEU D 219 " --> pdb=" O PHE D 206 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TRP D 208 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 280 through 282 removed outlier: 6.908A pdb=" N VAL D 260 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N TRP D 307 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N LEU D 262 " --> pdb=" O TRP D 307 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 627 through 629 removed outlier: 3.625A pdb=" N THR D 627 " --> pdb=" O ASN D 622 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN D 622 " --> pdb=" O THR D 627 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY D 615 " --> pdb=" O VAL D 605 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR D 602 " --> pdb=" O GLN D 590 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER D 606 " --> pdb=" O VAL D 586 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL D 586 " --> pdb=" O SER D 606 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N THR D 411 " --> pdb=" O LEU D 555 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ILE D 557 " --> pdb=" O THR D 411 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE D 413 " --> pdb=" O ILE D 557 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE D 515 " --> pdb=" O THR D 554 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AC1, first strand: chain 'E' and resid 161 through 163 removed outlier: 6.524A pdb=" N LEU E 204 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU E 221 " --> pdb=" O LEU E 204 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N PHE E 206 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LEU E 219 " --> pdb=" O PHE E 206 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TRP E 208 " --> pdb=" O ARG E 217 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 280 through 282 removed outlier: 6.875A pdb=" N VAL E 260 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N TRP E 307 " --> pdb=" O VAL E 260 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LEU E 262 " --> pdb=" O TRP E 307 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 627 through 629 removed outlier: 3.634A pdb=" N THR E 627 " --> pdb=" O ASN E 622 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN E 622 " --> pdb=" O THR E 627 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR E 602 " --> pdb=" O GLN E 590 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER E 606 " --> pdb=" O VAL E 586 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL E 586 " --> pdb=" O SER E 606 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR E 411 " --> pdb=" O LEU E 555 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE E 557 " --> pdb=" O THR E 411 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N PHE E 413 " --> pdb=" O ILE E 557 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE E 515 " --> pdb=" O THR E 554 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AC5, first strand: chain 'F' and resid 162 through 163 removed outlier: 6.463A pdb=" N LEU F 204 " --> pdb=" O LEU F 221 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU F 221 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE F 206 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N LEU F 219 " --> pdb=" O PHE F 206 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TRP F 208 " --> pdb=" O ARG F 217 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 280 through 282 removed outlier: 6.900A pdb=" N VAL F 260 " --> pdb=" O VAL F 305 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N TRP F 307 " --> pdb=" O VAL F 260 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N LEU F 262 " --> pdb=" O TRP F 307 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 627 through 629 removed outlier: 3.640A pdb=" N THR F 627 " --> pdb=" O ASN F 622 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN F 622 " --> pdb=" O THR F 627 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY F 615 " --> pdb=" O VAL F 605 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR F 602 " --> pdb=" O GLN F 590 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER F 606 " --> pdb=" O VAL F 586 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL F 586 " --> pdb=" O SER F 606 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N THR F 411 " --> pdb=" O LEU F 555 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE F 557 " --> pdb=" O THR F 411 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N PHE F 413 " --> pdb=" O ILE F 557 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE F 515 " --> pdb=" O THR F 554 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AC9, first strand: chain 'G' and resid 162 through 163 removed outlier: 6.565A pdb=" N LEU G 204 " --> pdb=" O LEU G 221 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU G 221 " --> pdb=" O LEU G 204 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE G 206 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LEU G 219 " --> pdb=" O PHE G 206 