Starting phenix.real_space_refine on Wed Jul 24 01:40:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9e_34564/07_2024/8h9e_34564_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9e_34564/07_2024/8h9e_34564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9e_34564/07_2024/8h9e_34564.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9e_34564/07_2024/8h9e_34564.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9e_34564/07_2024/8h9e_34564_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h9e_34564/07_2024/8h9e_34564_neut.cif" } resolution = 2.53 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= 0.029 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 13 5.49 5 Mg 5 5.21 5 S 87 5.16 5 C 15234 2.51 5 N 4210 2.21 5 O 4665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 7": "OE1" <-> "OE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A ARG 171": "NH1" <-> "NH2" Residue "A ASP 194": "OD1" <-> "OD2" Residue "A TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 439": "OE1" <-> "OE2" Residue "A GLU 440": "OE1" <-> "OE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 491": "OE1" <-> "OE2" Residue "A GLU 499": "OE1" <-> "OE2" Residue "A PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B ASP 79": "OD1" <-> "OD2" Residue "B GLU 102": "OE1" <-> "OE2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "B TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 224": "OD1" <-> "OD2" Residue "B TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 314": "OD1" <-> "OD2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 373": "NH1" <-> "NH2" Residue "B TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 439": "OE1" <-> "OE2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 15": "NH1" <-> "NH2" Residue "C ASP 20": "OD1" <-> "OD2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C ARG 30": "NH1" <-> "NH2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C GLU 144": "OE1" <-> "OE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C ASP 170": "OD1" <-> "OD2" Residue "C ASP 191": "OD1" <-> "OD2" Residue "C TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 224": "OD1" <-> "OD2" Residue "C TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "C PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 440": "OE1" <-> "OE2" Residue "C PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 494": "OD1" <-> "OD2" Residue "C PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 29": "OD1" <-> "OD2" Residue "E GLU 30": "OE1" <-> "OE2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "E GLU 107": "OE1" <-> "OE2" Residue "E PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E GLU 125": "OE1" <-> "OE2" Residue "E PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "E PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 171": "OE1" <-> "OE2" Residue "E GLU 195": "OE1" <-> "OE2" Residue "E TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 202": "OE1" <-> "OE2" Residue "E GLU 227": "OE1" <-> "OE2" Residue "E GLU 244": "OE1" <-> "OE2" Residue "E TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 270": "OE1" <-> "OE2" Residue "E TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 318": "OD1" <-> "OD2" Residue "E ASP 322": "OD1" <-> "OD2" Residue "E ARG 359": "NH1" <-> "NH2" Residue "E ASP 362": "OD1" <-> "OD2" Residue "E TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 401": "OE1" <-> "OE2" Residue "E GLU 402": "OE1" <-> "OE2" Residue "E ARG 411": "NH1" <-> "NH2" Residue "E PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 425": "OE1" <-> "OE2" Residue "E GLU 451": "OE1" <-> "OE2" Residue "E GLU 457": "OE1" <-> "OE2" Residue "E TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 468": "OE1" <-> "OE2" Residue "F PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 45": "OE1" <-> "OE2" Residue "F ARG 74": "NH1" <-> "NH2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "F GLU 122": "OE1" <-> "OE2" Residue "F GLU 125": "OE1" <-> "OE2" Residue "F PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 171": "OE1" <-> "OE2" Residue "F ARG 192": "NH1" <-> "NH2" Residue "F GLU 195": "OE1" <-> "OE2" Residue "F TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 202": "OE1" <-> "OE2" Residue "F TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 227": "OE1" <-> "OE2" Residue "F ARG 232": "NH1" <-> "NH2" Residue "F ARG 247": "NH1" <-> "NH2" Residue "F PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 263": "NH1" <-> "NH2" Residue "F PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 318": "OD1" <-> "OD2" Residue "F PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 369": "OE1" <-> "OE2" Residue "F TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 398": "OE1" <-> "OE2" Residue "F ASP 403": "OD1" <-> "OD2" Residue "F PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 425": "OE1" <-> "OE2" Residue "F GLU 451": "OE1" <-> "OE2" Residue "F PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 468": "OE1" <-> "OE2" Residue "D PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 40": "OE1" <-> "OE2" Residue "D GLU 45": "OE1" <-> "OE2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 122": "OE1" <-> "OE2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D GLU 195": "OE1" <-> "OE2" Residue "D TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 244": "OE1" <-> "OE2" Residue "D PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 247": "NH1" <-> "NH2" Residue "D ASP 248": "OD1" <-> "OD2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 277": "NH1" <-> "NH2" Residue "D TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 340": "NH1" <-> "NH2" Residue "D ASP 355": "OD1" <-> "OD2" Residue "D TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 397": "OD1" <-> "OD2" Residue "D GLU 398": "OE1" <-> "OE2" Residue "D GLU 401": "OE1" <-> "OE2" Residue "D PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 425": "OE1" <-> "OE2" Residue "D GLU 439": "OE1" <-> "OE2" Residue "D GLU 451": "OE1" <-> "OE2" Residue "D TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 468": "OE1" <-> "OE2" Residue "D GLU 479": "OE1" <-> "OE2" Residue "G ASP 233": "OD1" <-> "OD2" Residue "G GLU 241": "OE1" <-> "OE2" Residue "G PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 261": "OE1" <-> "OE2" Residue "O TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 91": "OE1" <-> "OE2" Residue "O PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 127": "OE1" <-> "OE2" Residue "O PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 16": "NH1" <-> "NH2" Residue "J PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 29": "OE1" <-> "OE2" Residue "J ARG 32": "NH1" <-> "NH2" Residue "J TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 35": "NH1" <-> "NH2" Residue "J ARG 39": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 24214 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3830 Classifications: {'peptide': 503} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 484} Chain breaks: 1 Chain: "B" Number of atoms: 3639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3639 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 458} Chain breaks: 1 Chain: "C" Number of atoms: 3714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3714 Classifications: {'peptide': 487} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 468} Chain breaks: 1 Chain: "E" Number of atoms: 3458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3458 Classifications: {'peptide': 456} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 430} Chain breaks: 1 Chain: "F" Number of atoms: 3529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3529 Classifications: {'peptide': 466} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 440} Chain: "D" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3562 Classifications: {'peptide': 470} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 444} Chain: "G" Number of atoms: 623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 623 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain breaks: 1 Chain: "O" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1437 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain: "J" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 270 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.62, per 1000 atoms: 0.65 Number of scatterers: 24214 At special positions: 0 Unit cell: (132.86, 124.1, 134.