Starting phenix.real_space_refine on Sat Mar 23 22:45:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vol_21268/03_2024/6vol_21268_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vol_21268/03_2024/6vol_21268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vol_21268/03_2024/6vol_21268.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vol_21268/03_2024/6vol_21268.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vol_21268/03_2024/6vol_21268_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vol_21268/03_2024/6vol_21268_updated.pdb" } resolution = 4.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 129 5.16 5 C 24741 2.51 5 N 6646 2.21 5 O 7459 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 46": "OD1" <-> "OD2" Residue "A TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A ASP 290": "OD1" <-> "OD2" Residue "A PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A ARG 455": "NH1" <-> "NH2" Residue "A GLU 485": "OE1" <-> "OE2" Residue "A GLU 499": "OE1" <-> "OE2" Residue "B ARG 5": "NH1" <-> "NH2" Residue "B ARG 14": "NH1" <-> "NH2" Residue "B GLU 18": "OE1" <-> "OE2" Residue "B GLU 55": "OE1" <-> "OE2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B ASP 171": "OD1" <-> "OD2" Residue "B ASP 182": "OD1" <-> "OD2" Residue "B TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 230": "OD1" <-> "OD2" Residue "B GLU 386": "OE1" <-> "OE2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B GLU 419": "OE1" <-> "OE2" Residue "B TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 450": "OE1" <-> "OE2" Residue "B ASP 452": "OD1" <-> "OD2" Residue "B TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "C ASP 46": "OD1" <-> "OD2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 171": "OD1" <-> "OD2" Residue "C TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "C ASP 263": "OD1" <-> "OD2" Residue "C GLU 285": "OE1" <-> "OE2" Residue "C ASP 290": "OD1" <-> "OD2" Residue "C GLU 311": "OE1" <-> "OE2" Residue "C PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 392": "OE1" <-> "OE2" Residue "C TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D GLU 116": "OE1" <-> "OE2" Residue "D ASP 125": "OD1" <-> "OD2" Residue "D ARG 127": "NH1" <-> "NH2" Residue "D GLU 218": "OE1" <-> "OE2" Residue "D TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 491": "OE1" <-> "OE2" Residue "E ASP 32": "OD1" <-> "OD2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E ASP 83": "OD1" <-> "OD2" Residue "E ARG 109": "NH1" <-> "NH2" Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 204": "OE1" <-> "OE2" Residue "E GLU 311": "OE1" <-> "OE2" Residue "E TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 386": "OE1" <-> "OE2" Residue "E TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 53": "OD1" <-> "OD2" Residue "F GLU 64": "OE1" <-> "OE2" Residue "F PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 163": "NH1" <-> "NH2" Residue "F GLU 204": "OE1" <-> "OE2" Residue "F TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 284": "OE1" <-> "OE2" Residue "F ASP 333": "OD1" <-> "OD2" Residue "F ASP 369": "OD1" <-> "OD2" Residue "F PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 77": "NH1" <-> "NH2" Residue "d GLU 100": "OE1" <-> "OE2" Residue "d PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 130": "OD1" <-> "OD2" Residue "d ASP 151": "OD1" <-> "OD2" Residue "d PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 208": "NH1" <-> "NH2" Residue "d TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 234": "OD1" <-> "OD2" Residue "d GLU 243": "OE1" <-> "OE2" Residue "g ARG 48": "NH1" <-> "NH2" Residue "g ARG 73": "NH1" <-> "NH2" Residue "g GLU 98": "OE1" <-> "OE2" Residue "g ARG 144": "NH1" <-> "NH2" Residue "g ARG 171": "NH1" <-> "NH2" Residue "g PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 181": "OD1" <-> "OD2" Residue "g PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 208": "OD1" <-> "OD2" Residue "g ASP 248": "OD1" <-> "OD2" Residue "g ARG 256": "NH1" <-> "NH2" Residue "g GLU 267": "OE1" <-> "OE2" Residue "g ARG 306": "NH1" <-> "NH2" Residue "e ARG 12": "NH1" <-> "NH2" Residue "e ARG 68": "NH1" <-> "NH2" Residue "e GLU 73": "OE1" <-> "OE2" Residue "e GLU 82": "OE1" <-> "OE2" Residue "e GLU 107": "OE1" <-> "OE2" Residue "e ARG 110": "NH1" <-> "NH2" Residue "e GLU 127": "OE1" <-> "OE2" Residue "I ARG 59": "NH1" <-> "NH2" Residue "I GLU 68": "OE1" <-> "OE2" Residue "I GLU 69": "OE1" <-> "OE2" Residue "I ARG 71": "NH1" <-> "NH2" Residue "I GLU 76": "OE1" <-> "OE2" Residue "I GLU 79": "OE1" <-> "OE2" Residue "I ARG 82": "NH1" <-> "NH2" Residue "I ASP 91": "OD1" <-> "OD2" Residue "I TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 119": "OE1" <-> "OE2" Residue "I TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 163": "OE1" <-> "OE2" Residue "J TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 114": "OD1" <-> "OD2" Residue "J ASP 117": "OD1" <-> "OD2" Residue "J GLU 125": "OE1" <-> "OE2" Residue "J GLU 165": "OE1" <-> "OE2" Residue "J GLU 169": "OE1" <-> "OE2" Residue "J GLU 193": "OE1" <-> "OE2" Residue "J ASP 204": "OD1" <-> "OD2" Residue "J ASP 212": "OD1" <-> "OD2" Residue "a ARG 59": "NH1" <-> "NH2" Residue "a PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 178": "OE1" <-> "OE2" Residue "a ASP 197": "OD1" <-> "OD2" Residue "a PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 44": "OE1" <-> "OE2" Residue "N PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 37": "OE1" <-> "OE2" Residue "O GLU 44": "OE1" <-> "OE2" Residue "O PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 37": "OE1" <-> "OE2" Residue "P PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 44": "OE1" <-> "OE2" Residue "T GLU 61": "OE1" <-> "OE2" Residue "V GLU 37": "OE1" <-> "OE2" Residue "V GLU 46": "OE1" <-> "OE2" Residue "W GLU 44": "OE1" <-> "OE2" Residue "Y PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 38991 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 3818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3818 Classifications: {'peptide': 497} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 478} Chain: "B" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3851 Classifications: {'peptide': 501} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 482} Chain: "C" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3843 Classifications: {'peptide': 500} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 481} Chain: "D" Number of atoms: 3627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3627 Classifications: {'peptide': 479} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 452} Chain: "E" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3636 Classifications: {'peptide': 480} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 453} Chain: "F" Number of atoms: 3619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3619 Classifications: {'peptide': 478} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 451} Chain: "d" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1383 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 4, 'TRANS': 174} Chain: "g" Number of atoms: 2497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2497 Classifications: {'peptide': 321} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 308} Chain: "e" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1010 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "I" Number of atoms: 1213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1213 Classifications: {'peptide': 150} Link IDs: {'TRANS': 149} Chain: "J" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1041 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "a" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1629 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 14, 'TRANS': 195} Chain: "M" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "N" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "O" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "P" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "Q" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "R" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "S" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "T" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "U" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "V" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "W" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "X" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "Y" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "Z" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'ATP': 1, 'TTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 18.85, per 1000 atoms: 0.48 Number of scatterers: 38991 At special positions: 0 Unit cell: (225.342, 138.996, 154.791, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 129 16.00 P 16 15.00 O 7459 8.00 N 6646 7.00 C 24741 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.00 Conformation dependent library (CDL) restraints added in 6.3 seconds 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9386 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 173 helices and 28 sheets defined 56.3% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.77 Creating SS restraints... Processing helix chain 'A' and resid 11 through 24 removed outlier: 3.817A pdb=" N TYR A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 176 through 188 removed outlier: 4.475A pdb=" N GLN A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 233 through 252 Proline residue: A 240 - end of helix removed outlier: 3.663A pdb=" N PHE A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 4.733A pdb=" N LEU A 278 " --> pdb=" O MET A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 301 removed outlier: 4.223A pdb=" N PHE A 292 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR A 293 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU A 294 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU A 300 " --> pdb=" O ARG A 297 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG A 301 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 336 Processing helix chain 'A' and resid 347 through 352 Processing helix chain 'A' and resid 368 through 371 No H-bonds generated for 'chain 'A' and resid 368 through 371' Processing helix chain 'A' and resid 374 through 394 removed outlier: 4.551A pdb=" N LYS A 382 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 383 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU A 385 " --> pdb=" O GLY A 381 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 400 No H-bonds generated for 'chain 'A' and resid 397 through 400' Processing helix chain 'A' and resid 407 through 421 Processing helix chain 'A' and resid 431 through 442 Processing helix chain 'A' and resid 451 through 467 removed outlier: 4.360A pdb=" N ARG A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 478 Processing helix chain 'A' and resid 484 through 500 Processing helix chain 'B' and resid 12 through 18 Processing helix chain 'B' and resid 57 through 59 No H-bonds generated for 'chain 'B' and resid 57 through 59' Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 176 through 188 removed outlier: 4.197A pdb=" N GLN B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 218 through 221 removed outlier: 3.543A pdb=" N TYR B 221 " --> pdb=" O ALA B 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 218 through 221' Processing helix chain 'B' and resid 233 through 252 Proline residue: B 240 - end of helix removed outlier: 3.691A pdb=" N PHE B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 277 Processing helix chain 'B' and resid 284 through 286 No H-bonds generated for 'chain 'B' and resid 284 through 286' Processing helix chain 'B' and resid 289 through 300 removed outlier: 4.156A pdb=" N PHE B 292 " --> pdb=" O GLY B 289 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS B 295 " --> pdb=" O PHE B 292 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU B 300 " --> pdb=" O ARG B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 338 Processing helix chain 'B' and resid 347 through 351 Processing helix chain 'B' and resid 368 through 370 No H-bonds generated for 'chain 'B' and resid 368 through 370' Processing helix chain 'B' and resid 374 through 396 removed outlier: 4.526A pdb=" N LYS B 382 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ALA B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N PHE B 396 " --> pdb=" O GLU B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 405 through 420 removed outlier: 3.524A pdb=" N GLU B 419 " --> pdb=" O GLN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 Processing helix chain 'B' and resid 453 through 468 Processing helix chain 'B' and resid 470 through 479 removed outlier: 3.657A pdb=" N GLU B 474 " --> pdb=" O PRO B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 503 Processing helix chain 'C' and resid 6 through 18 removed outlier: 4.051A pdb=" N SER C 10 " --> pdb=" O ALA C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 176 through 189 removed outlier: 4.016A pdb=" N GLN C 187 " --> pdb=" O THR C 183 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLN C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLY C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 233 through 252 Proline residue: C 240 - end of helix removed outlier: 3.781A pdb=" N PHE C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 277 Processing helix chain 'C' and resid 284 through 286 No H-bonds generated for 'chain 'C' and resid 284 through 286' Processing helix chain 'C' and resid 289 through 301 removed outlier: 4.558A pdb=" N PHE C 292 " --> pdb=" O GLY C 289 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG C 297 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU C 300 " --> pdb=" O ARG C 297 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG C 301 " --> pdb=" O LEU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 