Starting phenix.real_space_refine on Sat Jul 27 03:42:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5b_33615/07_2024/7y5b_33615_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5b_33615/07_2024/7y5b_33615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5b_33615/07_2024/7y5b_33615.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5b_33615/07_2024/7y5b_33615.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5b_33615/07_2024/7y5b_33615_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5b_33615/07_2024/7y5b_33615_neut.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 17 5.49 5 Mg 5 5.21 5 S 106 5.16 5 C 22813 2.51 5 N 6242 2.21 5 O 6776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 45": "OE1" <-> "OE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "A GLU 443": "OE1" <-> "OE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B ASP 300": "OD1" <-> "OD2" Residue "B TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 45": "OE1" <-> "OE2" Residue "D PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 108": "OD1" <-> "OD2" Residue "E ASP 285": "OD1" <-> "OD2" Residue "E ASP 317": "OD1" <-> "OD2" Residue "F PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 313": "OD1" <-> "OD2" Residue "F PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 104": "OE1" <-> "OE2" Residue "a TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 61": "OE1" <-> "OE2" Residue "b GLU 86": "OE1" <-> "OE2" Residue "5 PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 35959 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 3843 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 20, 'TRANS': 495} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3790 Classifications: {'peptide': 505} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 20, 'TRANS': 484} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 3822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3822 Classifications: {'peptide': 514} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 22, 'TRANS': 491} Chain breaks: 2 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 7, 'UNK:plan-1': 11, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "D" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3503 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 23, 'TRANS': 440} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 43 Chain: "E" Number of atoms: 3508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3508 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 23, 'TRANS': 440} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 42 Chain: "F" Number of atoms: 3528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3528 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 440} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "G" Number of atoms: 2220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2220 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 282} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "H" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 862 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 3, 'TRANS': 113} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 32 Chain: "a" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1604 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 196} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "b" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1055 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 141} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 16 Chain: "d" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3010 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 11, 'TRANS': 419} Chain breaks: 3 Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 292 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 17, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 144 Chain: "1" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 560 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "2" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 552 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "3" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 548 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 76} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "4" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 564 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "5" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 554 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "6" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "7" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 556 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "8" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 573 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 78} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "9" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 564 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.95, per 1000 atoms: 0.50 Number of scatterers: 35959 At special positions: 0 Unit cell: (180.4, 123.2, 233.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 106 16.00 P 17 15.00 Mg 5 11.99 O 6776 8.00 N 6242 7.00 C 22813 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: 14.37 Conformation dependent library (CDL) restraints added in 6.2 seconds 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8730 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 29 sheets defined 58.9% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.74 Creating SS restraints... Processing helix chain 'A' and resid 5 through 21 Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 177 through 188 Processing helix chain 'A' and resid 189 through 195 removed outlier: 3.543A pdb=" N THR A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 227 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 263 removed outlier: 3.746A pdb=" N LYS A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Proline residue: A 250 - end of helix removed outlier: 3.592A pdb=" N TRP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN A 263 " --> pdb=" O HIS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 288 Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 298 through 299 No H-bonds generated for 'chain 'A' and resid 298 through 299' Processing helix chain 'A' and resid 300 through 310 removed outlier: 3.924A pdb=" N GLU A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 356 through 362 removed outlier: 3.915A pdb=" N PHE A 360 " --> pdb=" O GLU A 356 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.540A pdb=" N ALA A 380 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 391 removed outlier: 4.205A pdb=" N GLY A 391 " --> pdb=" O LYS A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 407 removed outlier: 4.124A pdb=" N ASP A 396 " --> pdb=" O SER A 392 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 431 Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'A' and resid 454 through 459 removed outlier: 4.400A pdb=" N SER A 458 " --> pdb=" O HIS A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 479 removed outlier: 3.661A pdb=" N PHE A 467 " --> pdb=" O ASP A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 490 Processing helix chain 'A' and resid 493 through 510 removed outlier: 3.942A pdb=" N GLY A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 22 removed outlier: 4.368A pdb=" N PHE B 22 " --> pdb=" O TYR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 160 removed outlier: 3.616A pdb=" N ASP B 157 " --> pdb=" O ILE B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 195 removed outlier: 4.090A pdb=" N ARG B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLU B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 227 Processing helix chain 'B' and resid 242 through 262 removed outlier: 3.844A pdb=" N LYS B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) Proline residue: B 250 - end of helix removed outlier: 3.613A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 287 Processing helix chain 'B' and resid 293 through 297 removed outlier: 3.531A pdb=" N ALA B 296 " --> pdb=" O GLY B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 311 removed outlier: 4.128A pdb=" N ARG B 311 " --> pdb=" O ARG B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'B' and resid 356 through 363 removed outlier: 3.944A pdb=" N PHE B 360 " --> pdb=" O GLU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 382 removed outlier: 3.636A pdb=" N ALA B 381 " --> pdb=" O GLY B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 392 through 404 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 417 through 431 Processing helix chain 'B' and resid 440 through 454 removed outlier: 3.527A pdb=" N GLY B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 458 removed outlier: 4.244A pdb=" N SER B 458 " --> pdb=" O HIS B 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 