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 87 16.00 P 13 15.00 Mg 5 11.99 O 4665 8.00 N 4210 7.00 C 15234 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: 9.13 Conformation dependent library (CDL) restraints added in 3.9 seconds 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5740 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 20 sheets defined 51.5% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.94 Creating SS restraints... Processing helix chain 'A' and resid 8 through 18 Processing helix chain 'A' and resid 78 through 82 removed outlier: 3.858A pdb=" N LEU A 81 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.508A pdb=" N LEU A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.806A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 209 through 223 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 239 through 260 Proline residue: A 247 - end of helix removed outlier: 3.993A pdb=" N PHE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 285 removed outlier: 3.661A pdb=" N GLN A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.520A pdb=" N GLY A 317 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.589A pdb=" N ALA A 377 " --> pdb=" O VAL A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 401 removed outlier: 3.994A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 411 through 428 Processing helix chain 'A' and resid 437 through 450 Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing helix chain 'A' and resid 460 through 476 Processing helix chain 'A' and resid 476 through 487 Processing helix chain 'A' and resid 490 through 508 Processing helix chain 'B' and resid 78 through 82 Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.638A pdb=" N LEU B 103 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 194 through 198 removed outlier: 3.625A pdb=" N LYS B 198 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 223 Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 239 through 260 Proline residue: B 247 - end of helix removed outlier: 3.990A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 297 through 307 removed outlier: 3.743A pdb=" N HIS B 302 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 336 through 346 Processing helix chain 'B' and resid 353 through 359 Processing helix chain 'B' and resid 380 through 401 removed outlier: 4.384A pdb=" N THR B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 429 removed outlier: 3.631A pdb=" N LYS B 429 " --> pdb=" O THR B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 450 Processing helix chain 'B' and resid 451 through 455 removed outlier: 3.680A pdb=" N LYS B 455 " --> pdb=" O TYR B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 459 No H-bonds generated for 'chain 'B' and resid 457 through 459' Processing helix chain 'B' and resid 460 through 476 Processing helix chain 'B' and resid 476 through 487 Processing helix chain 'B' and resid 490 through 507 Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.758A pdb=" N LEU C 81 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.556A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.738A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 191 Processing helix chain 'C' and resid 194 through 197 removed outlier: 3.543A pdb=" N LYS C 197 " --> pdb=" O ASP C 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 194 through 197' Processing helix chain 'C' and resid 209 through 223 Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 239 through 260 Proline residue: C 247 - end of helix removed outlier: 4.128A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 285 removed outlier: 3.651A pdb=" N GLN C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 297 through 307 removed outlier: 3.788A pdb=" N LEU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 Processing helix chain 'C' and resid 336 through 346 Processing helix chain 'C' and resid 353 through 359 Processing helix chain 'C' and resid 374 through 379 Processing helix chain 'C' and resid 380 through 400 removed outlier: 4.031A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 429 Processing helix chain 'C' and resid 437 through 450 Processing helix chain 'C' and resid 457 through 459 No H-bonds generated for 'chain 'C' and resid 457 through 459' Processing helix chain 'C' and resid 460 through 476 Processing helix chain 'C' and resid 476 through 487 Processing helix chain 'C' and resid 490 through 508 Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'E' and resid 125 through 129 Processing helix chain 'E' and resid 140 through 147 Processing helix chain 'E' and resid 164 through 180 Processing helix chain 'E' and resid 192 through 206 Processing helix chain 'E' and resid 228 through 249 removed outlier: 4.897A pdb=" N ALA E 236 " --> pdb=" O ARG E 232 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LEU E 237 " --> pdb=" O ALA E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 275 removed outlier: 3.601A pdb=" N PHE E 264 " --> pdb=" O ASN E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 284 removed outlier: 3.518A pdb=" N TYR E 284 " --> pdb=" O ALA E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 297 Processing helix chain 'E' and resid 315 through 319 Processing helix chain 'E' and resid 322 through 329 Processing helix chain 'E' and resid 339 through 344 Processing helix chain 'E' and resid 362 through 367 Processing helix chain 'E' and resid 367 through 391 removed outlier: 3.582A pdb=" N ILE E 390 " --> pdb=" O SER E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 418 removed outlier: 3.940A pdb=" N SER E 418 " --> pdb=" O GLN E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 423 No H-bonds generated for 'chain 'E' and resid 421 through 423' Processing helix chain 'E' and resid 424 through 429 Processing helix chain 'E' and resid 436 through 450 Processing helix chain 'E' and resid 456 through 460 removed outlier: 3.533A pdb=" N PHE E 460 " --> pdb=" O GLU E 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 465 through 475 removed outlier: 3.716A pdb=" N LYS E 475 " --> pdb=" O ALA E 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 125 through 129 Processing helix chain 'F' and resid 140 through 147 Processing helix chain 'F' and resid 164 through 177 Processing helix chain 'F' and resid 192 through 206 Processing helix chain 'F' and resid 228 through 249 removed outlier: 4.939A pdb=" N ALA F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 275 removed outlier: 4.021A pdb=" N THR F 265 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU F 274 " --> pdb=" O GLU F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 284 Processing helix chain 'F' and resid 287 through 297 Processing helix chain 'F' and resid 316 through 319 Processing helix chain 'F' and resid 322 through 329 Processing helix chain 'F' and resid 330 through 332 No H-bonds generated for 'chain 'F' and resid 330 through 332' Processing helix chain 'F' and resid 339 through 345 Processing helix chain 'F' and resid 362 through 394 removed outlier: 7.794A pdb=" N SER F 368 " --> pdb=" O ASN F 364 " (cutoff:3.500A) removed outlier: 9.402A pdb=" N GLU F 369 " --> pdb=" O ILE F 365 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N HIS F 370 " --> pdb=" O VAL F 366 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASP F 389 " --> pdb=" O LYS F 385 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ILE F 390 " --> pdb=" O SER F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 399 removed outlier: 3.895A pdb=" N GLU F 398 " --> pdb=" O GLY F 395 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU F 399 " --> pdb=" O MET F 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 395 through 399' Processing helix chain 'F' and resid 400 through 418 