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TRP G 208 " --> pdb=" O ARG G 217 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 280 through 282 removed outlier: 6.859A pdb=" N VAL G 260 " --> pdb=" O VAL G 305 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N TRP G 307 " --> pdb=" O VAL G 260 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LEU G 262 " --> pdb=" O TRP G 307 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 627 through 629 removed outlier: 3.610A pdb=" N THR G 627 " --> pdb=" O ASN G 622 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN G 622 " --> pdb=" O THR G 627 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER G 606 " --> pdb=" O VAL G 586 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL G 586 " --> pdb=" O SER G 606 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR G 411 " --> pdb=" O LEU G 555 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE G 557 " --> pdb=" O THR G 411 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N PHE G 413 " --> pdb=" O ILE G 557 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE G 515 " --> pdb=" O THR G 554 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 71 through 72 Processing sheet with id=AD4, first strand: chain 'H' and resid 162 through 163 removed outlier: 6.533A pdb=" N LEU H 204 " --> pdb=" O LEU H 221 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU H 221 " --> pdb=" O LEU H 204 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE H 206 " --> pdb=" O LEU H 219 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LEU H 219 " --> pdb=" O PHE H 206 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TRP H 208 " --> pdb=" O ARG H 217 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 280 through 282 removed outlier: 6.873A pdb=" N VAL H 260 " --> pdb=" O VAL H 305 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N TRP H 307 " --> pdb=" O VAL H 260 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LEU H 262 " --> pdb=" O TRP H 307 " (cutoff:3.500A) 1389 hydrogen bonds defined for protein. 3813 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: 13.65 Time building geometry restraints manager: 12.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 10937 1.34 - 1.46: 7705 1.46 - 1.58: 14939 1.58 - 1.69: 0 1.69 - 1.81: 176 Bond restraints: 33757 Sorted by residual: bond pdb=" CA PRO F 291 " pdb=" C PRO F 291 " ideal model delta sigma weight residual 1.517 1.508 0.009 6.70e-03 2.23e+04 1.86e+00 bond pdb=" C ARG G 199 " pdb=" N PRO G 200 " ideal model delta sigma weight residual 1.335 1.346 -0.010 1.36e-02 5.41e+03 5.77e-01 bond pdb=" C ARG A 199 " pdb=" N PRO A 200 " ideal model delta sigma weight residual 1.335 1.346 -0.010 1.36e-02 5.41e+03 5.70e-01 bond pdb=" C ARG C 199 " pdb=" N PRO C 200 " ideal model delta sigma weight residual 1.335 1.346 -0.010 1.36e-02 5.41e+03 5.61e-01 bond pdb=" CA GLU E 153 " pdb=" CB GLU E 153 " ideal model delta sigma weight residual 1.522 1.532 -0.010 1.32e-02 5.74e+03 5.41e-01 ... (remaining 33752 not shown) Histogram of bond angle deviations from ideal: 100.19 - 106.95: 1084 106.95 - 113.71: 18160 113.71 - 120.47: 12958 120.47 - 127.23: 13088 127.23 - 134.00: 407 Bond angle restraints: 45697 Sorted by residual: angle pdb=" N PRO C 54 " pdb=" CA PRO C 54 " pdb=" CB PRO C 54 " ideal model delta sigma weight residual 103.00 110.46 -7.46 1.10e+00 8.26e-01 4.60e+01 angle pdb=" N PRO D 54 " pdb=" CA PRO D 54 " pdb=" CB PRO D 54 " ideal model delta sigma weight residual 103.00 110.44 -7.44 1.10e+00 8.26e-01 4.57e+01 angle pdb=" N PRO G 54 " pdb=" CA PRO G 54 " pdb=" CB PRO G 54 " ideal model delta sigma weight residual 103.00 110.43 -7.43 1.10e+00 8.26e-01 4.56e+01 angle pdb=" N PRO F 54 " pdb=" CA PRO F 54 " pdb=" CB PRO F 54 " ideal model delta sigma weight residual 103.00 110.43 -7.43 1.10e+00 8.26e-01 4.56e+01 angle pdb=" N PRO B 54 " pdb=" CA PRO B 54 " pdb=" CB PRO B 54 " ideal model delta sigma weight residual 103.00 110.42 -7.42 1.10e+00 8.26e-01 4.55e+01 ... (remaining 45692 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.04: 19193 16.04 - 32.07: 801 32.07 - 48.11: 116 48.11 - 64.15: 17 64.15 - 80.18: 8 Dihedral angle restraints: 20135 sinusoidal: 8255 harmonic: 11880 Sorted by residual: dihedral pdb=" CA ASP A 516 " pdb=" CB ASP A 516 " pdb=" CG ASP A 516 " pdb=" OD1 ASP A 516 " ideal model delta sinusoidal sigma weight residual -30.00 -88.78 58.78 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA GLU F 479 " pdb=" C GLU F 479 " pdb=" N ASP F 480 " pdb=" CA ASP F 480 " ideal model delta harmonic sigma weight residual 180.00 163.77 16.23 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA GLU H 479 " pdb=" C GLU H 479 " pdb=" N ASP H 480 " pdb=" CA ASP H 480 " ideal model delta harmonic sigma weight residual 180.00 164.14 15.86 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 20132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 4232 0.047 - 0.094: 596 0.094 - 0.141: 224 0.141 - 0.188: 0 0.188 - 0.236: 