455 through 458' Processing helix chain 'B' and resid 463 through 478 Processing helix chain 'B' and resid 480 through 489 Processing helix chain 'B' and resid 493 through 510 removed outlier: 3.628A pdb=" N GLY B 510 " --> pdb=" O GLU B 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 22 removed outlier: 3.858A pdb=" N UNK C 22 " --> pdb=" O UNK C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.870A pdb=" N PHE C 106 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU C 107 " --> pdb=" O ASP C 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 107' Processing helix chain 'C' and resid 153 through 160 removed outlier: 3.667A pdb=" N ASP C 157 " --> pdb=" O ILE C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 195 removed outlier: 4.219A pdb=" N VAL C 181 " --> pdb=" O GLY C 177 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N CYS C 182 " --> pdb=" O LYS C 178 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ARG C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLU C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ALA C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N THR C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 200 Processing helix chain 'C' and resid 212 through 227 Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 242 through 264 removed outlier: 3.839A pdb=" N LYS C 246 " --> pdb=" O ALA C 242 " (cutoff:3.500A) Proline residue: C 250 - end of helix removed outlier: 3.743A pdb=" N TRP C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN C 263 " --> pdb=" O HIS C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 Processing helix chain 'C' and resid 293 through 297 Processing helix chain 'C' and resid 300 through 310 Processing helix chain 'C' and resid 316 through 320 Processing helix chain 'C' and resid 339 through 347 removed outlier: 3.646A pdb=" N THR C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER C 347 " --> pdb=" O THR C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 363 Processing helix chain 'C' and resid 383 through 390 Processing helix chain 'C' and resid 392 through 407 removed outlier: 3.638A pdb=" N ASP C 396 " --> pdb=" O SER C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 431 removed outlier: 3.549A pdb=" N LEU C 431 " --> pdb=" O LEU C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 453 Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 463 through 476 removed outlier: 3.972A pdb=" N GLU C 473 " --> pdb=" O SER C 469 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS C 476 " --> pdb=" O LEU C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 490 removed outlier: 3.686A pdb=" N ASP C 484 " --> pdb=" O SER C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 511 Processing helix chain 'D' and resid 141 through 148 Processing helix chain 'D' and resid 165 through 181 removed outlier: 3.660A pdb=" N LEU D 169 " --> pdb=" O GLY D 165 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE D 181 " --> pdb=" O ILE D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 207 Processing helix chain 'D' and resid 223 through 246 removed outlier: 3.935A pdb=" N ARG D 227 " --> pdb=" O PRO D 223 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ALA D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 270 removed outlier: 3.512A pdb=" N LEU D 270 " --> pdb=" O VAL D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 292 removed outlier: 3.529A pdb=" N GLU D 286 " --> pdb=" O THR D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 314 removed outlier: 4.255A pdb=" N ASP D 313 " --> pdb=" O VAL D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 324 Processing helix chain 'D' and resid 325 through 327 No H-bonds generated for 'chain 'D' and resid 325 through 327' Processing helix chain 'D' and resid 335 through 341 Processing helix chain 'D' and resid 357 through 362 Processing helix chain 'D' and resid 362 through 389 removed outlier: 4.541A pdb=" N ASP D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ILE D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 413 removed outlier: 4.089A pdb=" N SER D 413 " --> pdb=" O GLU D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 424 Processing helix chain 'D' and resid 431 through 443 Processing helix chain 'D' and resid 444 through 450 removed outlier: 6.317A pdb=" N PHE D 447 " --> pdb=" O LYS D 444 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP D 448 " --> pdb=" O GLY D 445 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N HIS D 449 " --> pdb=" O GLU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 456 removed outlier: 3.741A pdb=" N PHE D 456 " --> pdb=" O GLN D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 470 Processing helix chain 'E' and resid 91 through 95 removed outlier: 3.832A pdb=" N VAL E 94 " --> pdb=" O GLY E 91 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS E 95 " --> pdb=" O ASP E 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 91 through 95' Processing helix chain 'E' and resid 126 through 130 Processing helix chain 'E' and resid 141 through 148 removed outlier: 3.816A pdb=" N ASP E 145 " --> pdb=" O LEU E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 181 removed outlier: 3.741A pdb=" N LEU E 169 " --> pdb=" O GLY E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 207 Processing helix chain 'E' and resid 209 through 211 No H-bonds generated for 'chain 'E' and resid 209 through 211' Processing helix chain 'E' and resid 223 through 244 removed outlier: 3.762A pdb=" N ARG E 227 " --> pdb=" O PRO E 223 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU E 232 " --> pdb=" O MET E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 271 removed outlier: 3.884A pdb=" N THR E 260 " --> pdb=" O ILE E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 292 Processing helix chain 'E' and resid 310 through 314 removed outlier: 3.980A pdb=" N ASP E 313 " --> pdb=" O VAL E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 324 removed outlier: 3.606A pdb=" N ALA E 321 " --> pdb=" O ASP E 317 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 327 No H-bonds generated for 'chain 'E' and resid 325 through 327' Processing helix chain 'E' and resid 334 through 341 removed outlier: 3.615A pdb=" N GLY E 341 " --> pdb=" O VAL E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 387 removed outlier: 3.522A pdb=" N TYR E 366 " --> pdb=" O GLY E 362 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ILE E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 412 removed outlier: 4.381A pdb=" N LEU E 401 " --> pdb=" O GLU E 397 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU E 412 " --> pdb=" O ILE E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 418 No H-bonds generated for 'chain 'E' and resid 416 through 418' Processing helix chain 'E' and resid 419 through 424 Processing helix chain 'E' and resid 431 through 445 removed outlier: 3.554A pdb=" N GLY E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 450 removed outlier: 4.135A pdb=" N HIS E 449 " --> pdb=" O GLU E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 456 removed outlier: 3.512A pdb=" N ALA E 454 " --> pdb=" O PRO E 451 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE E 456 " --> pdb=" O GLN E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 471 Processing helix chain 'F' and resid 91 through 95 Processing helix chain 'F' and resid 126 through 130 removed outlier: 3.553A pdb=" N ASP F 129 " --> pdb=" O ALA F 126 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU F 130 " --> pdb=" O PHE F 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 126 through 130' Processing helix chain 'F' and resid 141 through 147 Processing helix chain 'F' and resid 165 through 179 removed outlier: 4.121A pdb=" N ARG F 179 " --> pdb=" O ASN F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 206 removed outlier: 3.524A pdb=" N GLY F 197 " --> pdb=" O ARG F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 211 removed outlier: 3.757A pdb=" N LYS F 211 " --> pdb=" O ASN F 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 208 through 211' Processing helix chain 'F' and resid 223 through 228 removed outlier: 3.868A pdb=" N ARG F 227 " --> pdb=" O PRO F 223 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET F 228 " --> pdb=" O PRO F 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 223 through 228' Processing helix chain 'F' and resid 229 through 246 removed outlier: 3.653A pdb=" N GLU F 244 " --> pdb=" O PHE F 240 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN F 245 " --> pdb=" O PHE F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 271 removed outlier: 3.827A pdb=" N THR F 260 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU F 269 " --> pdb=" O GLU F 265 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY F 271 " --> pdb=" O SER F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 