removed outlier: 3.786A pdb=" N SER F 418 " --> pdb=" O GLN F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 450 Processing helix chain 'F' and resid 456 through 460 Processing helix chain 'F' and resid 465 through 477 Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 140 through 147 Processing helix chain 'D' and resid 164 through 180 Processing helix chain 'D' and resid 192 through 206 Processing helix chain 'D' and resid 228 through 249 removed outlier: 4.872A pdb=" N ALA D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N LEU D 237 " --> pdb=" O ALA D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 273 removed outlier: 4.038A pdb=" N THR D 265 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA D 273 " --> pdb=" O SER D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 276 No H-bonds generated for 'chain 'D' and resid 274 through 276' Processing helix chain 'D' and resid 280 through 284 removed outlier: 3.724A pdb=" N GLY D 283 " --> pdb=" O SER D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 297 Processing helix chain 'D' and resid 316 through 319 Processing helix chain 'D' and resid 322 through 329 Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 339 through 345 Processing helix chain 'D' and resid 367 through 395 removed outlier: 4.177A pdb=" N ASP D 389 " --> pdb=" O LYS D 385 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE D 390 " --> pdb=" O SER D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 399 removed outlier: 3.856A pdb=" N LEU D 399 " --> pdb=" O MET D 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 396 through 399' Processing helix chain 'D' and resid 400 through 418 removed outlier: 3.666A pdb=" N SER D 418 " --> pdb=" O GLN D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 423 No H-bonds generated for 'chain 'D' and resid 421 through 423' Processing helix chain 'D' and resid 424 through 429 Processing helix chain 'D' and resid 436 through 450 Processing helix chain 'D' and resid 456 through 461 Processing helix chain 'D' and resid 465 through 480 Processing helix chain 'G' and resid 3 through 32 removed outlier: 3.683A pdb=" N ALA G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 271 Processing helix chain 'O' and resid 12 through 28 Processing helix chain 'O' and resid 31 through 48 removed outlier: 3.748A pdb=" N GLU O 48 " --> pdb=" O GLN O 44 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 56 Processing helix chain 'O' and resid 61 through 76 removed outlier: 3.715A pdb=" N GLU O 76 " --> pdb=" O ILE O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 92 Processing helix chain 'O' and resid 94 through 96 No H-bonds generated for 'chain 'O' and resid 94 through 96' Processing helix chain 'O' and resid 97 through 113 Processing helix chain 'O' and resid 127 through 139 Processing helix chain 'O' and resid 140 through 142 No H-bonds generated for 'chain 'O' and resid 140 through 142' Processing helix chain 'O' and resid 155 through 159 removed outlier: 3.663A pdb=" N ILE O 158 " --> pdb=" O ASP O 155 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 188 removed outlier: 3.749A pdb=" N LYS O 178 " --> pdb=" O SER O 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 18 Processing helix chain 'J' and resid 20 through 45 removed outlier: 3.948A pdb=" N ALA J 44 " --> pdb=" O GLU J 40 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 66 removed outlier: 3.920A pdb=" N GLU A 51 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N MET A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARG A 40 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE A 38 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL A 74 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N SER A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ARG E 62 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N HIS E 55 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N THR E 60 " --> pdb=" O HIS E 55 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL E 23 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL E 19 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASP E 25 " --> pdb=" O VAL E 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.087A pdb=" N THR A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.522A pdb=" N ALA A 264 " --> pdb=" O THR A 322 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LEU A 324 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE A 266 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N VAL A 326 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TYR A 268 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N GLU A 328 " --> pdb=" O TYR A 268 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU A 166 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU A 352 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE A 168 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 66 removed outlier: 4.117A pdb=" N GLU B 51 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N MET B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG B 40 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ILE B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE B 38 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LYS B 60 " --> pdb=" O PHE B 76 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG F 62 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N HIS F 55 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N THR F 60 " --> pdb=" O HIS F 55 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL F 23 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL F 19 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASP F 25 " --> pdb=" O VAL F 17 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.138A pdb=" N THR B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 109 removed outlier: 6.515A pdb=" N ALA B 264 " --> pdb=" O THR B 322 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N LEU B 324 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE B 266 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N VAL B 326 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TYR B 268 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N GLU B 328 " --> pdb=" O TYR B 268 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU B 166 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LEU B 352 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE B 168 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 145 through 146 removed outlier: 4.472A pdb=" N ILE B 159 " --> pdb=" O MET B 146 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 26 through 35 removed outlier: 6.622A pdb=" N ARG C 40 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 38 through 43 current: chain 'C' and resid 60 through 66 removed outlier: 5.751A pdb=" N SER C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL C 74 " --> pdb=" O SER C 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 71 through 75 current: chain 'D' and resid 23 through 28 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 23 through 28 current: chain 'D' and resid 49 through 57 removed outlier: 6.592A pdb=" N ARG D 62 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N HIS D 55 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N THR D 60 " --> pdb=" O HIS D 55 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 60 through 65 current: chain 'O' and resid 147 through 150 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 147 through 150 current: chain 'O' and resid 169 through 172 Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.089A pdb=" N THR C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 107 through 108 removed outlier: 6.505A pdb=" N VAL C 108 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA C 264 " --> pdb=" O THR C 322 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU C 324 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE C 266 " --> pdb=" O LEU C 324 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL C 326 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TYR C 268 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLU C 328 " --> pdb=" O TYR C 268 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU C 166 " --> pdb=" O ILE C 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 145 through 146 removed outlier: 4.458A pdb=" N ILE C 159 " --> pdb=" O MET C 146 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 86 through 89 removed outlier: 4.548A pdb=" N GLN E 115 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 97 through 98 removed outlier: 6.417A pdb=" N MET E 98 " --> pdb=" O TYR E 222 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N GLN E 224 " --> pdb=" O MET E 98 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL E 185 " --> pdb=" O PHE E 257 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ASP E 259 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ALA E 187 " --> pdb=" O ASP E 259 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL E 254 " --> pdb=" O THR E 308 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N VAL E 310 " --> pdb=" O VAL E 254 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU E 256 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ALA E 312 " --> pdb=" O LEU E 256 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE E 258 " --> pdb=" O ALA E 312 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ILE E 155 " --> pdb=" O GLN E 311 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LYS E 154 " --> pdb=" O ALA E 334 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N THR E 336 " --> pdb=" O LYS E 154 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLY E 156 " --> pdb=" O THR E 336 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 135 through 136 removed outlier: 4.372A pdb=" N TYR E 149 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 86 through 89 removed outlier: 4.337A pdb=" N GLN F 115 " --> pdb=" O VAL F 89 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 97 through 98 removed outlier: 6.400A pdb=" N MET F 98 " --> pdb=" O TYR F 222 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL F 254 " --> pdb=" O THR F 308 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N VAL F 310 " --> pdb=" O VAL F 254 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU F 256 " --> pdb=" O VAL F 310 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ALA F 312 " --> pdb=" O LEU F 256 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE F 258 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N TYR F 314 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS F 154 " --> pdb=" O ALA F 334 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N THR F 336 " --> pdb=" O LYS F 154 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLY F 156 " --> pdb=" O THR F 336 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 135 through 136 removed outlier: 4.218A pdb=" N TYR F 149 " --> pdb=" O LEU F 136 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 86 through 89 removed outlier: 4.398A pdb=" N GLN D 115 " --> pdb=" O VAL D 89 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 97 through 98 removed outlier: 6.316A pdb=" N MET D 98 " --> pdb=" O TYR D 222 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL D 254 " --> pdb=" O THR D 308 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL D 310 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU D 256 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ALA D 312 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE D 258 " --> pdb=" O ALA D 312 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N TYR D 314 " --> pdb=" O ILE D 258 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE D 158 " --> pdb=" O LEU D 338 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 135 through 136 removed outlier: 4.238A pdb=" N TYR D 149 " --> pdb=" O LEU D 136 " (cutoff:3.500A) 1225 hydrogen bonds defined for protein. 3489 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: 9.84 Time building geometry restraints manager: 10.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5119 1.33 - 1.45: 4927 1.45 - 1.57: 14323 1.57 - 1.69: 21 1.69 - 1.81: 167 Bond restraints: 24557 Sorted by residual: bond pdb=" C6 ATP B 601 " pdb=" N6 ATP B 601 " ideal model delta sigma weight residual 1.337 1.459 -0.122 1.10e-02 8.26e+03 1.23e+02 bond pdb=" C6 ATP C 601 " pdb=" N6 ATP C 601 " ideal model delta sigma weight residual 1.337 1.459 -0.122 1.10e-02 8.26e+03 1.23e+02 bond pdb=" C6 ATP A 601 " pdb=" N6 ATP A 601 " ideal model delta sigma weight residual 1.337 1.457 -0.120 1.10e-02 8.26e+03 1.20e+02 bond pdb=" C4 ATP C 601 " pdb=" N9 ATP C 601 " ideal model delta sigma weight residual 1.374 1.284 0.090 1.00e-02 1.00e+04 8.01e+01 bond pdb=" C8 ATP C 601 " pdb=" N9 ATP C 601 " ideal model delta sigma weight residual 1.370 1.263 0.107 1.20e-02 6.94e+03 7.98e+01 ... (remaining 24552 not shown) Histogram of bond angle deviations from ideal: 98.02 - 105.94: 525 105.94 - 113.85: 14454 113.85 - 121.77: 13178 121.77 - 129.68: 4995 129.68 - 137.60: 61 Bond angle restraints: 33213 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 122.61 17.26 1.00e+00 1.00e+00 2.98e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 123.58 16.29 1.00e+00 1.00e+00 2.65e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 124.89 14.98 1.00e+00 1.00e+00 2.24e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 125.71 11.12 1.00e+00 1.00e+00 1.24e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 125.74 11.09 1.00e+00 1.00e+00 1.23e+02 ... (remaining 33208 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.15: 14750 35.15 - 70.30: 283 70.30 - 105.45: 40 105.45 - 140.60: 0 140.60 - 175.75: 3 Dihedral angle restraints: 15076 sinusoidal: 6097 harmonic: 8979 Sorted by residual: dihedral pdb=" C5' ADP F 501 " pdb=" O5' ADP F 501 " pdb=" PA ADP F 501 " pdb=" O2A ADP F 501 " ideal model delta sinusoidal sigma weight residual -60.00 115.76 -175.75 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP F 501 " pdb=" O3A ADP F 501 " pdb=" PA ADP F 501 " pdb=" PB ADP F 501 " ideal model delta sinusoidal sigma weight residual -60.00 109.33 -169.33 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O2A ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PA ADP D 501 " pdb=" PB ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 86.99 -146.98 1 2.00e+01 2.50e-03 4.41e+01 ... (remaining 15073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2824 0.050 - 0.101: 848 0.101 - 0.151: 188 0.151 - 0.202: 7 0.202 - 0.252: 4 Chirality restraints: 3871 Sorted by residual: chirality pdb=" C2' ATP C 601 " pdb=" C1' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" O2' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.43 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C2' ATP A 601 " pdb=" C1' ATP A 601 " pdb=" C3' ATP A 601 " pdb=" O2' ATP A 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.44 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA ILE D 278 " pdb=" N ILE D 278 " pdb=" C ILE D 278 " pdb=" CB ILE D 278 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 3868 not shown) Planarity restraints: 4292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 188 " 0.630 9.50e-02 1.11e+02 2.82e-01 4.87e+01 pdb=" NE ARG A 188 " -0.039 2.00e-02 2.50e+03 pdb=" CZ ARG A 188 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 188 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 188 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 16 " -0.584 9.50e-02 1.11e+02 2.62e-01 4.18e+01 pdb=" NE ARG J 16 " 0.035 2.00e-02 2.50e+03 pdb=" CZ ARG J 16 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG J 16 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG J 16 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 25 " -0.270 9.50e-02 1.11e+02 1.21e-01 9.02e+00 pdb=" NE ARG J 25 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG J 25 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG J 25 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG J 25 " -0.009 2.00e-02 2.50e+03 ... (remaining 4289 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 147 2.54 - 3.13: 18858 3.13 - 3.72: 37674 3.72 - 4.31: 58276 4.31 - 4.90: 