7 Chirality restraints: 5059 Sorted by residual: chirality pdb=" CA PRO G 54 " pdb=" N PRO G 54 " pdb=" C PRO G 54 " pdb=" CB PRO G 54 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA PRO D 54 " pdb=" N PRO D 54 " pdb=" C PRO D 54 " pdb=" CB PRO D 54 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA PRO B 54 " pdb=" N PRO B 54 " pdb=" C PRO B 54 " pdb=" CB PRO B 54 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 5056 not shown) Planarity restraints: 5909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 295 " 0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO B 296 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 296 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 296 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 199 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.37e+00 pdb=" N PRO C 200 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO C 200 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 200 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 199 " -0.019 5.00e-02 4.00e+02 2.90e-02 1.35e+00 pdb=" N PRO D 200 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO D 200 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 200 " -0.016 5.00e-02 4.00e+02 ... (remaining 5906 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2700 2.74 - 3.28: 33034 3.28 - 3.82: 53427 3.82 - 4.36: 63066 4.36 - 4.90: 104951 Nonbonded interactions: 257178 Sorted by model distance: nonbonded pdb=" O THR H 423 " pdb=" OG SER H 426 " model vdw 2.205 2.440 nonbonded pdb=" O THR B 423 " pdb=" OG SER B 426 " model vdw 2.211 2.440 nonbonded pdb=" O THR G 423 " pdb=" OG SER G 426 " model vdw 2.213 2.440 nonbonded pdb=" O THR F 423 " pdb=" OG SER F 426 " model vdw 2.219 2.440 nonbonded pdb=" O THR D 423 " pdb=" OG SER D 426 " model vdw 2.226 2.440 ... (remaining 257173 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 54 and (name N or name CA or name C or name O or name CB \ )) or resid 55 through 486 or (resid 487 through 488 and (name N or name CA or n \ ame C or name O or name CB )) or resid 492 through 631)) selection = (chain 'B' and (resid 54 through 522 or (resid 523 and (name N or name CA )) or \ resid 529 through 600 or (resid 601 and (name N or name CA or name C or name O o \ r name CB )) or resid 602 through 622 or (resid 623 and (name N or name CA or na \ me C or name O or name CB )) or resid 624 through 631)) selection = (chain 'C' and (resid 54 through 522 or (resid 523 and (name N or name CA )) or \ resid 529 through 600 or (resid 601 and (name N or name CA or name C or name O o \ r name CB )) or resid 602 through 622 or (resid 623 and (name N or name CA or na \ me C or name O or name CB )) or resid 624 through 631)) selection = (chain 'D' and (resid 54 through 522 or (resid 523 and (name N or name CA )) or \ resid 529 through 600 or (resid 601 and (name N or name CA or name C or name O o \ r name CB )) or resid 602 through 622 or (resid 623 and (name N or name CA or na \ me C or name O or name CB )) or resid 624 through 631)) selection = (chain 'E' and (resid 54 through 522 or (resid 523 and (name N or name CA )) or \ resid 529 through 600 or (resid 601 and (name N or name CA or name C or name O o \ r name CB )) or resid 602 through 622 or (resid 623 and (name N or name CA or na \ me C or name O or name CB )) or resid 624 through 631)) selection = (chain 'F' and (resid 54 through 522 or (resid 523 and (name N or name CA )) or \ resid 529 through 600 or (resid 601 and (name N or name CA or name C or name O o \ r name CB )) or resid 602 through 622 or (resid 623 and (name N or name CA or na \ me C or name O or name CB )) or resid 624 through 631)) selection = (chain 'G' and (resid 54 through 522 or (resid 523 and (name N or name CA )) or \ resid 529 through 600 or (resid 601 and (name N or name CA or name C or name O o \ r name CB )) or resid 602 through 622 or (resid 623 and (name N or name CA or na \ me C or name O or name CB )) or resid 624 through 631)) selection = (chain 'H' and (resid 54 through 522 or (resid 523 and (name N or name CA )) or \ resid 529 through 600 or (resid 601 and (name N or name CA or name C or name O o \ r name CB )) or resid 602 through 622 or (resid 623 and (name N or name CA or na \ me C or name O or name CB )) or resid 624 through 631)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.550 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: 0.030 Extract box with map and model: 15.020 Check model and map are aligned: 0.500 Set scattering table: 0.270 Process input model: 84.910 Find NCS groups from input model: 2.600 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 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 : 0.002 0.025 33757 Z= 0.105 Angle : 0.466 7.457 45697 Z= 0.255 Chirality : 0.039 0.236 5059 Planarity : 0.003 0.030 5909 Dihedral : 8.770 80.182 12419 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.27 % Favored : 95.55 % Rotamer: Outliers : 1.40 % Allowed : 4.47 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.14), residues: 4004 helix: 0.50 (0.13), residues: 1429 sheet: -0.18 (0.18), residues: 940 loop : -0.76 (0.16), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 158 HIS 0.003 0.000 HIS G 503 PHE 0.009 0.001 PHE H 111 TYR 0.005 0.001 TYR C 428 ARG 0.002 0.000 ARG E 334 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1503 residues out of total 3610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 1453 time to evaluate : 3.