282 through 292 removed outlier: 3.556A pdb=" N GLU F 286 " --> pdb=" O THR F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 314 removed outlier: 4.297A pdb=" N ASP F 313 " --> pdb=" O VAL F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 325 removed outlier: 4.087A pdb=" N ALA F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 341 removed outlier: 3.766A pdb=" N PHE F 338 " --> pdb=" O SER F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 390 removed outlier: 3.699A pdb=" N TYR F 366 " --> pdb=" O GLY F 362 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ASP F 384 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ILE F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 394 Processing helix chain 'F' and resid 395 through 412 Processing helix chain 'F' and resid 416 through 421 removed outlier: 4.068A pdb=" N GLN F 421 " --> pdb=" O ALA F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 445 removed outlier: 3.738A pdb=" N THR F 435 " --> pdb=" O PRO F 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 456 removed outlier: 3.547A pdb=" N PHE F 456 " --> pdb=" O GLN F 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 470 Processing helix chain 'G' and resid 5 through 41 removed outlier: 3.998A pdb=" N ALA G 34 " --> pdb=" O THR G 30 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU G 41 " --> pdb=" O GLN G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 60 removed outlier: 4.235A pdb=" N ALA G 60 " --> pdb=" O GLU G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 109 removed outlier: 3.757A pdb=" N ASP G 109 " --> pdb=" O SER G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 130 Processing helix chain 'G' and resid 146 through 163 removed outlier: 3.749A pdb=" N ALA G 150 " --> pdb=" O THR G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 176 Processing helix chain 'G' and resid 227 through 302 Proline residue: G 237 - end of helix removed outlier: 3.809A pdb=" N LEU G 248 " --> pdb=" O VAL G 244 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU G 249 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU G 250 " --> pdb=" O ALA G 246 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ARG G 261 " --> pdb=" O ALA G 257 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA G 262 " --> pdb=" O SER G 258 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET G 263 " --> pdb=" O ARG G 259 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASP G 272 " --> pdb=" O ASP G 268 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU G 273 " --> pdb=" O ASN G 269 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE G 274 " --> pdb=" O ALA G 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 101 removed outlier: 3.851A pdb=" N SER H 101 " --> pdb=" O GLU H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 116 Processing helix chain 'a' and resid 33 through 53 removed outlier: 3.812A pdb=" N ALA a 51 " --> pdb=" O PHE a 47 " (cutoff:3.500A) Processing helix chain 'a' and resid 62 through 81 Processing helix chain 'a' and resid 88 through 106 removed outlier: 3.593A pdb=" N LEU a 92 " --> pdb=" O PHE a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 107 through 109 No H-bonds generated for 'chain 'a' and resid 107 through 109' Processing helix chain 'a' and resid 130 through 154 removed outlier: 3.973A pdb=" N VAL a 134 " --> pdb=" O ASP a 130 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA a 148 " --> pdb=" O CYS a 144 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG a 153 " --> pdb=" O GLY a 149 " (cutoff:3.500A) Processing helix chain 'a' and resid 156 through 164 Processing helix chain 'a' and resid 170 through 206 Proline residue: a 182 - end of helix removed outlier: 4.438A pdb=" N PHE a 206 " --> pdb=" O LEU a 202 " (cutoff:3.500A) Processing helix chain 'a' and resid 212 through 246 removed outlier: 3.622A pdb=" N THR a 220 " --> pdb=" O ALA a 216 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU a 246 " --> pdb=" O SER a 242 " (cutoff:3.500A) Processing helix chain 'b' and resid 31 through 48 removed outlier: 3.970A pdb=" N LEU b 35 " --> pdb=" O PHE b 31 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 59 removed outlier: 4.086A pdb=" N ILE b 53 " --> pdb=" O VAL b 49 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS b 55 " --> pdb=" O PRO b 51 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL b 56 " --> pdb=" O PRO b 52 " (cutoff:3.500A) Processing helix chain 'b' and resid 59 through 145 removed outlier: 3.834A pdb=" N MET b 63 " --> pdb=" O GLU b 59 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU b 64 " --> pdb=" O ARG b 60 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG b 72 " --> pdb=" O ALA b 68 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER b 74 " --> pdb=" O ASP b 70 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ALA b 75 " --> pdb=" O ASN b 71 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN b 131 " --> pdb=" O THR b 127 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER b 134 " --> pdb=" O ASP b 130 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN b 139 " --> pdb=" O ALA b 135 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU b 145 " --> pdb=" O ARG b 141 " (cutoff:3.500A) Processing helix chain 'b' and resid 147 through 161 Processing helix chain 'd' and resid 3 through 18 removed outlier: 4.131A pdb=" N ILE d 9 " --> pdb=" O ILE d 5 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLY d 10 " --> pdb=" O GLY d 6 " (cutoff:3.500A) Processing helix chain 'd' and resid 22 through 54 removed outlier: 3.689A pdb=" N VAL d 26 " --> pdb=" O VAL d 22 " (cutoff:3.500A) Processing helix chain 'd' and resid 56 through 136 removed outlier: 4.431A pdb=" N LYS d 60 " --> pdb=" O ALA d 56 " (cutoff:3.500A) Processing helix chain 'd' and resid 139 through 157 removed outlier: 3.868A pdb=" N GLN d 143 " --> pdb=" O ASP d 139 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER d 144 " --> pdb=" O PRO d 140 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ALA d 145 " --> pdb=" O GLN d 141 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 191 Processing helix chain 'd' and resid 197 through 216 removed outlier: 3.546A pdb=" N GLU d 216 " --> pdb=" O LEU d 212 " (cutoff:3.500A) Processing helix chain 'd' and resid 217 through 224 Processing helix chain 'd' and resid 230 through 240 Processing helix chain 'd' and resid 246 through 259 Processing helix chain 'd' and resid 263 through 285 removed outlier: 4.136A pdb=" N VAL d 271 " --> pdb=" O LEU d 267 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU d 272 " --> pdb=" O ILE d 268 " (cutoff:3.500A) Processing helix chain 'd' and resid 289 through 306 removed outlier: 3.615A pdb=" N GLU d 306 " --> pdb=" O VAL d 302 " (cutoff:3.500A) Processing helix chain 'd' and resid 306 through 313 removed outlier: 3.656A pdb=" N SER d 310 " --> pdb=" O GLU d 306 " (cutoff:3.500A) Processing helix chain 'd' and resid 321 through 331 Processing helix chain 'd' and resid 338 through 351 Processing helix chain 'd' and resid 356 through 372 removed outlier: 4.019A pdb=" N ARG d 372 " --> pdb=" O ALA d 368 " (cutoff:3.500A) Processing helix chain 'd' and resid 386 through 401 Processing helix chain 'd' and resid 431 through 442 Processing helix chain '1' and resid 6 through 46 removed outlier: 4.014A pdb=" N ALA 1 44 " --> pdb=" O ILE 1 40 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG 1 45 " --> pdb=" O SER 1 41 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN 1 46 " --> pdb=" O GLY 1 42 " (cutoff:3.500A) Processing helix chain '1' and resid 49 through 52 Processing helix chain '1' and resid 53 through 81 removed outlier: 3.574A pdb=" N PHE 1 57 " --> pdb=" O LEU 1 53 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL 1 64 " --> pdb=" O THR 1 60 " (cutoff:3.500A) Processing helix chain '2' and resid 6 through 46 Processing helix chain '2' and resid 50 through 79 removed outlier: 4.249A pdb=" N THR 2 55 " --> pdb=" O GLY 2 51 " (cutoff:3.500A) Proline residue: 2 56 - end of helix Processing helix chain '3' and resid 6 through 46 Processing helix chain '3' and resid 48 through 52 removed outlier: 4.064A pdb=" N GLY 3 51 " --> pdb=" O GLU 3 48 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG 3 52 " --> pdb=" O ALA 3 49 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 48 through 52' Processing helix chain '3' and resid 53 through 81 removed outlier: 3.906A pdb=" N PHE 3 57 " --> pdb=" O LEU 3 53 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE 3 80 " --> pdb=" O ALA 3 76 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA 3 81 " --> pdb=" O LEU 3 77 " (cutoff:3.500A) Processing helix chain '4' and resid 6 through 46 Processing helix chain '4' and resid 54 through 79 removed outlier: 3.925A pdb=" N PHE 4 58 " --> pdb=" O PHE 4 54 