94733 Nonbonded interactions: 209688 Sorted by model distance: nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 602 " model vdw 1.956 2.170 nonbonded pdb=" O1B ADP F 501 " pdb="MG MG F 502 " model vdw 2.048 2.170 nonbonded pdb=" O3G ATP B 601 " pdb="MG MG B 602 " model vdw 2.084 2.170 nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 602 " model vdw 2.086 2.170 nonbonded pdb=" OG1 THR D 166 " pdb="MG MG D 502 " model vdw 2.097 2.170 ... (remaining 209683 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 24 through 401 or resid 417 through 508 or resid 601 throu \ gh 602)) selection = (chain 'B' and (resid 24 through 401 or resid 417 through 508 or resid 601 throu \ gh 602)) selection = (chain 'C' and (resid 24 through 508 or resid 601 through 602)) } ncs_group { reference = (chain 'D' and (resid 12 through 391 or resid 400 through 475)) selection = chain 'E' selection = (chain 'F' and (resid 12 through 391 or resid 400 through 475)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.010 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 69.340 Find NCS groups from input model: 1.880 Set up NCS constraints: 0.320 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: 0.000 Load rotamer database and sin/cos tables:11.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 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 : 0.008 0.145 24557 Z= 0.528 Angle : 0.803 17.256 33213 Z= 0.515 Chirality : 0.049 0.252 3871 Planarity : 0.008 0.282 4292 Dihedral : 14.539 175.753 9336 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.68 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: -1.86 (0.13), residues: 3134 helix: -0.92 (0.12), residues: 1361 sheet: -0.96 (0.22), residues: 479 loop : -1.52 (0.15), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 180 PHE 0.015 0.002 PHE F 444 TYR 0.012 0.002 TYR A 446 ARG 0.005 0.001 ARG F 298 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 425 time to evaluate : 2.593 Fit side-chains REVERT: A 359 LYS cc_start: 0.8232 (mttt) cc_final: 0.7955 (mttm) REVERT: A 399 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7438 (tp30) REVERT: A 419 SER cc_start: 0.8511 (m) cc_final: 0.8303 (m) REVERT: A 488 LYS cc_start: 0.8627 (pttt) cc_final: 0.8295 (ptpt) REVERT: C 8 MET cc_start: 0.4229 (ptt) cc_final: 0.3757 (ptp) REVERT: D 212 LYS cc_start: 0.7863 (ptpp) cc_final: 0.7655 (ptpp) REVERT: D 470 VAL cc_start: 0.7787 (m) cc_final: 0.7579 (t) REVERT: O 69 LEU cc_start: 0.6587 (mm) cc_final: 0.6218 (mm) outliers start: 0 outliers final: 0 residues processed: 425 average time/residue: 1.7648 time to fit residues: 834.9369 Evaluate side-chains 303 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 2.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 3.9990 chunk 236 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 159 optimal weight: 0.6980 chunk 126 optimal weight: 0.9980 chunk 244 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 148 optimal weight: 0.0170 chunk 182 optimal weight: 4.9990 chunk 283 optimal weight: 0.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN A 405 GLN A 416 GLN A 492 GLN A 503 ASN B 466 ASN C 208 GLN C 503 ASN F 115 GLN F 224 GLN F 249 GLN F 296 GLN F 331 HIS D 201 HIS D 252 GLN D 266 GLN D 446 GLN D 458 GLN O 87 ASN O 99 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24557 Z= 0.163 Angle : 0.511 7.283 33213 Z= 0.264 Chirality : 0.043 0.137 3871 Planarity : 0.004 0.045 4292 Dihedral : 8.136 153.211 3541 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.79 % Favored : 98.12 % Rotamer: Outliers : 1.56 % Allowed : 10.75 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.15), residues: 3134 helix: 0.74 (0.14), residues: 1350 sheet: -0.45 (0.22), residues: 520 loop : -0.75 (0.16), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 476 PHE 0.015 0.001 PHE J 34 TYR 0.011 0.001 TYR A 446 ARG 0.007 0.000 ARG F 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 341 time to evaluate : 2.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 LYS cc_start: 0.8619 (pttt) cc_final: 0.8297 (ptpt) REVERT: B 455 LYS cc_start: 0.8251 (mmtp) cc_final: 0.7830 (mmpt) REVERT: C 8 MET cc_start: 0.4203 (ptt) cc_final: 0.3731 (ptp) REVERT: E 112 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7986 (mtpt) REVERT: E 249 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7602 (mp10) REVERT: E 415 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7001 (mpt180) REVERT: F 422 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7045 (mt0) REVERT: D 414 GLN cc_start: 0.7682 (tt0) cc_final: 0.7427 (tt0) REVERT: D 470 VAL cc_start: 0.7773 (m) cc_final: 0.7538 (t) REVERT: G 18 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7583 (tptt) REVERT: G 229 MET cc_start: 0.8055 (ttp) cc_final: 0.7850 (ttp) REVERT: G 264 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7791 (mt-10) outliers start: 40 outliers final: 10 residues processed: 358 average time/residue: 1.6487 time to fit residues: 662.0710 Evaluate side-chains 314 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 299 time to evaluate : 2.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 422 GLN Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 18 LYS Chi-restraints excluded: chain O residue 39 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 235 optimal weight: 0.7980 chunk 192 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 283 optimal weight: 4.9990 chunk 306 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 281 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 227 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN B 78 ASN E 388 GLN E 445 GLN D 252 GLN O 97 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24557 Z= 0.243 Angle : 0.527 10.102 33213 Z= 0.271 Chirality : 0.044 0.140 3871 Planarity : 0.004 0.046 4292 Dihedral : 7.746 148.193 3541 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.01 % Favored : 97.89 % Rotamer: Outliers : 2.34 % Allowed : 12.54 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.15), residues: 3134 helix: 1.17 (0.14), residues: 1348 sheet: -0.33 (0.22), residues: 513 loop : -0.47 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 476 PHE 0.013 0.001 PHE J 34 TYR 0.020 0.001 TYR B 446 ARG 0.006 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 312 time to evaluate : 2.800 Fit side-chains revert: symmetry clash REVERT: A 8 MET cc_start: 0.6734 (mtp) cc_final: 0.6284 (mmt) REVERT: A 488 LYS cc_start: 0.8627 (pttt) cc_final: 0.8310 (ptpt) REVERT: B 455 LYS cc_start: 0.8289 (mmtp) cc_final: 0.7888 (mmpt) REVERT: C 8 MET cc_start: 0.4149 (ptt) cc_final: 0.3679 (ptp) REVERT: C 498 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7167 (ttpp) REVERT: C 499 GLU cc_start: 0.6296 (OUTLIER) cc_final: 0.5978 (mt-10) REVERT: E 112 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.8007 (mtpt) REVERT: E 415 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.6888 (mpt180) REVERT: D 458 GLN cc_start: 0.7345 (pm20) cc_final: 0.6713 (tp40) REVERT: D 470 VAL cc_start: 0.7745 (m) cc_final: 0.7510 (t) REVERT: G 264 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7826 (mt-10) REVERT: O 28 LYS cc_start: 0.6552 (OUTLIER) cc_final: 0.5861 (mptt) REVERT: O 69 LEU cc_start: 0.6773 (mm) cc_final: 0.6390 (mm) REVERT: O 126 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7335 (mt) outliers start: 60 outliers final: 16 residues processed: 343 average time/residue: 1.6660 time to fit residues: 640.6903 Evaluate side-chains 313 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 291 time to evaluate : 2.