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 34 residues processed: 1496 average time/residue: 0.5538 time to fit residues: 1235.3864 Evaluate side-chains 1257 residues out of total 3610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 1223 time to evaluate : 3.719 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.3267 time to fit residues: 25.6657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 0.0040 chunk 309 optimal weight: 0.0970 chunk 171 optimal weight: 0.0980 chunk 105 optimal weight: 0.8980 chunk 208 optimal weight: 5.9990 chunk 165 optimal weight: 0.9980 chunk 319 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 238 optimal weight: 0.5980 chunk 370 optimal weight: 3.9990 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 ASN A 399 ASN A 622 ASN B 67 HIS ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 ASN B 502 GLN C 383 ASN C 399 ASN ** C 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 HIS D 273 ASN D 351 ASN D 383 ASN D 399 ASN ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 ASN E 351 ASN E 383 ASN E 399 ASN E 535 GLN F 67 HIS F 273 ASN F 338 GLN ** F 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 ASN F 372 GLN ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 624 ASN ** G 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 351 ASN G 383 ASN G 399 ASN H 67 HIS H 351 ASN H 372 GLN ** H 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 535 GLN H 622 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33757 Z= 0.194 Angle : 0.636 7.379 45697 Z= 0.326 Chirality : 0.044 0.204 5059 Planarity : 0.005 0.052 5909 Dihedral : 3.781 16.379 4491 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.34 % Favored : 94.48 % Rotamer: Outliers : 2.63 % Allowed : 14.48 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.14), residues: 4004 helix: 0.62 (0.13), residues: 1481 sheet: -0.16 (0.18), residues: 947 loop : -0.79 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 474 HIS 0.010 0.001 HIS A 67 PHE 0.019 0.001 PHE F 542 TYR 0.022 0.002 TYR B 484 ARG 0.016 0.001 ARG C 160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1349 residues out of total 3610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1255 time to evaluate : 3.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 94 outliers final: 60 residues processed: 1295 average time/residue: 0.5288 time to fit residues: 1034.0014 Evaluate side-chains 1186 residues out of total 3610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 1126 time to evaluate : 3.734 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 0.3376 time to fit residues: 41.2277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 308 optimal weight: 7.9990 chunk 252 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 371 optimal weight: 0.7980 chunk 400 optimal weight: 5.9990 chunk 330 optimal weight: 0.0570 chunk 368 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 297 optimal weight: 2.9990 overall best weight: 1.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN A 174 GLN A 338 GLN A 467 GLN ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN A 624 ASN ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 GLN B 383 ASN B 386 GLN B 467 GLN B 519 GLN B 535 GLN ** B 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 ASN C 399 ASN C 458 GLN ** C 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 GLN ** C 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 GLN D 174 GLN D 273 ASN D 338 GLN D 372 GLN ** D 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 467 GLN D 549 ASN ** D 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 HIS E 399 ASN E 519 GLN E 535 GLN ** E 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 273 ASN F 347 ASN F 372 GLN F 383 ASN ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 519 GLN G 386 GLN G 502 GLN G 558 HIS H 67 HIS H 338 GLN H 372 GLN H 383 ASN ** H 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 467 GLN H 519 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 33757 Z= 0.383 Angle : 0.689 8.110 45697 Z= 0.363 Chirality : 0.047 0.225 5059 Planarity : 0.005 0.109 5909 Dihedral : 4.382 18.858 4491 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.72 % Favored : 94.11 % Rotamer: Outliers : 3.02 % Allowed : 18.33 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.13), residues: 4004 helix: 0.43 (0.13), residues: 1474 sheet: -0.37 (0.18), residues: 912 loop : -1.03 (0.16), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F 474 HIS 0.010 0.002 HIS E 67 PHE 0.031 0.002 PHE D 301 TYR 0.022 0.002 TYR B 484 ARG 0.010 0.001 ARG G 240 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1289 residues out of total 3610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1181 time to evaluate : 3.