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA 4 67 " --> pdb=" O LEU 4 63 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR 4 68 " --> pdb=" O VAL 4 64 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU 4 77 " --> pdb=" O ALA 4 73 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE 4 78 " --> pdb=" O PHE 4 74 " (cutoff:3.500A) Processing helix chain '5' and resid 6 through 43 removed outlier: 3.830A pdb=" N ILE 5 43 " --> pdb=" O LEU 5 39 " (cutoff:3.500A) Processing helix chain '5' and resid 54 through 81 removed outlier: 3.648A pdb=" N ALA 5 81 " --> pdb=" O LEU 5 77 " (cutoff:3.500A) Processing helix chain '6' and resid 6 through 44 Processing helix chain '6' and resid 53 through 81 removed outlier: 3.634A pdb=" N LEU 6 63 " --> pdb=" O ILE 6 59 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL 6 64 " --> pdb=" O THR 6 60 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA 6 81 " --> pdb=" O LEU 6 77 " (cutoff:3.500A) Processing helix chain '7' and resid 6 through 46 removed outlier: 4.124A pdb=" N THR 7 10 " --> pdb=" O ASN 7 6 " (cutoff:3.500A) Processing helix chain '7' and resid 53 through 81 removed outlier: 3.569A pdb=" N PHE 7 57 " --> pdb=" O LEU 7 53 " (cutoff:3.500A) Processing helix chain '8' and resid 4 through 44 removed outlier: 4.098A pdb=" N ILE 8 8 " --> pdb=" O ASP 8 4 " (cutoff:3.500A) Processing helix chain '8' and resid 49 through 52 Processing helix chain '8' and resid 53 through 82 removed outlier: 3.864A pdb=" N PHE 8 57 " --> pdb=" O LEU 8 53 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU 8 63 " --> pdb=" O ILE 8 59 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL 8 64 " --> pdb=" O THR 8 60 " (cutoff:3.500A) Processing helix chain '9' and resid 8 through 46 removed outlier: 4.354A pdb=" N GLY 9 12 " --> pdb=" O ILE 9 8 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN 9 46 " --> pdb=" O GLY 9 42 " (cutoff:3.500A) Processing helix chain '9' and resid 53 through 81 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 4.049A pdb=" N GLU A 29 " --> pdb=" O VAL d 427 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL d 379 " --> pdb=" O HIS d 410 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 36 removed outlier: 6.782A pdb=" N HIS A 43 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 42 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY A 64 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 102 Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.861A pdb=" N ALA A 236 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 233 " --> pdb=" O CYS A 204 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 268 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 270 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR A 325 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE A 271 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU A 169 " --> pdb=" O CYS A 353 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LEU A 355 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE A 171 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 31 through 36 removed outlier: 3.665A pdb=" N GLU B 45 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N HIS B 43 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU B 63 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU B 57 " --> pdb=" O LYS B 92 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS B 92 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 99 through 102 removed outlier: 3.646A pdb=" N ARG B 130 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B 128 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.414A pdb=" N VAL B 111 " --> pdb=" O ALA B 236 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 329 through 330 removed outlier: 6.440A pdb=" N ILE B 170 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 33 through 38 removed outlier: 6.432A pdb=" N VAL C 34 " --> pdb=" O GLU C 45 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N GLU C 45 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP C 36 " --> pdb=" O HIS C 43 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N SER C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LEU C 69 " --> pdb=" O SER C 73 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N GLY C 75 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA C 66 " --> pdb=" O GLU C 54 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU C 54 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU C 55 " --> pdb=" O THR C 94 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR C 94 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS C 92 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 99 through 102 removed outlier: 3.691A pdb=" N THR C 128 " --> pdb=" O VAL C 102 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 110 through 111 removed outlier: 6.364A pdb=" N VAL C 111 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 9.268A pdb=" N THR C 233 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N CYS C 204 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N VAL C 235 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TYR C 206 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ALA C 237 " --> pdb=" O TYR C 206 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA C 208 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ARG C 203 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N VAL C 270 " --> pdb=" O ARG C 203 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL C 205 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE C 271 " --> pdb=" O LEU C 327 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 329 through 331 removed outlier: 6.302A pdb=" N ILE C 170 " --> pdb=" O ILE C 330 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 171 " --> pdb=" O CYS C 353 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 534 through 535 removed outlier: 6.165A pdb=" N GLU C 534 " --> pdb=" O ARG G 202 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N VAL G 186 " --> pdb=" O GLY G 78 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU G 80 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 9.259A pdb=" N THR G 188 " --> pdb=" O LEU G 80 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA G 77 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 9.575A pdb=" N TRP G 138 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL G 118 " --> pdb=" O TRP G 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 538 through 540 removed outlier: 6.501A pdb=" N VAL C 538 " --> pdb=" O GLU G 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 16 removed outlier: 5.684A pdb=" N VAL D 12 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLU D 23 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG D 14 " --> pdb=" O ASP D 21 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL D 20 " --> pdb=" O CYS D 64 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU D 61 " --> pdb=" O HIS D 56 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N HIS D 56 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ARG D 63 " --> pdb=" O ALA D 54 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA D 54 " --> pdb=" O ARG D 63 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS D 47 " --> pdb=" O ILE D 40 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS D 37 " --> pdb=" O THR D 80 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N GLU D 39 " --> pdb=" O GLU D 78 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N GLU D 78 " --> pdb=" O GLU D 39 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 87 through 90 Processing sheet with id=AB8, first strand: chain 'D' and resid 98 through 99 removed outlier: 3.749A pdb=" N PHE D 217 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA D 214 " --> pdb=" O SER D 185 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU D 250 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE D 156 " --> pdb=" O GLN D 306 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA D 329 " --> pdb=" O LYS D 155 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER D 352 " --> pdb=" O THR D 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 136 through 137 removed outlier: 4.530A pdb=" N TYR D 150 " --> pdb=" O LEU D 137 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 10 through 16 removed outlier: 5.566A pdb=" N VAL E 12 " --> pdb=" O GLU E 23 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLU E 23 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARG E 14 " --> pdb=" O ASP E 21 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU E 61 " --> pdb=" O HIS E 56 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N HIS E 56 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG E 63 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS E 47 " --> pdb=" O ILE E 40 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLU E 39 " --> pdb=" O GLU E 78 