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain O residue 28 LYS Chi-restraints excluded: chain O residue 126 LEU Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 6.9990 chunk 213 optimal weight: 3.9990 chunk 147 optimal weight: 0.0070 chunk 31 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 190 optimal weight: 1.9990 chunk 284 optimal weight: 2.9990 chunk 301 optimal weight: 4.9990 chunk 148 optimal weight: 0.4980 chunk 269 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 overall best weight: 1.2602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN B 78 ASN C 503 ASN E 388 GLN E 445 GLN D 458 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24557 Z= 0.207 Angle : 0.510 9.792 33213 Z= 0.262 Chirality : 0.043 0.138 3871 Planarity : 0.004 0.047 4292 Dihedral : 7.458 149.649 3541 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.85 % Favored : 98.12 % Rotamer: Outliers : 2.02 % Allowed : 14.14 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.15), residues: 3134 helix: 1.43 (0.14), residues: 1351 sheet: -0.23 (0.22), residues: 519 loop : -0.30 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 476 PHE 0.019 0.001 PHE B 468 TYR 0.011 0.001 TYR A 446 ARG 0.006 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 311 time to evaluate : 2.930 Fit side-chains revert: symmetry clash REVERT: A 8 MET cc_start: 0.6728 (mtp) cc_final: 0.6277 (mmt) REVERT: A 488 LYS cc_start: 0.8636 (pttt) cc_final: 0.8316 (ptpt) REVERT: B 455 LYS cc_start: 0.8207 (mmtp) cc_final: 0.7818 (mmpt) REVERT: B 475 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.6669 (mp-120) REVERT: C 8 MET cc_start: 0.4133 (ptt) cc_final: 0.3346 (mmt) REVERT: C 498 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7181 (ttpp) REVERT: E 112 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7991 (mtpt) REVERT: E 249 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7674 (mp10) REVERT: E 415 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.6911 (mpt180) REVERT: D 202 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6541 (tp30) REVERT: D 458 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.6701 (tp40) REVERT: D 470 VAL cc_start: 0.7736 (m) cc_final: 0.7491 (t) REVERT: G 264 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7811 (mt-10) REVERT: O 46 LEU cc_start: 0.6113 (OUTLIER) cc_final: 0.5877 (mp) REVERT: O 69 LEU cc_start: 0.6735 (mm) cc_final: 0.6363 (mm) outliers start: 52 outliers final: 15 residues processed: 339 average time/residue: 1.5834 time to fit residues: 603.5964 Evaluate side-chains 326 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 303 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 458 GLN Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 257 optimal weight: 5.9990 chunk 208 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 153 optimal weight: 4.9990 chunk 270 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN B 78 ASN C 503 ASN E 388 GLN E 445 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 24557 Z= 0.333 Angle : 0.561 10.413 33213 Z= 0.288 Chirality : 0.045 0.150 3871 Planarity : 0.004 0.045 4292 Dihedral : 7.796 152.949 3541 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.11 % Favored : 97.86 % Rotamer: Outliers : 2.49 % Allowed : 14.49 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.15), residues: 3134 helix: 1.31 (0.14), residues: 1350 sheet: -0.25 (0.22), residues: 519 loop : -0.31 (0.17), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS B 476 PHE 0.016 0.002 PHE J 34 TYR 0.020 0.002 TYR B 446 ARG 0.005 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 301 time to evaluate : 2.861 Fit side-chains revert: symmetry clash REVERT: A 8 MET cc_start: 0.6786 (mtp) cc_final: 0.6315 (mmt) REVERT: A 390 MET cc_start: 0.8765 (ttt) cc_final: 0.8518 (ttt) REVERT: A 393 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7706 (mt-10) REVERT: A 411 ASP cc_start: 0.7376 (OUTLIER) cc_final: 0.6984 (p0) REVERT: A 488 LYS cc_start: 0.8633 (pttt) cc_final: 0.8316 (ptpt) REVERT: B 54 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6931 (tm-30) REVERT: B 355 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6861 (tt0) REVERT: B 455 LYS cc_start: 0.8236 (mmtp) cc_final: 0.7825 (mmpt) REVERT: B 475 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.6689 (mp-120) REVERT: C 8 MET cc_start: 0.4233 (ptt) cc_final: 0.3451 (mmt) REVERT: C 498 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7199 (ttpp) REVERT: E 112 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.8014 (mtpt) REVERT: E 249 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7682 (mp10) REVERT: E 415 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.6976 (mpt180) REVERT: F 27 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: D 202 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6553 (tp30) REVERT: D 318 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8152 (m-30) REVERT: D 458 GLN cc_start: 0.7432 (pm20) cc_final: 0.7101 (pm20) REVERT: D 470 VAL cc_start: 0.7769 (m) cc_final: 0.7527 (t) REVERT: G 264 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7867 (mt-10) REVERT: O 46 LEU cc_start: 0.6065 (OUTLIER) cc_final: 0.5837 (mp) REVERT: O 69 LEU cc_start: 0.6774 (mm) cc_final: 0.6406 (mm) outliers start: 64 outliers final: 27 residues processed: 341 average time/residue: 1.6756 time to fit residues: 645.2875 Evaluate side-chains 331 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 291 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 355 ASP Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 1.9990 chunk 271 optimal weight: 0.4980 chunk 59 optimal weight: 0.8980 chunk 177 optimal weight: 7.9990 chunk 74 optimal weight: 0.8980 chunk 301 optimal weight: 20.0000 chunk 250 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 158 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: A 349 GLN A 492 GLN B 78 ASN C 432 GLN C 503 ASN E 388 GLN E 445 GLN F 42 GLN D 201 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24557 Z= 0.187 Angle : 0.503 10.704 33213 Z= 0.257 Chirality : 0.043 0.137 3871 Planarity : 0.004 0.045 4292 Dihedral : 7.348 153.845 3541 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.82 % Favored : 98.15 % Rotamer: Outliers : 2.14 % Allowed : 15.07 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.15), residues: 3134 helix: 1.56 (0.14), residues: 1358 sheet: -0.16 (0.22), residues: 523 loop : -0.16 (0.17), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS B 476 PHE 0.021 0.001 PHE B 468 TYR 0.010 0.001 TYR A 446 ARG 0.006 0.000 ARG F 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 304 time to evaluate : 2.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.6752 (mtp) cc_final: 0.6287 (mmt) REVERT: A 393 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7671 (mt-10) REVERT: A 411 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.6857 (p0) REVERT: A 488 LYS cc_start: 0.8632 (pttt) cc_final: 0.8318 (ptpt) REVERT: B 54 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6928 (tm-30) REVERT: B 195 GLU cc_start: 0.7024 (tp30) cc_final: 0.6705 (tp30) REVERT: B 355 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6855 (tt0) REVERT: B 392 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8320 (tm) REVERT: B 455 LYS cc_start: 0.8215 (mmtp) cc_final: 0.7819 (mmpt) REVERT: B 465 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7443 (tm-30) REVERT: B 475 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.6791 (mp-120) REVERT: B 476 HIS cc_start: 0.7902 (m-70) cc_final: 0.7660 (m-70) REVERT: C 8 MET cc_start: 0.4186 (ptt) cc_final: 0.3404 (mmt) REVERT: C 498 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7164 (ttpp) REVERT: E 112 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7987 (mtpt) REVERT: E 249 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7663 (mp10) REVERT: E 340 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6734 (tpp-160) REVERT: E 415 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.6856 (mpt180) REVERT: D 202 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.6489 (tp30) REVERT: D 318 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.8093 (m-30) REVERT: D 458 GLN cc_start: 0.7417 (pm20) cc_final: 0.7110 (pm20) REVERT: D 470 VAL cc_start: 0.7755 (m) cc_final: 0.7506 (t) REVERT: G 18 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7654 (tptt) REVERT: G 264 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7877 (mt-10) REVERT: O 36 GLU cc_start: 0.6586 (tt0) cc_final: 0.5873 (mt-10) REVERT: O 69 LEU cc_start: 0.6752 (mm) cc_final: 0.6372 (mm) REVERT: O 153 LYS cc_start: 0.7356 (OUTLIER) cc_final: 0.6597 (pttt) outliers start: 55 outliers final: 22 residues processed: 337 average time/residue: 1.5878 time to fit residues: 602.8898 Evaluate side-chains 334 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 296 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 355 ASP Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 18 LYS Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain O residue 153 LYS Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 220 optimal weight: 0.5980 chunk 170 optimal weight: 1.9990 chunk 254 optimal weight: 5.9990 chunk 168 optimal weight: 0.8980 chunk 300 optimal weight: 9.9990 chunk 188 optimal weight: 0.9980 chunk 183 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN A 492 GLN B 78 ASN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 503 ASN E 388 GLN E 445 GLN D 260 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24557 Z= 0.186 Angle : 0.506 11.141 33213 Z= 0.257 Chirality : 0.043 0.156 3871 Planarity : 0.004 0.044 4292 Dihedral : 7.193 155.242 3541 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.75 % Favored : 98.21 % Rotamer: Outliers : 2.02 % Allowed : 15.50 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.15), residues: 3134 helix: 1.64 (0.14), residues: 1357 sheet: -0.14 (0.23), residues: 517 loop : -0.07 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 476 PHE 0.013 0.001 PHE J 34 TYR 0.023 0.001 TYR B 446 ARG 0.007 0.000 ARG F 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 305 time to evaluate : 2.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.6761 (mtp) cc_final: 0.6284 (mmt) REVERT: A 393 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7653 (mt-10) REVERT: A 411 ASP cc_start: 0.7243 (OUTLIER) cc_final: 0.6781 (p0) REVERT: A 488 LYS cc_start: 0.8634 (pttt) cc_final: 0.8322 (ptpt) REVERT: B 54 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6922 (tm-30) REVERT: B 144 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8057 (mt-10) REVERT: B 355 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6848 (tt0) REVERT: B 392 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8309 (tm) REVERT: B 455 LYS cc_start: 0.8208 (mmtp) cc_final: 0.7810 (mmpt) REVERT: B 475 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.6829 (mp-120) REVERT: C 8 MET cc_start: 0.4161 (ptt) cc_final: 0.3403 (mmt) REVERT: C 498 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7192 (ttpp) REVERT: E 112 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.8004 (mtpt) REVERT: E 249 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7582 (mp10) REVERT: E 340 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6729 (tpp-160) REVERT: E 415 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.6851 (mpt180) REVERT: F 422 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.7040 (mt0) REVERT: D 202 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6476 (tp30) REVERT: D 458 GLN cc_start: 0.7403 (pm20) cc_final: 0.7090 (pm20) REVERT: D 470 VAL cc_start: 0.7711 (m) cc_final: 0.7468 (t) REVERT: O 69 LEU cc_start: 0.6772 (mm) cc_final: 0.6386 (mm) REVERT: O 153 LYS cc_start: 0.7359 (OUTLIER) cc_final: 0.6603 (pttt) outliers start: 52 outliers final: 23 residues processed: 337 average time/residue: 1.7059 time to fit residues: 645.1810 Evaluate side-chains 332 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 294 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 422 GLN Chi-restraints excluded: chain F residue 434 LEU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 18 LYS Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain O residue 153 LYS Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 59 optimal weight: 0.0070 chunk 58 optimal weight: 0.8980 chunk 191 optimal weight: 5.9990 chunk 204 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 236 optimal weight: 10.0000 overall best weight: 1.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN A 492 GLN B 477 GLN C 432 GLN C 503 ASN E 388 GLN E 445 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24557 Z= 0.267 Angle : 0.546 11.038 33213 Z= 0.277 Chirality : 0.044 0.140 3871 Planarity : 0.004 0.043 4292 Dihedral : 7.436 157.768 3541 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.98 % Favored : 97.99 % Rotamer: Outliers : 2.18 % Allowed : 15.42 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.15), residues: 3134 helix: 1.55 (0.14), residues: 1356 sheet: -0.14 (0.22), residues: 517 loop : -0.11 (0.17), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS B 476 PHE 0.022 0.002 PHE B 468 TYR 0.015 0.001 TYR E 384 ARG 0.007 0.000 ARG F 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 294 time to evaluate : 2.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.6794 (mtp) cc_final: 0.6310 (mmt) REVERT: A 393 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7655 (mt-10) REVERT: A 411 ASP cc_start: 0.7260 (OUTLIER) cc_final: 0.6795 (p0) REVERT: A 488 LYS cc_start: 0.8634 (pttt) cc_final: 0.8326 (ptpt) REVERT: B 54 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6920 (tm-30) REVERT: B 144 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8067 (mt-10) REVERT: B 355 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6869 (tt0) REVERT: B 392 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8357 (tm) REVERT: B 455 LYS cc_start: 0.8210 (mmtp) cc_final: 0.7805 (mmpt) REVERT: B 463 LYS cc_start: 0.7959 (ttmt) cc_final: 0.7394 (ptmm) REVERT: B 475 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.6871 (mp-120) REVERT: C 8 MET cc_start: 0.4259 (ptt) cc_final: 0.3499 (mmt) REVERT: C 498 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7235 (ttpp) REVERT: E 112 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7962 (mtpt) REVERT: E 249 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7674 (mp10) REVERT: E 340 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6743 (tpp-160) REVERT: E 415 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.6867 (mpt180) REVERT: F 422 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7055 (mt0) REVERT: D 132 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: D 202 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6470 (tp30) REVERT: D 318 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8139 (m-30) REVERT: D 458 GLN cc_start: 0.7413 (pm20) cc_final: 0.6714 (tp40) REVERT: D 470 VAL cc_start: 0.7768 (m) cc_final: 0.7529 (t) REVERT: G 262 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8306 (tt) REVERT: O 36 GLU cc_start: 0.6580 (tt0) cc_final: 0.6378 (mt-10) REVERT: O 69 LEU cc_start: 0.6762 (mm) cc_final: 0.6370 (mm) REVERT: O 153 LYS cc_start: 0.7421 (OUTLIER) cc_final: 0.6614 (pttt) outliers start: 56 outliers final: 24 residues processed: 330 average time/residue: 1.6835 time to fit residues: 623.5314 Evaluate side-chains 331 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 289 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 422 GLN Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 18 LYS Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain O residue 153 LYS Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 2.9990 chunk 288 optimal weight: 1.9990 chunk 262 optimal weight: 0.7980 chunk 280 optimal weight: 1.9990 chunk 168 optimal weight: 0.4980 chunk 122 optimal weight: 3.9990 chunk 220 optimal weight: 0.7980 chunk 85 optimal weight: 8.9990 chunk 253 optimal weight: 1.9990 chunk 265 optimal weight: 3.9990 chunk 279 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN A 492 GLN C 432 GLN C 503 ASN E 388 GLN E 445 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24557 Z= 0.181 Angle : 0.514 12.011 33213 Z= 0.259 Chirality : 0.043 0.208 3871 Planarity : 0.004 0.044 4292 Dihedral : 7.147 157.982 3541 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.72 % Favored : 98.25 % Rotamer: Outliers : 1.95 % Allowed : 15.93 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 1.03 (0.15), residues: 3134 helix: 1.70 (0.14), residues: 1357 sheet: -0.05 (0.23), residues: 518 loop : -0.01 (0.18), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS B 476 PHE 0.030 0.001 PHE B 464 TYR 0.023 0.001 TYR B 446 ARG 0.008 0.000 ARG F 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 303 time to evaluate : 2.