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 108 outliers final: 58 residues processed: 1223 average time/residue: 0.5406 time to fit residues: 1004.6148 Evaluate side-chains 1203 residues out of total 3610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 1145 time to evaluate : 3.612 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 0 residues processed: 58 average time/residue: 0.3488 time to fit residues: 42.2491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 3.9990 chunk 279 optimal weight: 0.7980 chunk 192 optimal weight: 0.0070 chunk 41 optimal weight: 0.9990 chunk 177 optimal weight: 0.7980 chunk 249 optimal weight: 1.9990 chunk 372 optimal weight: 0.8980 chunk 394 optimal weight: 1.9990 chunk 194 optimal weight: 0.5980 chunk 353 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN A 519 GLN ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN A 624 ASN ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 ASN C 386 GLN ** C 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 GLN ** C 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 386 GLN ** E 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 549 ASN ** E 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 HIS F 273 ASN F 458 GLN ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 HIS ** G 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 519 GLN G 549 ASN H 67 HIS H 338 GLN H 624 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 33757 Z= 0.223 Angle : 0.635 9.345 45697 Z= 0.327 Chirality : 0.044 0.225 5059 Planarity : 0.005 0.058 5909 Dihedral : 4.230 23.442 4491 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.00 % Favored : 94.81 % Rotamer: Outliers : 2.32 % Allowed : 20.32 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 4004 helix: 0.59 (0.13), residues: 1481 sheet: -0.34 (0.18), residues: 912 loop : -0.89 (0.16), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP E 474 HIS 0.007 0.001 HIS G 67 PHE 0.029 0.002 PHE D 301 TYR 0.026 0.002 TYR H 602 ARG 0.019 0.001 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1258 residues out of total 3610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1175 time to evaluate : 3.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 48 residues processed: 1206 average time/residue: 0.5280 time to fit residues: 961.6019 Evaluate side-chains 1166 residues out of total 3610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1118 time to evaluate : 3.444 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.3355 time to fit residues: 33.1540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 1.9990 chunk 223 optimal weight: 0.2980 chunk 5 optimal weight: 5.9990 chunk 293 optimal weight: 0.4980 chunk 162 optimal weight: 0.9990 chunk 336 optimal weight: 0.9980 chunk 272 optimal weight: 0.0870 chunk 0 optimal weight: 8.9990 chunk 201 optimal weight: 8.9990 chunk 353 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 GLN ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 GLN ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 GLN ** C 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN D 347 ASN D 386 GLN ** D 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 492 GLN D 549 ASN ** D 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 535 GLN ** G 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33757 Z= 0.215 Angle : 0.637 8.610 45697 Z= 0.327 Chirality : 0.044 0.231 5059 Planarity : 0.004 0.053 5909 Dihedral : 4.214 20.373 4491 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.29 % Favored : 94.56 % Rotamer: Outliers : 1.70 % Allowed : 22.00 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.14), residues: 4004 helix: 0.63 (0.13), residues: 1481 sheet: -0.34 (0.18), residues: 912 loop : -0.84 (0.16), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP C 474 HIS 0.011 0.001 HIS G 110 PHE 0.032 0.001 PHE D 301 TYR 0.018 0.002 TYR B 602 ARG 0.009 0.001 ARG G 255 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1203 residues out of total 3610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 1142 time to evaluate : 3.