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLU E 78 " --> pdb=" O GLU E 39 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 87 through 90 Processing sheet with id=AC3, first strand: chain 'E' and resid 98 through 99 removed outlier: 3.575A pdb=" N THR E 303 " --> pdb=" O VAL E 249 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 136 through 137 removed outlier: 3.792A pdb=" N TYR E 150 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 306 through 308 removed outlier: 6.293A pdb=" N ILE E 156 " --> pdb=" O GLN E 306 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL E 308 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU E 158 " --> pdb=" O VAL E 308 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 11 through 16 removed outlier: 3.864A pdb=" N VAL F 13 " --> pdb=" O ASP F 21 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ASP F 21 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ILE F 15 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N VAL F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU F 61 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE F 65 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N VAL F 53 " --> pdb=" O ILE F 65 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS F 47 " --> pdb=" O ILE F 40 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE F 40 " --> pdb=" O LYS F 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 87 through 89 removed outlier: 3.610A pdb=" N VAL F 88 " --> pdb=" O TRP F 118 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TRP F 118 " --> pdb=" O VAL F 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'F' and resid 98 through 99 removed outlier: 6.418A pdb=" N PHE F 99 " --> pdb=" O PHE F 217 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL F 249 " --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N MET F 305 " --> pdb=" O VAL F 249 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU F 251 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N ALA F 307 " --> pdb=" O LEU F 251 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE F 253 " --> pdb=" O ALA F 307 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE F 156 " --> pdb=" O GLN F 306 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LYS F 155 " --> pdb=" O ALA F 329 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 136 through 137 removed outlier: 3.656A pdb=" N LEU F 137 " --> pdb=" O TYR F 150 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR F 150 " --> pdb=" O LEU F 137 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'H' and resid 14 through 19 removed outlier: 4.507A pdb=" N TRP H 16 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG H 78 " --> pdb=" O SER H 71 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER H 71 " --> pdb=" O ARG H 78 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 31 through 33 removed outlier: 3.613A pdb=" N THR H 25 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE H 22 " --> pdb=" O GLU H 54 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG H 26 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N MET H 50 " --> pdb=" O ARG H 26 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA H 64 " --> pdb=" O GLN H 85 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN H 85 " --> pdb=" O ALA H 64 " (cutoff:3.500A) 2166 hydrogen bonds defined for protein. 6345 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: 12.95 Time building geometry restraints manager: 15.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8329 1.33 - 1.45: 7032 1.45 - 1.57: 20978 1.57 - 1.69: 28 1.69 - 1.82: 192 Bond restraints: 36559 Sorted by residual: bond pdb=" N LYS D 95 " pdb=" CA LYS D 95 " ideal model delta sigma weight residual 1.458 1.476 -0.018 1.35e-02 5.49e+03 1.72e+00 bond pdb=" CD GLN d 86 " pdb=" OE1 GLN d 86 " ideal model delta sigma weight residual 1.231 1.209 0.022 1.90e-02 2.77e+03 1.31e+00 bond pdb=" CD GLU d 96 " pdb=" OE1 GLU d 96 " ideal model delta sigma weight residual 1.249 1.227 0.022 1.90e-02 2.77e+03 1.29e+00 bond pdb=" CA ASP G 271 " pdb=" C ASP G 271 " ideal model delta sigma weight residual 1.523 1.538 -0.015 1.30e-02 5.92e+03 1.27e+00 bond pdb=" C THR G 267 " pdb=" O THR G 267 " ideal model delta sigma weight residual 1.237 1.250 -0.013 1.17e-02 7.31e+03 1.25e+00 ... (remaining 36554 not shown) Histogram of bond angle deviations from ideal: 97.39 - 105.89: 857 105.89 - 114.38: 21745 114.38 - 122.88: 24452 122.88 - 131.38: 2542 131.38 - 139.87: 45 Bond angle restraints: 49641 Sorted by residual: angle pdb=" N GLN d 86 " pdb=" CA GLN d 86 " pdb=" CB GLN d 86 " ideal model delta sigma weight residual 110.28 116.82 -6.54 1.55e+00 4.16e-01 1.78e+01 angle pdb=" C ALA d 95 " pdb=" N GLU d 96 " pdb=" CA GLU d 96 " ideal model delta sigma weight residual 120.72 114.24 6.48 1.67e+00 3.59e-01 1.50e+01 angle pdb=" N GLU d 96 " pdb=" CA GLU d 96 " pdb=" CB GLU d 96 " ideal model delta sigma weight residual 110.39 116.83 -6.44 1.66e+00 3.63e-01 1.50e+01 angle pdb=" C VAL D 94 " pdb=" N LYS D 95 " pdb=" CA LYS D 95 " ideal model delta sigma weight residual 123.47 129.17 -5.70 1.53e+00 4.27e-01 1.39e+01 angle pdb=" C ILE a 71 " pdb=" N GLN a 72 " pdb=" CA GLN a 72 " ideal model delta sigma weight residual 120.31 114.77 5.54 1.52e+00 4.33e-01 1.33e+01 ... (remaining 49636 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.85: 20746 26.85 - 53.69: 1012 53.69 - 80.54: 104 80.54 - 107.38: 20 107.38 - 134.23: 1 Dihedral angle restraints: 21883 sinusoidal: 8258 harmonic: 13625 Sorted by residual: dihedral pdb=" C5' ADP D 601 " pdb=" O5' ADP D 601 " pdb=" PA ADP D 601 " pdb=" O2A ADP D 601 " ideal model delta sinusoidal sigma weight residual 300.00 165.77 134.23 1 2.00e+01 2.50e-03 4.07e+01 dihedral pdb=" O2A ADP D 601 " pdb=" O3A ADP D 601 " pdb=" PA ADP D 601 " pdb=" PB ADP D 601 " ideal model delta sinusoidal sigma weight residual -60.00 -134.32 74.32 1 2.00e+01 2.50e-03 1.75e+01 dihedral pdb=" CA ASP E 114 " pdb=" CB ASP E 114 " pdb=" CG ASP E 114 " pdb=" OD1 ASP E 114 " ideal model delta sinusoidal sigma weight residual -30.00 -87.80 57.80 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 21880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 3899 0.032 - 0.064: 1292 0.064 - 0.097: 430 0.097 - 0.129: 187 0.129 - 0.161: 18 Chirality restraints: 5826 Sorted by residual: chirality pdb=" CA THR 1 55 " pdb=" N THR 1 55 " pdb=" C THR 1 55 " pdb=" CB THR 1 55 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.50e-01 chirality pdb=" CA THR 3 55 " pdb=" N THR 3 55 " pdb=" C THR 3 55 " pdb=" CB THR 3 55 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.15e-01 chirality pdb=" CA THR 2 55 " pdb=" N THR 2 55 " pdb=" C THR 2 55 " pdb=" CB THR 2 55 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.09e-01 ... (remaining 5823 not shown) Planarity restraints: 6454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 112 " -0.038 5.00e-02 4.00e+02 5.83e-02 5.45e+00 pdb=" N PRO A 113 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 113 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 113 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY 9 29 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.20e+00 pdb=" C GLY 9 29 " -0.039 2.00e-02 2.50e+03 pdb=" O GLY 9 29 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE 9 30 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP 9 32 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.90e+00 pdb=" C ASP 9 32 " 0.038 2.00e-02 2.50e+03 pdb=" O ASP 9 32 " -0.014 2.00e-02 2.50e+03 pdb=" N GLY 9 33 " -0.013 2.00e-02 2.50e+03 ... (remaining 6451 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 154 2.49 - 3.09: 26143 3.09 - 3.70: 54112 3.70 - 4.30: 69283 4.30 - 4.90: 115995 Nonbonded interactions: 265687 Sorted by model distance: nonbonded pdb=" O1B ATP F 601 " pdb="MG MG F 602 " model vdw 1.888 2.170 nonbonded pdb=" OG1 THR F 167 " pdb="MG MG F 602 " model vdw 1.963 2.170 nonbonded pdb=" O3G ATP F 601 " pdb="MG MG F 602 " model vdw 1.980 2.170 nonbonded pdb=" O3A ATP B 601 " pdb="MG MG B 602 " model vdw 1.982 2.170 nonbonded pdb=" O1G ATP A 601 " pdb="MG MG A 602 " model vdw 1.984 2.170 ... (remaining 265682 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 '1' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 49 or (resid 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '2' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 84)) selection = (chain '3' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '4' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '5' and (resid 5 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 49 or (resid 50 and (name N or name \ CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '6' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '7' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 49 or (resid 