309 No H-bonds generated for 'chain 'C' and resid 307 through 309' Processing helix chain 'C' and resid 323 through 325 No H-bonds generated for 'chain 'C' and resid 323 through 325' Processing helix chain 'C' and resid 330 through 338 Processing helix chain 'C' and resid 347 through 351 Processing helix chain 'C' and resid 360 through 362 No H-bonds generated for 'chain 'C' and resid 360 through 362' Processing helix chain 'C' and resid 368 through 371 Processing helix chain 'C' and resid 374 through 380 Processing helix chain 'C' and resid 383 through 396 Processing helix chain 'C' and resid 405 through 420 Processing helix chain 'C' and resid 431 through 443 Processing helix chain 'C' and resid 454 through 468 Processing helix chain 'C' and resid 470 through 478 Processing helix chain 'C' and resid 484 through 503 Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 139 through 141 No H-bonds generated for 'chain 'D' and resid 139 through 141' Processing helix chain 'D' and resid 154 through 158 Processing helix chain 'D' and resid 178 through 191 Processing helix chain 'D' and resid 206 through 218 Processing helix chain 'D' and resid 243 through 262 removed outlier: 3.763A pdb=" N MET D 247 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU D 251 " --> pdb=" O MET D 247 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE D 260 " --> pdb=" O MET D 256 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 289 Processing helix chain 'D' and resid 302 through 310 removed outlier: 3.716A pdb=" N LEU D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) 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 337 through 343 Processing helix chain 'D' and resid 354 through 359 Processing helix chain 'D' and resid 377 through 380 No H-bonds generated for 'chain 'D' and resid 377 through 380' Processing helix chain 'D' and resid 382 through 401 Processing helix chain 'D' and resid 404 through 408 Processing helix chain 'D' and resid 415 through 430 Processing helix chain 'D' and resid 439 through 442 No H-bonds generated for 'chain 'D' and resid 439 through 442' Processing helix chain 'D' and resid 451 through 462 Processing helix chain 'D' and resid 471 through 474 Processing helix chain 'D' and resid 480 through 495 Processing helix chain 'E' and resid 104 through 106 No H-bonds generated for 'chain 'E' and resid 104 through 106' Processing helix chain 'E' and resid 154 through 159 Processing helix chain 'E' and resid 178 through 192 removed outlier: 5.365A pdb=" N LYS E 191 " --> pdb=" O ASN E 187 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA E 192 " --> pdb=" O ASN E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 218 Processing helix chain 'E' and resid 243 through 263 removed outlier: 5.205A pdb=" N GLY E 250 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU E 251 " --> pdb=" O MET E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 289 removed outlier: 3.998A pdb=" N ALA E 287 " --> pdb=" O SER E 283 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LEU E 288 " --> pdb=" O GLU E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 312 removed outlier: 3.677A pdb=" N ARG E 312 " --> pdb=" O SER E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 332 No H-bonds generated for 'chain 'E' and resid 330 through 332' Processing helix chain 'E' and resid 337 through 345 removed outlier: 4.316A pdb=" N ALA E 344 " --> pdb=" O ALA E 340 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS E 345 " --> pdb=" O THR E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 358 Processing helix chain 'E' and resid 377 through 380 No H-bonds generated for 'chain 'E' and resid 377 through 380' Processing helix chain 'E' and resid 382 through 408 removed outlier: 5.206A pdb=" N ASP E 403 " --> pdb=" O LYS E 399 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ILE E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 430 Processing helix chain 'E' and resid 437 through 442 removed outlier: 4.006A pdb=" N VAL E 440 " --> pdb=" O VAL E 437 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR E 442 " --> pdb=" O GLU E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 463 Processing helix chain 'E' and resid 471 through 474 Processing helix chain 'E' and resid 480 through 495 removed outlier: 3.590A pdb=" N LYS E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 106 No H-bonds generated for 'chain 'F' and resid 104 through 106' Processing helix chain 'F' and resid 154 through 159 Processing helix chain 'F' and resid 178 through 192 removed outlier: 4.362A pdb=" N LYS F 191 " --> pdb=" O ASN F 187 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ALA F 192 " --> pdb=" O ASN F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 218 Processing helix chain 'F' and resid 249 through 264 Processing helix chain 'F' and resid 275 through 289 removed outlier: 3.661A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 312 removed outlier: 3.607A pdb=" N LEU F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG F 312 " --> pdb=" O SER F 308 " (cutoff:3.500A) 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 337 through 342 Processing helix chain 'F' and resid 354 through 359 Processing helix chain 'F' and resid 377 through 380 No H-bonds generated for 'chain 'F' and resid 377 through 380' Processing helix chain 'F' and resid 382 through 407 removed outlier: 4.477A pdb=" N ASP F 403 " --> pdb=" O LYS F 399 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ILE F 404 " --> pdb=" O GLU F 400 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE F 407 " --> pdb=" O ASP F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 412 No H-bonds generated for 'chain 'F' and resid 410 through 412' Processing helix chain 'F' and resid 415 through 430 Processing helix chain 'F' and resid 451 through 463 removed outlier: 3.913A pdb=" N ARG F 456 " --> pdb=" O ALA F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 465 through 468 removed outlier: 4.324A pdb=" N SER F 468 " --> pdb=" O GLU F 465 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 465 through 468' Processing helix chain 'F' and resid 472 through 474 No H-bonds generated for 'chain 'F' and resid 472 through 474' Processing helix chain 'F' and resid 480 through 492 Processing helix chain 'd' and resid 74 through 89 Processing helix chain 'd' and resid 92 through 107 removed outlier: 3.572A pdb=" N ASP d 98 " --> pdb=" O ALA d 94 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG d 104 " --> pdb=" O GLU d 100 " (cutoff:3.500A) Processing helix chain 'd' and resid 109 through 116 Processing helix chain 'd' and resid 122 through 136 Processing helix chain 'd' and resid 140 through 152 Processing helix chain 'd' and resid 155 through 173 removed outlier: 5.166A pdb=" N LYS d 159 " --> pdb=" O ASN d 156 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE d 165 " --> pdb=" O LEU d 162 " (cutoff:3.500A) Processing helix chain 'd' and resid 188 