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 31 residues processed: 1176 average time/residue: 0.5275 time to fit residues: 937.3117 Evaluate side-chains 1143 residues out of total 3610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1112 time to evaluate : 3.708 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.3222 time to fit residues: 24.1408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 1.9990 chunk 355 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 231 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 394 optimal weight: 0.5980 chunk 327 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 207 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 GLN ** C 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 ASN E 399 ASN ** E 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 GLN F 492 GLN ** G 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 372 GLN H 535 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 33757 Z= 0.238 Angle : 0.656 8.440 45697 Z= 0.337 Chirality : 0.045 0.236 5059 Planarity : 0.005 0.086 5909 Dihedral : 4.315 21.575 4491 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.47 % Favored : 94.43 % Rotamer: Outliers : 1.76 % Allowed : 23.31 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.14), residues: 4004 helix: 0.65 (0.13), residues: 1475 sheet: -0.34 (0.18), residues: 912 loop : -0.82 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP F 474 HIS 0.006 0.001 HIS A 75 PHE 0.018 0.002 PHE D 301 TYR 0.024 0.002 TYR H 602 ARG 0.010 0.001 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1198 residues out of total 3610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 1135 time to evaluate : 4.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 40 residues processed: 1165 average time/residue: 0.5390 time to fit residues: 951.0120 Evaluate side-chains 1129 residues out of total 3610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1089 time to evaluate : 4.001 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.3677 time to fit residues: 31.3668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 224 optimal weight: 0.7980 chunk 288 optimal weight: 0.9990 chunk 223 optimal weight: 0.9990 chunk 332 optimal weight: 2.9990 chunk 220 optimal weight: 0.7980 chunk 393 optimal weight: 0.6980 chunk 246 optimal weight: 0.5980 chunk 239 optimal weight: 0.6980 chunk 181 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 GLN C 67 HIS ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 GLN E 174 GLN E 399 ASN ** E 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 492 GLN ** G 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 372 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 33757 Z= 0.232 Angle : 0.675 8.501 45697 Z= 0.344 Chirality : 0.045 0.205 5059 Planarity : 0.005 0.086 5909 Dihedral : 4.293 24.434 4491 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.57 % Favored : 94.33 % Rotamer: Outliers : 1.51 % Allowed : 24.26 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.14), residues: 4004 helix: 0.64 (0.13), residues: 1475 sheet: -0.33 (0.18), residues: 912 loop : -0.80 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP E 474 HIS 0.004 0.001 HIS A 75 PHE 0.031 0.001 PHE D 444 TYR 0.024 0.002 TYR A 484 ARG 0.015 0.001 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1154 residues out of total 3610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 1100 time to evaluate : 3.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 29 residues processed: 1123 average time/residue: 0.5525 time to fit residues: 938.4721 Evaluate side-chains 1114 residues out of total 3610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 1085 time to evaluate : 3.865 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.3174 time to fit residues: 22.7100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 0.4980 chunk 157 optimal weight: 1.9990 chunk 234 optimal weight: 0.4980 chunk 118 optimal weight: 0.9990 chunk 77 optimal weight: 0.0980 chunk 76 optimal weight: 0.8980 chunk 250 optimal weight: 2.9990 chunk 267 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 309 optimal weight: 5.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 GLN ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN ** C 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 GLN ** E 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33757 Z= 0.218 Angle : 0.687 10.114 45697 Z= 0.349 Chirality : 0.044 0.258 5059 Planarity : 0.004 0.061 5909 Dihedral : 4.287 23.814 4491 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.27 % Favored : 94.68 % Rotamer: Outliers : 0.84 % Allowed : 25.24 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.14), residues: 4004 helix: 0.71 (0.14), residues: 1469 sheet: -0.30 (0.18), residues: 912 loop : -0.77 (0.16), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP E 474 HIS 0.005 0.001 HIS H 405 PHE 0.021 0.001 PHE D 206 TYR 0.030 0.002 TYR G 484 ARG 0.013 0.001 ARG F 453 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1132 residues out of total 3610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1102 time to evaluate : 4.