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '8' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 49 or (resid 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) selection = (chain '9' and (resid 5 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (nam \ e N or name CA or name C or name O or name CB )) or resid 51 through 84)) } ncs_group { reference = (chain 'A' and ((resid 29 and (name N or name CA or name C or name O or name CB \ )) or resid 30 through 132 or (resid 133 and (name N or name CA or name C or nam \ e O or name CB )) or resid 134 through 355 or (resid 356 and (name N or name CA \ or name C or name O or name CB )) or resid 357 or (resid 358 and (name N or name \ CA or name C or name O or name CB )) or resid 359 through 400 or (resid 401 thr \ ough 402 and (name N or name CA or name C or name O or name CB )) or resid 403 t \ hrough 411 or (resid 412 and (name N or name CA or name C or name O or name CB ) \ ) or resid 413 through 416 or (resid 417 through 419 and (name N or name CA or n \ ame C or name O or name CB )) or resid 420 through 461 or (resid 462 through 463 \ and (name N or name CA or name C or name O or name CB )) or resid 464 through 4 \ 67 or (resid 468 and (name N or name CA or name C or name O or name CB )) or res \ id 469 or (resid 470 and (name N or name CA or name C or name O or name CB )) or \ resid 471 through 494 or (resid 495 through 499 and (name N or name CA or name \ C or name O or name CB )) or resid 500 through 505 or (resid 506 and (name N or \ name CA or name C or name O or name CB )) or resid 507 through 516 or resid 518 \ through 520 or resid 601 through 602)) selection = (chain 'B' and ((resid 29 and (name N or name CA or name C or name O or name CB \ )) or resid 30 through 132 or (resid 133 and (name N or name CA or name C or nam \ e O or name CB )) or resid 134 through 190 or (resid 191 through 192 and (name N \ or name CA or name C or name O or name CB )) or resid 193 through 316 or (resid \ 317 through 318 and (name N or name CA or name C or name O or name CB )) or res \ id 319 through 355 or (resid 356 and (name N or name CA or name C or name O or n \ ame CB )) or resid 357 or (resid 358 and (name N or name CA or name C or name O \ or name CB )) or resid 359 through 401 or (resid 402 and (name N or name CA or n \ ame C or name O or name CB )) or resid 403 through 411 or (resid 412 and (name N \ or name CA or name C or name O or name CB )) or resid 413 through 416 or (resid \ 417 through 419 and (name N or name CA or name C or name O or name CB )) or res \ id 420 through 456 or (resid 457 and (name N or name CA or name C or name O or n \ ame CB )) or resid 458 through 467 or (resid 468 and (name N or name CA or name \ C or name O or name CB )) or resid 469 through 493 or (resid 494 through 499 and \ (name N or name CA or name C or name O or name CB )) or resid 500 through 505 o \ r (resid 506 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 07 through 516 or resid 518 through 520 or resid 601 through 602)) selection = (chain 'C' and (resid 29 through 190 or (resid 191 through 192 and (name N or na \ me CA or name C or name O or name CB )) or resid 193 through 316 or (resid 317 t \ hrough 318 and (name N or name CA or name C or name O or name CB )) or resid 319 \ through 400 or (resid 401 through 402 and (name N or name CA or name C or name \ O or name CB )) or resid 403 through 456 or (resid 457 and (name N or name CA or \ name C or name O or name CB )) or resid 458 through 469 or (resid 470 and (name \ N or name CA or name C or name O or name CB )) or resid 471 through 493 or (res \ id 494 through 499 and (name N or name CA or name C or name O or name CB )) or r \ esid 500 through 516 or resid 537 through 538 or resid 540 or resid 601 through \ 602)) } ncs_group { reference = (chain 'D' and (resid 8 through 103 or (resid 104 and (name N or name CA or name \ C or name O or name CB )) or resid 105 through 106 or (resid 107 and (name N or \ name CA or name C or name O or name CB )) or resid 108 through 198 or (resid 19 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 200 through \ 202 or (resid 203 and (name N or name CA or name C or name O or name CB )) or re \ sid 204 through 285 or (resid 286 and (name N or name CA or name C or name O or \ name CB )) or resid 287 through 362 or (resid 363 through 364 and (name N or nam \ e CA or name C or name O or name CB )) or resid 365 through 369 or (resid 370 th \ rough 371 and (name N or name CA or name C or name O or name CB )) or resid 372 \ through 380 or (resid 381 and (name N or name CA or name C or name O or name CB \ )) or resid 382 through 402 or (resid 403 and (name N or name CA or name C or na \ me O or name CB )) or resid 404 through 424 or (resid 425 and (name N or name CA \ or name C or name O or name CB )) or resid 426 through 471)) selection = (chain 'E' and (resid 8 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )) or resid 108 through 220 or (resid 221 through 222 an \ d (name N or name CA or name C or name O or name CB )) or resid 223 through 284 \ or (resid 285 through 286 and (name N or name CA or name C or name O or name CB \ )) or resid 287 through 288 or (resid 289 and (name N or name CA or name C or na \ me O or name CB )) or resid 290 through 291 or (resid 292 and (name N or name CA \ or name C or name O or name CB )) or resid 293 through 370 or (resid 371 and (n \ ame N or name CA or name C or name O or name CB )) or resid 372 through 395 or ( \ resid 396 through 398 and (name N or name CA or name C or name O or name CB )) o \ r resid 399 through 461 or (resid 462 and (name N or name CA or name C or name O \ or name CB )) or resid 463 through 465 or (resid 466 and (name N or name CA or \ name C or name O or name CB )) or resid 467 through 471)) selection = (chain 'F' and (resid 8 through 103 or (resid 104 and (name N or name CA or name \ C or name O or name CB )) or resid 105 through 134 or (resid 135 and (name N or \ name CA or name C or name O or name CB )) or resid 136 through 198 or (resid 19 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 200 through \ 202 or (resid 203 and (name N or name CA or name C or name O or name CB )) or re \ sid 204 through 220 or (resid 221 through 222 and (name N or name CA or name C o \ r name O or name CB )) or resid 223 through 291 or (resid 292 and (name N or nam \ e CA or name C or name O or name CB )) or resid 293 through 362 or (resid 363 th \ rough 364 and (name N or name CA or name C or name O or name CB )) or resid 365 \ through 369 or (resid 370 through 371 and (name N or name CA or name C or name O \ or name CB )) or resid 372 through 380 or (resid 381 and (name N or name CA or \ name C or name O or name CB )) or resid 382 through 383 or (resid 384 and (name \ N or name CA or name C or name O or name CB )) or resid 385 through 395 or (resi \ d 396 through 398 and (name N or name CA or name C or name O or name CB )) or re \ sid 399 through 402 or (resid 403 and (name N or name CA or name C or name O or \ name CB )) or resid 404 through 432 or (resid 433 and (name N or name CA or name \ C or name O or name CB )) or resid 434 through 461 or (resid 462 and (name N or \ name CA or name C or name O or name CB )) or resid 463 through 465 or (resid 46 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 467 through \ 471)) } 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: 21.530 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 87.990 Find NCS groups from input model: 3.380 Set up NCS constraints: 0.150 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 0.034 36559 Z= 0.155 Angle : 0.557 9.140 49641 Z= 0.284 Chirality : 0.040 0.161 5826 Planarity : 0.004 0.058 6454 Dihedral : 15.008 134.229 13153 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.12), residues: 4784 helix: 2.12 (0.11), residues: 2490 sheet: 0.90 (0.24), residues: 484 loop : -1.01 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP a 218 HIS 0.005 0.001 HIS a 146 PHE 0.020 0.001 PHE 7 57 TYR 0.022 0.001 TYR a 145 ARG 0.007 0.000 ARG a 188 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 350 time to evaluate : 4.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 15 ILE cc_start: 0.4093 (mt) cc_final: 0.3893 (mt) REVERT: 1 58 PHE cc_start: 0.7221 (m-10) cc_final: 0.7014 (m-10) REVERT: 3 75 MET cc_start: 0.6914 (tmm) cc_final: 0.6283 (tmm) outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.4210 time to fit residues: 261.5020 Evaluate side-chains 260 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 3.