through 202 Processing helix chain 'd' and resid 238 through 247 removed outlier: 4.067A pdb=" N GLN d 247 " --> pdb=" O GLU d 243 " (cutoff:3.500A) Processing helix chain 'g' and resid 44 through 99 removed outlier: 3.704A pdb=" N VAL g 80 " --> pdb=" O GLN g 76 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN g 81 " --> pdb=" O GLU g 77 " (cutoff:3.500A) Proline residue: g 84 - end of helix removed outlier: 3.514A pdb=" N MET g 96 " --> pdb=" O VAL g 92 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN g 97 " --> pdb=" O LEU g 93 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU g 98 " --> pdb=" O TYR g 94 " (cutoff:3.500A) Processing helix chain 'g' and resid 133 through 151 removed outlier: 3.619A pdb=" N LEU g 137 " --> pdb=" O PHE g 133 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU g 142 " --> pdb=" O LEU g 138 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS g 150 " --> pdb=" O ALA g 146 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU g 151 " --> pdb=" O GLU g 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 163 through 170 Processing helix chain 'g' and resid 189 through 203 Processing helix chain 'g' and resid 242 through 244 No H-bonds generated for 'chain 'g' and resid 242 through 244' Processing helix chain 'g' and resid 288 through 362 Proline residue: g 297 - end of helix removed outlier: 4.406A pdb=" N ASP g 328 " --> pdb=" O SER g 324 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY g 359 " --> pdb=" O GLU g 355 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA g 360 " --> pdb=" O ILE g 356 " (cutoff:3.500A) Processing helix chain 'e' and resid 84 through 86 No H-bonds generated for 'chain 'e' and resid 84 through 86' Processing helix chain 'e' and resid 89 through 105 Processing helix chain 'e' and resid 109 through 129 Processing helix chain 'I' and resid 34 through 156 removed outlier: 3.937A pdb=" N GLU I 106 " --> pdb=" O GLU I 102 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LYS I 107 " --> pdb=" O ILE I 103 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N MET I 108 " --> pdb=" O GLU I 104 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASN I 109 " --> pdb=" O ARG I 105 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN I 123 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TYR I 124 " --> pdb=" O GLN I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 181 Processing helix chain 'J' and resid 89 through 109 Processing helix chain 'J' and resid 111 through 212 Processing helix chain 'a' and resid 37 through 59 removed outlier: 4.706A pdb=" N THR a 42 " --> pdb=" O GLN a 38 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL a 45 " --> pdb=" O ILE a 41 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA a 55 " --> pdb=" O LEU a 51 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA a 57 " --> pdb=" O SER a 53 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL a 58 " --> pdb=" O ALA a 54 " (cutoff:3.500A) Processing helix chain 'a' and resid 69 through 86 Processing helix chain 'a' and resid 89 through 113 removed outlier: 4.582A pdb=" N ARG a 92 " --> pdb=" O GLU a 89 " (cutoff:3.500A) Proline residue: a 93 - end of helix Proline residue: a 96 - end of helix removed outlier: 4.200A pdb=" N THR a 100 " --> pdb=" O PHE a 97 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU a 103 " --> pdb=" O THR a 100 " (cutoff:3.500A) Processing helix chain 'a' and resid 130 through 132 No H-bonds generated for 'chain 'a' and resid 130 through 132' Processing helix chain 'a' and resid 134 through 154 Processing helix chain 'a' and resid 172 through 207 Proline residue: a 183 - end of helix removed outlier: 4.231A pdb=" N LEU a 190 " --> pdb=" O LEU a 186 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN a 193 " --> pdb=" O ARG a 189 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL a 202 " --> pdb=" O GLU a 198 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU a 207 " --> pdb=" O VAL a 203 " (cutoff:3.500A) Processing helix chain 'a' and resid 214 through 243 removed outlier: 4.506A pdb=" N GLY a 225 " --> pdb=" O LEU a 221 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE a 226 " --> pdb=" O PHE a 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 20 removed outlier: 3.882A pdb=" N VAL M 17 " --> pdb=" O ALA M 13 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 41 removed outlier: 4.685A pdb=" N VAL M 26 " --> pdb=" O ILE M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 75 removed outlier: 4.196A pdb=" N GLY M 47 " --> pdb=" O GLU M 44 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY M 51 " --> pdb=" O LYS M 48 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA M 62 " --> pdb=" O PHE M 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 41 removed outlier: 4.747A pdb=" N VAL N 17 " --> pdb=" O ALA N 13 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY N 18 " --> pdb=" O GLY N 14 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE N 22 " --> pdb=" O GLY N 18 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N GLY N 23 " --> pdb=" O LEU N 19 " (cutoff:3.500A) Proline residue: N 24 - end of helix Processing helix chain 'N' and resid 43 through 75 removed outlier: 4.586A pdb=" N GLY N 47 " --> pdb=" O GLU N 44 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLY N 51 " --> pdb=" O LYS N 48 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA N 62 " --> pdb=" O PHE N 59 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR N 64 " --> pdb=" O GLU N 61 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA N 73 " --> pdb=" O VAL N 70 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 41 removed outlier: 4.483A pdb=" N SER O 21 " --> pdb=" O VAL O 17 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE O 22 " --> pdb=" O GLY O 18 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLY O 23 " --> pdb=" O LEU O 19 " (cutoff:3.500A) Proline residue: O 24 - end of helix removed outlier: 4.261A pdb=" N GLY O 29 " --> pdb=" O GLY O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 75 removed outlier: 4.063A pdb=" N GLY O 47 " --> pdb=" O GLU O 44 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ARG O 50 " --> pdb=" O GLY O 47 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA O 62 " --> pdb=" O PHE O 59 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TYR O 66 " --> pdb=" O LEU O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 39 removed outlier: 4.085A pdb=" N VAL P 17 " --> pdb=" O ALA P 13 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER P 21 " --> pdb=" O VAL P 17 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ILE P 22 " --> pdb=" O GLY P 18 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N GLY P 23 " --> pdb=" O LEU P 19 " (cutoff:3.500A) Proline residue: P 24 - end of helix removed outlier: 4.273A pdb=" N GLY P 29 " --> pdb=" O GLY P 25 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 75 removed outlier: 3.856A pdb=" N THR P 64 " --> pdb=" O MET P 60 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLY P 67 " --> pdb=" O LEU P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 41 Proline residue: Q 24 - end of helix removed outlier: 4.584A pdb=" N ALA Q 40 " --> pdb=" O VAL Q 36 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ARG Q 41 " --> pdb=" O GLU Q 37 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 75 removed outlier: 4.739A pdb=" N GLY Q 47 " --> pdb=" O GLU Q 44 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLY Q 51 " --> pdb=" O LYS Q 48 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR Q 52 " --> pdb=" O ILE Q 49 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA Q 62 " --> pdb=" O PHE Q 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 41 removed outlier: 3.872A pdb=" N SER R 9 " --> pdb=" O ILE R 5 " (cutoff:3.500A) Proline residue: R 24 - end of helix Processing helix chain 'R' and resid 43 through 75 removed outlier: 3.962A pdb=" N GLU R 46 " --> pdb=" O PRO R 43 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY R 47 " --> pdb=" O GLU R 44 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE R 49 " --> pdb=" O GLU R 46 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ARG R 50 " --> pdb=" O GLY R 47 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR R 52 " --> pdb=" O ILE R 49 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA R 62 " --> pdb=" O PHE R 59 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N TYR R 66 " --> pdb=" O LEU R 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 41 Proline residue: S 24 - end of helix Processing helix chain 'S' and resid 46 through 75 removed outlier: 3.756A pdb=" N THR S 52 " --> pdb=" O LYS S 48 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU S 63 " --> pdb=" O PHE S 59 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR S 64 " --> pdb=" O MET S 60 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY S 67 " --> pdb=" O LEU S 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 41 Proline residue: T 24 - end of helix Processing helix chain 'T' and resid 46 through 75 removed outlier: 3.500A pdb=" N GLY T 51 " --> pdb=" O GLY T 47 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU T 63 " --> pdb=" O PHE T 59 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR T 64 " --> pdb=" O MET T 60 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY T 67 " --> pdb=" O LEU T 63 " (cutoff:3.500A) Processing helix chain 'U' and resid 4 through 41 removed outlier: 4.025A pdb=" N VAL U 10 " --> pdb=" O ALA U 6 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE U 11 " --> pdb=" O ALA U 7 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA U 12 " --> pdb=" O ALA U 8 " (cutoff:3.500A) Proline residue: U 24 - end of helix Processing helix chain 'U' and resid 46 through 75 removed outlier: 3.764A pdb=" N THR U 52 " --> pdb=" O LYS U 48 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU U 63 " --> pdb=" O PHE U 59 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR U 64 " --> pdb=" O MET U 60 " (cutoff:3.500A) Processing helix chain 'V' and resid 5 through 40 removed outlier: 4.150A pdb=" N VAL V 10 " --> pdb=" O ALA V 6 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE V 11 " --> pdb=" O ALA V 7 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA V 12 " --> pdb=" O ALA V 8 " (cutoff:3.500A) Proline residue: V 24 - end of helix removed outlier: 3.857A pdb=" N ALA V 40 " --> pdb=" O VAL V 36 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 75 removed outlier: 4.907A pdb=" N GLY V 47 " --> pdb=" O GLU V 44 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 41 removed outlier: 3.514A pdb=" N VAL W 10 " --> pdb=" O ALA W 6 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE W 11 " --> pdb=" O ALA W 7 " (cutoff:3.500A) Proline residue: W 24 - end of helix Processing helix chain 'W' and resid 43 through 75 removed outlier: 5.953A pdb=" N GLY W 47 " --> pdb=" O GLU W 44 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG W 50 " --> pdb=" O GLY W 47 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY W 51 " --> pdb=" O LYS W 48 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU W 63 " --> pdb=" O MET W 60 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR W 66 " --> pdb=" O LEU W 63 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY W 67 " --> pdb=" O THR W 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 4 through 41 removed outlier: 4.098A pdb=" N VAL X 10 " --> pdb=" O ALA X 6 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE X 11 " --> pdb=" O ALA X 7 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA X 12 " --> pdb=" O ALA X 8 " (cutoff:3.500A) Proline residue: X 24 - end of helix Processing helix chain 'X' and resid 46 through 75 removed outlier: 4.368A pdb=" N GLY X 51 " --> pdb=" O GLY X 47 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR X 52 " --> pdb=" O LYS X 48 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU X 63 " --> pdb=" O PHE X 59 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR X 64 " --> pdb=" O MET X 60 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY X 67 " --> pdb=" O LEU X 63 " (cutoff:3.500A) Processing helix chain 'Y' and resid 4 through 41 removed outlier: 3.503A pdb=" N VAL Y 10 " --> pdb=" O ALA Y 6 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE Y 11 " --> pdb=" O ALA Y 7 " (cutoff:3.500A) Proline residue: Y 24 - end of helix Processing helix chain 'Y' and resid 43 through 75 removed outlier: 3.800A pdb=" N GLU Y 46 " --> pdb=" O PRO Y 43 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY Y 47 " --> pdb=" O GLU Y 44 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS Y 48 " --> pdb=" O ALA Y 45 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ARG Y 50 " --> pdb=" O GLY Y 47 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLY Y 51 " --> pdb=" O LYS Y 48 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA Y 62 " --> pdb=" O PHE Y 59 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR Y 66 " --> pdb=" O LEU Y 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 4 through 38 removed outlier: 3.631A pdb=" N VAL Z 10 " --> pdb=" O ALA Z 6 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE Z 11 " --> pdb=" O ALA Z 7 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLY Z 23 " --> pdb=" O LEU Z 19 " (cutoff:3.500A) Proline residue: Z 24 - end of helix removed outlier: 4.829A pdb=" N GLY Z 29 " --> pdb=" O GLY Z 25 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR Z 30 " --> pdb=" O VAL Z 26 " (cutoff:3.500A) Processing helix chain 'Z' and resid 44 through 75 removed outlier: 4.082A pdb=" N GLY Z 47 " --> pdb=" O GLU Z 44 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG Z 50 " --> pdb=" O GLY Z 47 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY Z 51 " --> pdb=" O LYS Z 48 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR Z 66 " --> pdb=" O LEU Z 63 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.598A