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 18 residues processed: 1109 average time/residue: 0.5521 time to fit residues: 926.6899 Evaluate side-chains 1091 residues out of total 3610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1073 time to evaluate : 3.368 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3936 time to fit residues: 17.2443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 0.0670 chunk 376 optimal weight: 0.6980 chunk 343 optimal weight: 1.9990 chunk 366 optimal weight: 3.9990 chunk 220 optimal weight: 0.0370 chunk 159 optimal weight: 0.9990 chunk 287 optimal weight: 3.9990 chunk 112 optimal weight: 0.5980 chunk 331 optimal weight: 2.9990 chunk 346 optimal weight: 0.0370 chunk 365 optimal weight: 2.9990 overall best weight: 0.2874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN ** C 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 492 GLN ** G 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 467 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33757 Z= 0.200 Angle : 0.701 10.317 45697 Z= 0.355 Chirality : 0.044 0.204 5059 Planarity : 0.004 0.048 5909 Dihedral : 4.222 19.983 4491 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.29 % Favored : 94.63 % Rotamer: Outliers : 0.56 % Allowed : 25.63 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.14), residues: 4004 helix: 0.84 (0.14), residues: 1462 sheet: -0.20 (0.18), residues: 947 loop : -0.84 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP C 474 HIS 0.008 0.001 HIS H 405 PHE 0.030 0.001 PHE D 444 TYR 0.027 0.002 TYR G 508 ARG 0.012 0.001 ARG G 240 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1112 residues out of total 3610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1092 time to evaluate : 3.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 1100 average time/residue: 0.5413 time to fit residues: 900.6372 Evaluate side-chains 1073 residues out of total 3610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1062 time to evaluate : 3.629 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3818 time to fit residues: 12.5527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 2.9990 chunk 387 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 chunk 183 optimal weight: 0.0060 chunk 269 optimal weight: 9.9990 chunk 406 optimal weight: 3.9990 chunk 374 optimal weight: 0.8980 chunk 323 optimal weight: 0.0020 chunk 33 optimal weight: 0.0970 chunk 250 optimal weight: 0.3980 chunk 198 optimal weight: 0.6980 overall best weight: 0.2402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 GLN A 549 ASN ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 338 GLN ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN ** C 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 273 ASN ** G 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33757 Z= 0.205 Angle : 0.728 10.873 45697 Z= 0.368 Chirality : 0.044 0.211 5059 Planarity : 0.005 0.066 5909 Dihedral : 4.237 19.455 4491 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.36 % Allowed : 26.38 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.14), residues: 4004 helix: 0.90 (0.14), residues: 1447 sheet: -0.14 (0.18), residues: 947 loop : -0.81 (0.16), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.003 TRP F 474 HIS 0.007 0.001 HIS H 405 PHE 0.018 0.001 PHE E 248 TYR 0.032 0.002 TYR G 508 ARG 0.015 0.001 ARG G 240 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1110 residues out of total 3610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1097 time to evaluate : 3.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 1103 average time/residue: 0.5718 time to fit residues: 954.2036 Evaluate side-chains 1074 residues out of total 3610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1066 time to evaluate : 3.943 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3663 time to fit residues: 10.6045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 8.9990 chunk 344 optimal weight: 0.6980 chunk 99 optimal weight: 8.9990 chunk 298 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 89 optimal weight: 0.0060 chunk 324 optimal weight: 0.3980 chunk 135 optimal weight: 0.6980 chunk 332 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 GLN ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN ** C 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 458 GLN ** G 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.142640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.117535 restraints weight = 59693.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.121602 restraints weight = 30590.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.124425 restraints weight = 19665.177| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33757 Z= 0.222 Angle : 0.743 15.178 45697 Z= 0.376 Chirality : 0.045 0.206 5059 Planarity : 0.005 0.075 5909 Dihedral : 4.262 20.667 4491 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.31 % Allowed : 27.08 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.14), residues: 4004 helix: 0.85 (0.14), residues: 1448 sheet: -0.09 (0.18), residues: 947 loop : -0.86 (0.16), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.003 TRP B 474 HIS 0.007 0.001 HIS A 405 PHE 0.024 0.001 PHE D 444 TYR 0.030 0.002 TYR G 508 ARG 0.015 0.001 ARG G 240 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13257.78 seconds wall clock time: 235 minutes 58.68 seconds (14158.68 seconds total)