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 404 optimal weight: 6.9990 chunk 363 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 244 optimal weight: 0.8980 chunk 193 optimal weight: 4.9990 chunk 375 optimal weight: 0.5980 chunk 145 optimal weight: 0.7980 chunk 228 optimal weight: 3.9990 chunk 279 optimal weight: 2.9990 chunk 434 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 ASN F 55 GLN a 229 GLN ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.0597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36559 Z= 0.181 Angle : 0.519 8.637 49641 Z= 0.265 Chirality : 0.040 0.224 5826 Planarity : 0.004 0.055 6454 Dihedral : 6.755 118.366 5333 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.03 % Allowed : 5.92 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.12), residues: 4784 helix: 2.42 (0.10), residues: 2505 sheet: 0.69 (0.23), residues: 505 loop : -1.01 (0.14), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 118 HIS 0.004 0.001 HIS C 474 PHE 0.015 0.001 PHE H 24 TYR 0.021 0.001 TYR a 145 ARG 0.004 0.000 ARG H 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 352 time to evaluate : 4.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 ASP cc_start: 0.7639 (t0) cc_final: 0.7325 (t0) REVERT: A 229 MET cc_start: 0.8269 (tpp) cc_final: 0.8044 (tpp) REVERT: D 309 TYR cc_start: 0.8326 (t80) cc_final: 0.8096 (t80) REVERT: 1 9 ILE cc_start: 0.2160 (mt) cc_final: 0.1892 (mt) REVERT: 3 75 MET cc_start: 0.6995 (tmm) cc_final: 0.6293 (tmm) REVERT: 5 15 ILE cc_start: 0.5576 (mm) cc_final: 0.5304 (mm) REVERT: 5 75 MET cc_start: 0.6373 (pmm) cc_final: 0.5875 (pmm) outliers start: 1 outliers final: 0 residues processed: 353 average time/residue: 0.4090 time to fit residues: 254.4506 Evaluate side-chains 264 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 3.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 241 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 362 optimal weight: 0.8980 chunk 296 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 435 optimal weight: 9.9990 chunk 470 optimal weight: 1.9990 chunk 388 optimal weight: 0.7980 chunk 432 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 349 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 GLN B 263 ASN D 175 ASN E 68 GLN F 55 GLN a 229 GLN ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 71 ASN ** 9 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 36559 Z= 0.255 Angle : 0.563 11.911 49641 Z= 0.288 Chirality : 0.041 0.251 5826 Planarity : 0.004 0.046 6454 Dihedral : 6.701 109.490 5333 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.08 % Allowed : 5.31 % Favored : 94.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.12), residues: 4784 helix: 2.34 (0.10), residues: 2505 sheet: 0.54 (0.23), residues: 501 loop : -1.10 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 118 HIS 0.006 0.001 HIS A 305 PHE 0.027 0.001 PHE E 324 TYR 0.022 0.001 TYR a 145 ARG 0.004 0.000 ARG C 93 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 351 time to evaluate : 4.509 Fit side-chains revert: symmetry clash REVERT: A 173 ASP cc_start: 0.7633 (t0) cc_final: 0.7349 (t0) REVERT: 1 9 ILE cc_start: 0.2018 (mt) cc_final: 0.1788 (mt) REVERT: 1 21 MET cc_start: 0.6973 (mmm) cc_final: 0.6720 (tpp) REVERT: 3 75 MET cc_start: 0.6929 (tmm) cc_final: 0.6330 (tmm) REVERT: 9 65 GLU cc_start: 0.7359 (mp0) cc_final: 0.7000 (mm-30) outliers start: 3 outliers final: 1 residues processed: 354 average time/residue: 0.3963 time to fit residues: 247.0313 Evaluate side-chains 256 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 255 time to evaluate : 3.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 430 optimal weight: 1.9990 chunk 327 optimal weight: 0.2980 chunk 226 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 292 optimal weight: 0.8980 chunk 437 optimal weight: 1.9990 chunk 463 optimal weight: 0.0370 chunk 228 optimal weight: 1.9990 chunk 414 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 ASN F 55 GLN a 229 GLN 6 71 ASN ** 9 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 36559 Z= 0.146 Angle : 0.523 10.271 49641 Z= 0.262 Chirality : 0.040 0.246 5826 Planarity : 0.003 0.048 6454 Dihedral : 6.397 101.059 5333 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.12), residues: 4784 helix: 2.51 (0.10), residues: 2504 sheet: 0.72 (0.23), residues: 493 loop : -1.04 (0.14), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 118 HIS 0.003 0.001 HIS a 146 PHE 0.017 0.001 PHE E 324 TYR 0.009 0.001 TYR A 18 ARG 0.004 0.000 ARG a 188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 378 time to evaluate : 3.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ASP cc_start: 0.7593 (t0) cc_final: 0.7263 (t0) REVERT: C 472 LEU cc_start: 0.8782 (tp) cc_final: 0.8572 (tp) REVERT: 1 9 ILE cc_start: 0.2314 (mt) cc_final: 0.1993 (mt) REVERT: 1 75 MET cc_start: 0.7827 (ppp) cc_final: 0.7553 (ppp) REVERT: 5 75 MET cc_start: 0.6380 (pmm) cc_final: 0.5980 (pmm) REVERT: 6 39 LEU cc_start: 0.8926 (mt) cc_final: 0.8654 (mt) REVERT: 9 48 GLU cc_start: 0.8273 (tp30) cc_final: 0.7924 (tm-30) REVERT: 9 70 ILE cc_start: 0.8531 (tp) cc_final: 0.8205 (tp) outliers start: 0 outliers final: 0 residues processed: 378 average time/residue: 0.4066 time to fit residues: 265.6238 Evaluate side-chains 268 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 5.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 385 optimal weight: 6.9990 chunk 262 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 344 optimal weight: 8.9990 chunk 191 optimal weight: 0.7980 chunk 395 optimal weight: 6.9990 chunk 320 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 236 optimal weight: 0.0670 chunk 415 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.3120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN D 175 ASN F 55 GLN G 301 ASN ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 36559 Z= 0.211 Angle : 0.548 11.088 49641 Z= 0.277 Chirality : 0.040 0.296 5826 Planarity : 0.004 0.061 6454 Dihedral : 6.246 96.033 5333 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.03 % Allowed : 3.43 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.12), residues: 4784 helix: 2.49 (0.10), residues: 2501 sheet: 0.64 (0.23), residues: 498 loop : -1.06 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 118 HIS 0.004 0.001 HIS B 305 PHE 0.021 0.001 PHE F 241 TYR 0.011 0.001 TYR A 206 ARG 0.006 0.000 ARG E 122 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 350 time to evaluate : 3.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ASP cc_start: 0.7633 (t0) cc_final: 0.7293 (t0) REVERT: 1 75 MET cc_start: 0.7671 (ppp) cc_final: 0.7448 (ppp) REVERT: 3 75 MET cc_start: 0.7033 (tmm) cc_final: 0.6394 (tmm) REVERT: 9 48 GLU cc_start: 0.8366 (tp30) cc_final: 0.7976 (tm-30) REVERT: 9 70 ILE cc_start: 0.8488 (tp) cc_final: 0.8179 (tp) outliers start: 1 outliers final: 0 residues processed: 351 average time/residue: 0.3876 time to fit residues: 238.1906 Evaluate side-chains 261 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 3.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 155 optimal weight: 4.9990 chunk 416 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 271 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 463 optimal weight: 1.9990 chunk 384 optimal weight: 4.9990 chunk 214 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 243 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 175 ASN F 55 GLN ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 36559 Z= 0.228 Angle : 0.570 11.490 49641 Z= 0.288 Chirality : 0.041 0.289 5826 Planarity : 0.004 0.075 6454 Dihedral : 6.117 87.060 5333 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.03 % Allowed : 2.35 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.12), residues: 4784 helix: 2.41 (0.10), residues: 2509 sheet: 0.52 (0.23), residues: 501 loop : -1.14 (0.14), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 118 HIS 0.004 0.001 HIS B 305 PHE 0.022 0.001 PHE F 324 TYR 0.015 0.001 TYR 1 68 ARG 0.009 0.000 ARG a 188 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 348 time to evaluate : 4.397 Fit side-chains revert: symmetry clash REVERT: A 173 ASP cc_start: 0.7652 (t0) cc_final: 0.7392 (t0) REVERT: A 229 MET cc_start: 0.8258 (tpp) cc_final: 0.7974 (tpp) REVERT: 1 9 ILE cc_start: 0.2346 (mt) cc_final: 0.2138 (mt) REVERT: 1 21 MET cc_start: 0.6308 (tpt) cc_final: 0.6057 (tpt) REVERT: 1 75 MET cc_start: 0.7777 (ppp) cc_final: 0.7492 (ppp) REVERT: 3 75 MET cc_start: 0.6981 (tmm) cc_final: 0.6288 (tmm) REVERT: 9 48 GLU cc_start: 0.8378 (tp30) cc_final: 0.7959 (tm-30) REVERT: 9 70 ILE cc_start: 0.8547 (tp) cc_final: 0.8209 (tp) outliers start: 1 outliers final: 0 residues processed: 349 average time/residue: 0.4037 time to fit residues: 248.2964 Evaluate side-chains 257 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 4.