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.6785 (mtp) cc_final: 0.6292 (mmt) REVERT: A 390 MET cc_start: 0.8748 (ttt) cc_final: 0.8487 (ttt) REVERT: A 393 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7642 (mt-10) REVERT: A 411 ASP cc_start: 0.7218 (OUTLIER) cc_final: 0.6767 (p0) REVERT: A 488 LYS cc_start: 0.8635 (pttt) cc_final: 0.8326 (ptpt) REVERT: B 54 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6912 (tm-30) REVERT: B 144 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8054 (mt-10) REVERT: B 195 GLU cc_start: 0.6904 (tp30) cc_final: 0.6641 (tp30) REVERT: B 355 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6855 (tt0) REVERT: B 392 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8313 (tm) REVERT: B 455 LYS cc_start: 0.8206 (mmtp) cc_final: 0.7807 (mmpt) REVERT: B 463 LYS cc_start: 0.7933 (ttmt) cc_final: 0.7414 (ptmm) REVERT: B 465 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7485 (tm-30) REVERT: B 475 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.6991 (mp-120) REVERT: C 8 MET cc_start: 0.4241 (ptt) cc_final: 0.3451 (mmt) REVERT: C 498 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7234 (ttpp) REVERT: E 112 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7995 (mtpt) REVERT: E 249 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7646 (mp10) REVERT: E 340 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.6744 (tpp-160) REVERT: E 415 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.6826 (mpt180) REVERT: D 132 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7142 (mp0) REVERT: D 202 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6492 (tp30) REVERT: D 318 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8093 (m-30) REVERT: D 458 GLN cc_start: 0.7372 (pm20) cc_final: 0.7050 (pm20) REVERT: D 470 VAL cc_start: 0.7714 (m) cc_final: 0.7475 (t) REVERT: O 36 GLU cc_start: 0.6520 (tt0) cc_final: 0.5958 (mt-10) REVERT: O 69 LEU cc_start: 0.6734 (mm) cc_final: 0.6353 (mm) REVERT: O 153 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.6606 (pttt) outliers start: 50 outliers final: 23 residues processed: 331 average time/residue: 1.6084 time to fit residues: 601.3963 Evaluate side-chains 335 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 295 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 18 LYS Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain O residue 153 LYS Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 0.7980 chunk 296 optimal weight: 7.9990 chunk 180 optimal weight: 1.9990 chunk 140 optimal weight: 0.2980 chunk 205 optimal weight: 0.8980 chunk 310 optimal weight: 0.9980 chunk 286 optimal weight: 4.9990 chunk 247 optimal weight: 0.0980 chunk 25 optimal weight: 4.9990 chunk 191 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN A 492 GLN B 492 GLN C 503 ASN E 252 GLN E 445 GLN F 197 ASN D 260 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24557 Z= 0.146 Angle : 0.497 12.081 33213 Z= 0.250 Chirality : 0.042 0.244 3871 Planarity : 0.004 0.051 4292 Dihedral : 6.819 157.120 3541 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.60 % Favored : 98.37 % Rotamer: Outliers : 1.52 % Allowed : 16.59 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % 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: 1.14 (0.15), residues: 3134 helix: 1.83 (0.14), residues: 1359 sheet: 0.02 (0.23), residues: 499 loop : -0.01 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS B 476 PHE 0.027 0.001 PHE B 468 TYR 0.019 0.001 TYR E 384 ARG 0.014 0.000 ARG F 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 307 time to evaluate : 2.757 Fit side-chains revert: symmetry clash REVERT: A 8 MET cc_start: 0.6722 (mtp) cc_final: 0.6218 (mmt) REVERT: A 390 MET cc_start: 0.8759 (ttt) cc_final: 0.8539 (ttt) REVERT: A 393 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7646 (mt-10) REVERT: A 488 LYS cc_start: 0.8632 (pttt) cc_final: 0.8322 (ptpt) REVERT: B 54 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6941 (tm-30) REVERT: B 144 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8072 (mt-10) REVERT: B 195 GLU cc_start: 0.6903 (tp30) cc_final: 0.6596 (tp30) REVERT: B 355 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6855 (tt0) REVERT: B 392 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8251 (tm) REVERT: B 455 LYS cc_start: 0.8223 (mmtp) cc_final: 0.7825 (mmpt) REVERT: B 463 LYS cc_start: 0.7918 (ttmt) cc_final: 0.7422 (ptmm) REVERT: B 475 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7214 (mp-120) REVERT: C 8 MET cc_start: 0.4192 (ptt) cc_final: 0.3406 (mmt) REVERT: C 498 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7232 (ttpp) REVERT: E 112 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7986 (mtpt) REVERT: E 249 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7616 (mp10) REVERT: E 340 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6741 (tpp-160) REVERT: E 415 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.6742 (mpt180) REVERT: D 202 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6555 (tp30) REVERT: D 318 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8039 (m-30) REVERT: D 458 GLN cc_start: 0.7346 (pm20) cc_final: 0.7027 (pm20) REVERT: D 470 VAL cc_start: 0.7734 (m) cc_final: 0.7483 (t) REVERT: O 69 LEU cc_start: 0.6753 (mm) cc_final: 0.6382 (mm) REVERT: O 153 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.6614 (pttt) outliers start: 39 outliers final: 17 residues processed: 330 average time/residue: 1.6623 time to fit residues: 616.5300 Evaluate side-chains 319 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 288 time to evaluate : 2.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain O residue 153 LYS Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.7072 > 50: distance: 52 - 56: 12.682 distance: 56 - 57: 22.170 distance: 57 - 58: 31.761 distance: 57 - 60: 20.746 distance: 58 - 59: 27.942 distance: 58 - 64: 29.351 distance: 60 - 61: 14.686 distance: 61 - 62: 8.276 distance: 61 - 63: 10.848 distance: 64 - 65: 52.707 distance: 65 - 66: 44.890 distance: 65 - 68: 29.489 distance: 66 - 67: 26.553 distance: 66 - 73: 24.514 distance: 68 - 69: 10.595 distance: 69 - 70: 10.564 distance: 70 - 71: 17.494 distance: 70 - 72: 9.388 distance: 73 - 74: 7.649 distance: 73 - 79: 15.403 distance: 74 - 75: 4.450 distance: 74 - 77: 9.089 distance: 75 - 76: 10.715 distance: 75 - 80: 13.752 distance: 77 - 78: 5.033 distance: 78 - 79: 13.835 distance: 80 - 81: 3.887 distance: 81 - 82: 3.694 distance: 81 - 84: 3.203 distance: 82 - 83: 3.676 distance: 82 - 86: 3.085 distance: 84 - 85: 5.642 distance: 87 - 88: 7.121 distance: 87 - 90: 5.343 distance: 88 - 95: 9.394 distance: 89 - 119: 5.929 distance: 95 - 96: 7.210 distance: 96 - 97: 10.422 distance: 96 - 99: 7.373 distance: 97 - 98: 8.419 distance: 97 - 103: 10.067 distance: 98 - 130: 4.092 distance: 99 - 100: 6.494 distance: 99 - 101: 4.420 distance: 100 - 102: 4.885 distance: 103 - 104: 4.459 distance: 104 - 105: 6.766 distance: 104 - 107: 5.837 distance: 105 - 106: 3.491 distance: 105 - 110: 5.742 distance: 106 - 139: 3.775 distance: 107 - 108: 6.132 distance: 107 - 109: 4.205 distance: 110 - 111: 5.729 distance: 111 - 112: 9.348 distance: 111 - 114: 5.325 distance: 112 - 113: 12.116 distance: 112 - 119: 12.242 distance: 113 - 145: 10.277 distance: 114 - 115: 6.698 distance: 115 - 116: 3.518 distance: 116 - 117: 4.464 distance: 119 - 120: 7.977 distance: 120 - 121: 5.686 distance: 120 - 123: 3.116 distance: 121 - 122: 7.619 distance: 121 - 130: 6.934 distance: 122 - 150: 5.851 distance: 124 - 125: 3.032 distance: 125 - 127: 5.016 distance: 126 - 128: 4.624 distance: 127 - 129: 4.348 distance: 128 - 129: 4.958 distance: 130 - 131: 4.567 distance: 131 - 132: 5.640 distance: 131 - 134: 11.425 distance: 132 - 133: 5.111 distance: 132 - 139: 5.015 distance: 133 - 157: 5.973 distance: 134 - 135: 8.377 distance: 135 - 136: 6.336 distance: 136 - 137: 8.676 distance: 136 - 138: 3.744