pdb=" N GLY A 30 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 89 " --> pdb=" O GLY A 30 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 32 through 36 removed outlier: 6.710A pdb=" N ARG A 41 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL A 35 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 97 through 99 Processing sheet with id= D, first strand: chain 'A' and resid 168 through 170 Processing sheet with id= E, first strand: chain 'A' and resid 256 through 259 removed outlier: 6.196A pdb=" N SER A 313 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ILE A 259 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N THR A 315 " --> pdb=" O ILE A 259 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 30 through 36 removed outlier: 3.587A pdb=" N HIS B 43 " --> pdb=" O THR B 31 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ARG B 41 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N VAL B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL B 75 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ALA B 64 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 97 through 99 Processing sheet with id= H, first strand: chain 'B' and resid 317 through 321 removed outlier: 6.701A pdb=" N GLU B 166 " --> pdb=" O PRO B 318 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL B 320 " --> pdb=" O GLU B 166 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE B 168 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLY B 341 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE B 169 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE B 343 " --> pdb=" O ILE B 169 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 313 through 316 Processing sheet with id= J, first strand: chain 'C' and resid 39 through 43 removed outlier: 6.933A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N MET C 77 " --> pdb=" O GLY C 62 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N GLY C 62 " --> pdb=" O MET C 77 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 97 through 100 removed outlier: 3.845A pdb=" N GLU C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 167 through 170 Processing sheet with id= M, first strand: chain 'C' and resid 222 through 226 removed outlier: 6.788A pdb=" N CYS C 194 " --> pdb=" O ILE C 223 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N VAL C 225 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR C 196 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N SER C 313 " --> pdb=" O THR C 257 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE C 259 " --> pdb=" O SER C 313 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N THR C 315 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N TYR C 261 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 90 through 92 removed outlier: 6.511A pdb=" N ASP D 32 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ILE D 26 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL D 30 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL D 77 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL D 65 " --> pdb=" O VAL D 77 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 49 through 52 Processing sheet with id= P, first strand: chain 'D' and resid 99 through 101 Processing sheet with id= Q, first strand: chain 'D' and resid 348 through 352 removed outlier: 3.546A pdb=" N PHE D 171 " --> pdb=" O THR D 350 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N ILE D 168 " --> pdb=" O ILE D 321 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N SER D 323 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU D 170 " --> pdb=" O SER D 323 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLN D 325 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N GLY D 172 " --> pdb=" O GLN D 325 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE D 272 " --> pdb=" O ILE D 324 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL D 198 " --> pdb=" O PHE D 271 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 20 through 22 removed outlier: 4.393A pdb=" N GLU E 90 " --> pdb=" O LYS E 50 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ARG E 75 " --> pdb=" O GLN E 66 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LEU E 68 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ARG E 73 " --> pdb=" O LEU E 68 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ALA E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ILE E 23 " --> pdb=" O ALA E 34 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 99 through 101 Processing sheet with id= T, first strand: chain 'E' and resid 348 through 351 removed outlier: 7.431A pdb=" N ILE E 168 " --> pdb=" O ILE E 321 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N SER E 323 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N LEU E 170 " --> pdb=" O SER E 323 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLN E 325 " --> pdb=" O LEU E 170 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N GLY E 172 " --> pdb=" O GLN E 325 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL E 327 " --> pdb=" O GLY E 172 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL E 268 " --> pdb=" O THR E 322 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ILE E 324 " --> pdb=" O VAL E 268 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N LEU E 270 " --> pdb=" O ILE E 324 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ALA E 326 " --> pdb=" O LEU E 270 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE E 272 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N TYR E 328 " --> pdb=" O ILE E 272 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL E 196 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N PHE E 271 " --> pdb=" O VAL E 196 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL E 198 " --> pdb=" O PHE E 271 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ASP E 273 " --> pdb=" O VAL E 198 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLY E 200 " --> pdb=" O ASP E 273 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 47 through 49 removed outlier: 3.522A pdb=" N GLY F 21 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASP F 32 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE F 26 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL F 77 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL F 65 " --> pdb=" O VAL F 77 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 99 through 101 Processing sheet with id= W, first strand: chain 'F' and resid 168 through 172 removed outlier: 3.998A pdb=" N LEU F 270 " --> pdb=" O THR F 322 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL F 196 " --> pdb=" O LEU F 269 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N PHE F 271 " --> pdb=" O VAL F 196 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL F 198 " --> pdb=" O PHE F 271 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'd' and resid 175 through 182 removed outlier: 7.225A pdb=" N ASN d 206 " --> pdb=" O GLU d 176 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ALA d 178 " --> pdb=" O ASN d 206 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ARG d 208 " --> pdb=" O ALA d 178 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL d 180 " --> pdb=" O ARG d 208 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS d 210 " --> pdb=" O VAL d 180 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N SER d 182 " --> pdb=" O LYS d 210 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL d 212 " --> pdb=" O SER d 182 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'd' and resid 221 through 224 removed outlier: 3.723A pdb=" N PHE d 221 " --> pdb=" O MET d 235 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'g' and resid 154 through 160 removed outlier: 7.058A pdb=" N GLU g 211 " --> pdb=" O MET g 121 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N VAL g 123 " --> pdb=" O GLU g 211 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU g 213 " --> pdb=" O VAL g 123 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N MET g 212 " --> pdb=" O THR g 229 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N THR g 229 " --> pdb=" O MET g 212 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N TYR g 214 " --> pdb=" O ILE g 227 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE g 227 " --> pdb=" O TYR g 214 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'e' and resid 5 through 8 removed outlier: 6.778A pdb=" N ILE e 74 " --> pdb=" O CYS e 6 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LEU e 8 " --> pdb=" O ILE e 74 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ILE e 76 " --> pdb=" O LEU e 8 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'e' and resid 30 through 33 removed outlier: 3.515A pdb=" N ILE e 22 " --> pdb=" O VAL e 33 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE e 23 " --> pdb=" O ARG e 50 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG e 50 " --> pdb=" O ILE e 23 " (cutoff:3.500A) 2177 hydrogen bonds defined for protein. 5673 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.75 Time building geometry restraints manager: 15.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11973 1.34 - 1.45: 4674 1.45 - 1.57: 22618 1.57 - 1.69: 26 1.69 - 1.81: 246 Bond restraints: 39537 Sorted by residual: bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.23e+01 bond pdb=" C4 ATP F 502 " pdb=" C5 ATP F 502 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.99e+01 bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.91e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.74e+01 bond pdb=" C5 ATP C 601 " pdb=" C6 ATP C 601 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.95e+01 ... (remaining 39532 not shown) Histogram of bond angle deviations from ideal: 96.53 - 104.51: 694 104.51 - 112.49: 20972 112.49 - 120.47: 17354 120.47 - 128.44: 14501 128.44 - 136.42: 102 Bond angle restraints: 53623 Sorted by residual: angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 118.07 21.80 1.00e+00 1.00e+00 4.75e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 119.20 20.67 1.00e+00 1.00e+00 4.27e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 119.67 20.20 1.00e+00 1.00e+00 4.08e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 117.26 19.57 1.00e+00 1.00e+00 3.83e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 118.19 18.64 1.00e+00 1.00e+00 3.48e+02 ... (remaining 53618 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.79: 23444 33.79 - 67.59: 601 67.59 - 101.38: 53 101.38 - 135.17: 3 135.17 - 168.96: 3 Dihedral angle restraints: 24104 sinusoidal: 9452 harmonic: 14652 Sorted by residual: dihedral pdb=" CA ALA F 295 " pdb=" C ALA F 295 " pdb=" N VAL F 296 " pdb=" CA VAL F 296 " ideal model delta harmonic sigma weight residual 180.00 -129.45 -50.55 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA ALA D 295 " pdb=" C ALA D 295 " pdb=" N VAL D 296 " pdb=" CA VAL D 296 " ideal model delta harmonic sigma weight residual -180.00 -139.93 -40.07 0 5.00e+00 4.00e-02 6.42e+01 dihedral pdb=" CA TYR B 20 " pdb=" C TYR B 20 " pdb=" N ASN B 21 " pdb=" CA ASN B 21 " ideal model delta harmonic sigma weight residual -180.00 -145.07 -34.93 0 5.00e+00 4.00e-02 4.88e+01 ... (remaining 24101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 4998 0.053 - 0.105: 1193 0.105 - 0.158: 205 0.158 - 0.211: 14 0.211 - 0.263: 7 Chirality restraints: 6417 Sorted by residual: chirality pdb=" CB ILE e 51 " pdb=" CA ILE e 51 " pdb=" CG1 ILE e 51 " pdb=" CG2 ILE e 51 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA THR J 110 " pdb=" N THR J 110 " pdb=" C THR J 110 " pdb=" CB THR J 110 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CB ILE A 354 " pdb=" CA ILE A 354 " pdb=" CG1 ILE A 354 " pdb=" CG2 ILE A 354 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 6414 not shown) Planarity restraints: 6914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 TTX F 501 " 0.684 2.00e-02 2.50e+03 6.32e-01 5.99e+03 pdb=" C12 TTX F 501 " -0.071 2.00e-02 2.50e+03 pdb=" C13 TTX F 501 " 0.880 2.00e-02 2.50e+03 pdb=" C9 TTX F 501 " -0.627 2.00e-02 2.50e+03 pdb=" N3 TTX F 501 " 0.005 2.00e-02 2.50e+03 pdb=" O3 TTX F 501 " -0.870 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C15 TTX F 501 " 0.332 2.00e-02 2.50e+03 3.97e-01 2.36e+03 pdb=" C5 TTX F 501 " -0.514 2.00e-02 2.50e+03 pdb=" C6 TTX F 501 " 0.079 2.00e-02 2.50e+03 pdb=" C7 TTX F 501 " -0.576 2.00e-02 2.50e+03 pdb=" N1 TTX F 501 " 0.325 2.00e-02 2.50e+03 pdb=" O1 TTX F 501 " 0.354 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C13 TTX F 501 " -0.544 2.00e-02 2.50e+03 2.72e-01 1.48e+03 pdb=" C14 TTX F 501 " 0.138 2.00e-02 2.50e+03 pdb=" C15 TTX F 501 " 0.094 2.00e-02 2.50e+03 pdb=" C16 TTX F 501 " -0.083 2.00e-02 2.50e+03 pdb=" C17 TTX F 501 " -0.175 2.00e-02 2.50e+03 pdb=" N1 TTX F 501 " 0.236 2.00e-02 2.50e+03 pdb=" N4 TTX F 501 " 0.412 2.00e-02 2.50e+03 pdb=" O4 TTX F 501 " -0.079 2.00e-02 2.50e+03 ... (remaining 6911 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1094 2.70 - 3.25: 41967 3.25 - 3.80: 64727 3.80 - 4.35: 83747 4.35 - 4.90: 135424 Nonbonded interactions: 326959 Sorted by model distance: nonbonded pdb=" O ALA D 295 " pdb=" N GLY D 297 " model vdw 2.148 2.520 nonbonded pdb=" O ASP A 402 " pdb=" OG1 THR A 407 " model vdw 2.149 2.440 nonbonded pdb=" OH TYR C 196 " pdb=" OD2 ASP C 262 " model vdw 2.174 2.440 nonbonded pdb=" OG1 THR B 149 " pdb=" OG1 THR B 183 " model vdw 2.178 2.440 nonbonded pdb=" O ALA E 295 " pdb=" N GLY E 297 " model vdw 2.204 2.520 ... (remaining 326954 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' selection = (chain 'B' and (resid 7 through 503 or resid 601)) selection = (chain 'C' and (resid 7 through 503 or resid 601)) } ncs_group { reference = (chain 'D' and resid 18 through 494) selection = (chain 'E' and resid 18 through 494) selection = (chain 'F' and resid 18 through 494) } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.710 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: 17.250 Check model and map are aligned: 0.580 Set scattering table: 0.350 Process input model: 93.850 Find NCS groups from input model: 2.470 Set up NCS constraints: 0.380 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 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 : 0.005 0.079 39537 Z= 0.341 Angle : 0.890 21.798 53623 Z= 0.556 Chirality : 0.046 0.263 6417 Planarity : 0.011 0.632 6914 Dihedral : 15.393 168.964 14718 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.20 % Favored : 94.66 % Rotamer: Outliers : 0.12 % Allowed : 7.24 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.18 (0.10), residues: 5113 helix: -1.50 (0.08), residues: 2855 sheet: -2.79 (0.19), residues: 504 loop : -2.69 (0.13), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP e 57 HIS 0.004 0.001 HIS F 133 PHE 0.027 0.002 PHE E 343 TYR 0.051 0.002 TYR J 109 ARG 0.007 0.001 ARG J 119 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 889 time to evaluate : 4.