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 446 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 264 optimal weight: 0.9990 chunk 338 optimal weight: 0.4980 chunk 262 optimal weight: 0.9990 chunk 390 optimal weight: 10.0000 chunk 258 optimal weight: 1.9990 chunk 461 optimal weight: 2.9990 chunk 288 optimal weight: 0.6980 chunk 281 optimal weight: 0.6980 chunk 213 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN F 55 GLN ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 36559 Z= 0.160 Angle : 0.540 10.905 49641 Z= 0.270 Chirality : 0.040 0.287 5826 Planarity : 0.004 0.062 6454 Dihedral : 5.913 76.054 5333 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.12), residues: 4784 helix: 2.49 (0.10), residues: 2507 sheet: 0.67 (0.23), residues: 493 loop : -1.07 (0.14), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 118 HIS 0.004 0.001 HIS A 259 PHE 0.038 0.001 PHE 5 80 TYR 0.015 0.001 TYR a 145 ARG 0.004 0.000 ARG b 115 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 time to evaluate : 4.103 Fit side-chains revert: symmetry clash REVERT: A 173 ASP cc_start: 0.7681 (t0) cc_final: 0.7352 (t0) REVERT: 1 9 ILE cc_start: 0.2248 (mt) cc_final: 0.2012 (mt) REVERT: 1 21 MET cc_start: 0.6315 (tpt) cc_final: 0.6105 (tpt) REVERT: 1 58 PHE cc_start: 0.7159 (m-10) cc_final: 0.6905 (m-10) REVERT: 1 75 MET cc_start: 0.7725 (ppp) cc_final: 0.7399 (ppp) REVERT: 3 75 MET cc_start: 0.6830 (tmm) cc_final: 0.6095 (tmm) REVERT: 9 48 GLU cc_start: 0.8277 (tp30) cc_final: 0.7865 (tm-30) REVERT: 9 70 ILE cc_start: 0.8579 (tp) cc_final: 0.8235 (tp) outliers start: 0 outliers final: 0 residues processed: 359 average time/residue: 0.4044 time to fit residues: 253.9051 Evaluate side-chains 261 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 4.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 285 optimal weight: 0.0870 chunk 184 optimal weight: 7.9990 chunk 275 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 293 optimal weight: 0.9990 chunk 314 optimal weight: 4.9990 chunk 228 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 362 optimal weight: 2.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN D 175 ASN F 55 GLN ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36559 Z= 0.178 Angle : 0.554 11.367 49641 Z= 0.276 Chirality : 0.040 0.285 5826 Planarity : 0.004 0.061 6454 Dihedral : 5.802 73.715 5333 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.95 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.12), residues: 4784 helix: 2.51 (0.10), residues: 2507 sheet: 0.71 (0.23), residues: 486 loop : -1.10 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 118 HIS 0.006 0.001 HIS A 305 PHE 0.031 0.001 PHE 5 80 TYR 0.015 0.001 TYR a 145 ARG 0.005 0.000 ARG b 115 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 4.240 Fit side-chains revert: symmetry clash REVERT: A 173 ASP cc_start: 0.7553 (t0) cc_final: 0.7222 (t0) REVERT: A 229 MET cc_start: 0.8296 (tpp) cc_final: 0.8058 (tpp) REVERT: D 355 ILE cc_start: 0.8955 (tp) cc_final: 0.8637 (tp) REVERT: 1 9 ILE cc_start: 0.2278 (mt) cc_final: 0.2034 (mt) REVERT: 1 58 PHE cc_start: 0.7007 (m-10) cc_final: 0.6768 (m-10) REVERT: 1 75 MET cc_start: 0.7714 (ppp) cc_final: 0.7466 (ppp) REVERT: 9 48 GLU cc_start: 0.8249 (tp30) cc_final: 0.7821 (tm-30) REVERT: 9 70 ILE cc_start: 0.8654 (tp) cc_final: 0.8314 (tp) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.4221 time to fit residues: 259.5208 Evaluate side-chains 260 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 4.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 419 optimal weight: 10.0000 chunk 442 optimal weight: 0.9990 chunk 403 optimal weight: 3.9990 chunk 430 optimal weight: 0.3980 chunk 258 optimal weight: 0.0980 chunk 187 optimal weight: 0.9990 chunk 337 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 388 optimal weight: 2.9990 chunk 406 optimal weight: 0.9990 chunk 428 optimal weight: 0.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN B 369 ASN D 175 ASN F 55 GLN F 377 GLN ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 36559 Z= 0.155 Angle : 0.553 12.274 49641 Z= 0.274 Chirality : 0.040 0.291 5826 Planarity : 0.003 0.061 6454 Dihedral : 5.697 71.787 5333 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.40 % Favored : 97.58 % Rotamer: Outliers : 0.03 % Allowed : 0.95 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.13), residues: 4784 helix: 2.54 (0.10), residues: 2510 sheet: 0.78 (0.23), residues: 486 loop : -1.05 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 118 HIS 0.004 0.001 HIS a 146 PHE 0.028 0.001 PHE 5 80 TYR 0.016 0.001 TYR a 145 ARG 0.004 0.000 ARG E 229 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 360 time to evaluate : 4.105 Fit side-chains REVERT: A 173 ASP cc_start: 0.7486 (t0) cc_final: 0.7185 (t0) REVERT: A 229 MET cc_start: 0.8252 (tpp) cc_final: 0.7995 (tpp) REVERT: D 355 ILE cc_start: 0.8939 (tp) cc_final: 0.8640 (tp) REVERT: b 61 GLU cc_start: 0.8271 (pm20) cc_final: 0.8022 (pm20) REVERT: 1 58 PHE cc_start: 0.7117 (m-10) cc_final: 0.6806 (m-10) REVERT: 1 75 MET cc_start: 0.7763 (ppp) cc_final: 0.7427 (ppp) REVERT: 9 48 GLU cc_start: 0.8236 (tp30) cc_final: 0.7807 (tm-30) REVERT: 9 65 GLU cc_start: 0.6551 (mp0) cc_final: 0.6299 (mp0) REVERT: 9 70 ILE cc_start: 0.8629 (tp) cc_final: 0.8317 (tp) outliers start: 1 outliers final: 1 residues processed: 361 average time/residue: 0.4088 time to fit residues: 258.2966 Evaluate side-chains 263 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 262 time to evaluate : 3.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 282 optimal weight: 0.2980 chunk 454 optimal weight: 6.9990 chunk 277 optimal weight: 0.8980 chunk 215 optimal weight: 0.0050 chunk 316 optimal weight: 2.9990 chunk 477 optimal weight: 5.9990 chunk 439 optimal weight: 3.9990 chunk 380 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 293 optimal weight: 0.0470 chunk 233 optimal weight: 0.3980 overall best weight: 0.3292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN C 258 GLN D 175 ASN F 55 GLN ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 36559 Z= 0.144 Angle : 0.555 10.797 49641 Z= 0.273 Chirality : 0.040 0.265 5826 Planarity : 0.003 0.062 6454 Dihedral : 5.572 68.664 5333 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.42 % Favored : 97.55 % Rotamer: Outliers : 0.03 % Allowed : 0.22 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.13), residues: 4784 helix: 2.55 (0.11), residues: 2513 sheet: 0.81 (0.23), residues: 484 loop : -0.97 (0.14), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 118 HIS 0.004 0.000 HIS a 146 PHE 0.027 0.001 PHE 5 80 TYR 0.016 0.001 TYR a 145 ARG 0.007 0.000 ARG H 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9568 Ramachandran restraints generated. 4784 Oldfield, 0 Emsley, 4784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 372 time to evaluate : 3.911 Fit side-chains REVERT: A 173 ASP cc_start: 0.7462 (t0) cc_final: 0.7140 (t0) REVERT: C 409 PHE cc_start: 0.8110 (m-10) cc_final: 0.7517 (t80) REVERT: D 355 ILE cc_start: 0.8951 (tp) cc_final: 0.8662 (tp) REVERT: E 327 LEU cc_start: 0.9065 (mm) cc_final: 0.8805 (mm) REVERT: 1 58 PHE cc_start: 0.7104 (m-10) cc_final: 0.6793 (m-10) REVERT: 1 75 MET cc_start: 0.7731 (ppp) cc_final: 0.7465 (ppp) REVERT: 6 39 LEU cc_start: 0.8949 (mt) cc_final: 0.8697 (mm) REVERT: 9 48 GLU cc_start: 0.8302 (tp30) cc_final: 0.7809 (tm-30) REVERT: 9 65 GLU cc_start: 0.6596 (mp0) cc_final: 0.6318 (mp0) REVERT: 9 70 ILE cc_start: 0.8688 (tp) cc_final: 0.8343 (tp) outliers start: 1 outliers final: 1 residues processed: 373 average time/residue: 0.3910 time to fit residues: 254.0125 Evaluate side-chains 274 residues out of total 3768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 273 time to evaluate : 3.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 479 random chunks: chunk 301 optimal weight: 5.9990 chunk 404 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 chunk 350 optimal weight: 0.0170 chunk 56 optimal weight: 0.7980 chunk 105 optimal weight: 0.0170 chunk 380 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 390 optimal weight: 9.9990 chunk 48 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN F 55 GLN G 301 ASN ** 6 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.083356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.067297 restraints weight = 142011.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.067482 restraints weight = 102663.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.067691 restraints weight = 74562.902| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 36559 Z= 0.145 Angle : 0.550 11.486 49641 Z= 0.270 Chirality : 0.040 0.262 5826 Planarity : 0.003 0.063 6454 Dihedral : 5.500 66.509 5333 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.30 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.13), residues: 4784 helix: 2.58 (0.11), residues: 2512 sheet: 0.86 (0.24), residues: 482 loop : -0.93 (0.14), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP a 218 HIS 0.004 0.000 HIS a 146 PHE 0.025 0.001 PHE 5 80 TYR 0.016 0.001 TYR a 145 ARG 0.004 0.000 ARG H 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6288.15 seconds wall clock time: 113 minutes 52.62 seconds (6832.62 seconds total)