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7068 (mm-30) REVERT: A 131 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7577 (tm-30) REVERT: A 293 TYR cc_start: 0.8554 (t80) cc_final: 0.8200 (t80) REVERT: A 430 THR cc_start: 0.8169 (p) cc_final: 0.7298 (p) REVERT: B 171 ASP cc_start: 0.5609 (t0) cc_final: 0.5386 (t0) REVERT: C 251 MET cc_start: 0.8566 (ttp) cc_final: 0.8311 (ttm) REVERT: C 321 GLU cc_start: 0.8469 (tm-30) cc_final: 0.7875 (tm-30) REVERT: C 498 MET cc_start: 0.6898 (tpp) cc_final: 0.6100 (ttp) REVERT: D 79 MET cc_start: 0.8218 (mmp) cc_final: 0.8007 (mmp) REVERT: D 239 MET cc_start: 0.7790 (mtt) cc_final: 0.7333 (mtm) REVERT: D 311 GLU cc_start: 0.7297 (mt-10) cc_final: 0.6912 (mm-30) REVERT: D 333 ASP cc_start: 0.8618 (t0) cc_final: 0.8386 (t0) REVERT: E 89 MET cc_start: 0.8262 (mtt) cc_final: 0.8002 (mtt) REVERT: E 254 LEU cc_start: 0.8683 (tp) cc_final: 0.8455 (tp) REVERT: E 273 ASP cc_start: 0.8613 (t70) cc_final: 0.8401 (t0) REVERT: F 254 LEU cc_start: 0.9104 (tp) cc_final: 0.8816 (tp) REVERT: F 301 THR cc_start: 0.9098 (p) cc_final: 0.8602 (t) REVERT: F 311 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7538 (mm-30) REVERT: F 374 MET cc_start: 0.8398 (mmp) cc_final: 0.8098 (mmp) REVERT: F 458 PHE cc_start: 0.7485 (m-80) cc_final: 0.7281 (m-80) REVERT: F 472 GLN cc_start: 0.7269 (mp10) cc_final: 0.6875 (tm-30) REVERT: d 72 ASP cc_start: 0.7950 (t0) cc_final: 0.7599 (t70) REVERT: g 96 MET cc_start: 0.6632 (tpp) cc_final: 0.6404 (mmp) REVERT: e 50 ARG cc_start: 0.6094 (pmt170) cc_final: 0.5430 (ptt180) REVERT: e 63 MET cc_start: 0.5351 (mmt) cc_final: 0.4758 (mmm) REVERT: e 110 ARG cc_start: 0.6919 (mtt180) cc_final: 0.6006 (mtp180) REVERT: I 105 ARG cc_start: 0.6157 (mtm-85) cc_final: 0.5226 (ttp80) REVERT: J 106 LYS cc_start: 0.4054 (ttpp) cc_final: 0.3786 (tptt) REVERT: J 182 GLU cc_start: 0.4770 (mt-10) cc_final: 0.3661 (tp30) REVERT: a 71 PHE cc_start: 0.5424 (t80) cc_final: 0.5134 (t80) REVERT: a 186 LEU cc_start: 0.4360 (tp) cc_final: 0.3898 (tp) REVERT: O 68 LEU cc_start: 0.4504 (tp) cc_final: 0.4131 (tt) REVERT: R 57 LEU cc_start: 0.6571 (mt) cc_final: 0.5912 (mp) REVERT: R 76 PHE cc_start: 0.3083 (m-10) cc_final: 0.1839 (t80) REVERT: S 60 MET cc_start: 0.2314 (tpp) cc_final: 0.1294 (tpp) REVERT: T 48 LYS cc_start: 0.5248 (mtmm) cc_final: 0.4727 (mmtm) REVERT: V 59 PHE cc_start: 0.6085 (m-80) cc_final: 0.5828 (m-80) REVERT: W 30 THR cc_start: 0.7137 (t) cc_final: 0.6850 (m) REVERT: X 49 ILE cc_start: 0.5538 (mt) cc_final: 0.5271 (mm) outliers start: 5 outliers final: 2 residues processed: 893 average time/residue: 0.5512 time to fit residues: 769.5557 Evaluate side-chains 600 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 598 time to evaluate : 4.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 422 optimal weight: 6.9990 chunk 378 optimal weight: 0.6980 chunk 210 optimal weight: 4.9990 chunk 129 optimal weight: 0.4980 chunk 255 optimal weight: 4.9990 chunk 202 optimal weight: 1.9990 chunk 391 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 238 optimal weight: 0.6980 chunk 291 optimal weight: 1.9990 chunk 454 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN A 256 HIS A 351 ASN A 389 GLN A 423 GLN A 434 GLN A 468 ASN A 497 GLN B 34 GLN B 201 GLN B 208 GLN B 212 ASN B 256 HIS B 295 HIS C 70 ASN C 201 GLN C 214 GLN C 295 HIS C 389 GLN C 425 GLN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN D 57 GLN D 133 HIS D 238 GLN D 264 ASN D 396 GLN E 25 GLN E 72 ASN E 188 ASN E 226 ASN E 238 GLN E 240 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 389 GLN F 25 GLN F 112 ASN ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 GLN ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 170 ASN d 240 GLN g 95 ASN g 134 ASN e 4 ASN e 27 ASN e 54 ASN I 55 ASN I 109 ASN I 120 GLN ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 161 ASN ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 145 ASN J 186 GLN a 86 GLN ** a 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 175 ASN O 28 GLN O 78 ASN P 28 GLN P 34 GLN ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 34 GLN ** Y 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 28 GLN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 39537 Z= 0.272 Angle : 0.687 10.793 53623 Z= 0.350 Chirality : 0.044 0.213 6417 Planarity : 0.006 0.061 6914 Dihedral : 8.139 165.704 5700 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.42 % Favored : 94.47 % Rotamer: Outliers : 0.15 % Allowed : 6.18 % Favored : 93.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.97 (0.11), residues: 5113 helix: -0.47 (0.09), residues: 2877 sheet: -2.30 (0.19), residues: 524 loop : -2.25 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP e 57 HIS 0.003 0.001 HIS a 36 PHE 0.024 0.002 PHE S 59 TYR 0.031 0.002 TYR J 109 ARG 0.006 0.000 ARG U 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 757 time to evaluate : 4.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7516 (tt0) REVERT: A 22 ARG cc_start: 0.6564 (ptt-90) cc_final: 0.5806 (tpt90) REVERT: A 25 LYS cc_start: 0.7513 (ttmt) cc_final: 0.7240 (mtpt) REVERT: A 230 ASP cc_start: 0.7228 (p0) cc_final: 0.6971 (p0) REVERT: B 182 ASP cc_start: 0.5850 (m-30) cc_final: 0.5640 (m-30) REVERT: C 321 GLU cc_start: 0.8510 (tm-30) cc_final: 0.7874 (tm-30) REVERT: C 498 MET cc_start: 0.7022 (tpp) cc_final: 0.5953 (ttp) REVERT: D 79 MET cc_start: 0.8195 (mmp) cc_final: 0.7707 (mmp) REVERT: D 239 MET cc_start: 0.7605 (mtt) cc_final: 0.7318 (mtm) REVERT: D 305 GLU cc_start: 0.6006 (mt-10) cc_final: 0.5770 (mt-10) REVERT: D 311 GLU cc_start: 0.7596 (mt-10) cc_final: 0.6972 (mt-10) REVERT: D 333 ASP cc_start: 0.8703 (t0) cc_final: 0.8397 (t0) REVERT: E 89 MET cc_start: 0.8395 (mtt) cc_final: 0.8171 (mtt) REVERT: E 273 ASP cc_start: 0.8577 (t70) cc_final: 0.8365 (t0) REVERT: E 313 ILE cc_start: 0.7962 (mt) cc_final: 0.7710 (mt) REVERT: F 254 LEU cc_start: 0.9099 (tp) cc_final: 0.8831 (tp) REVERT: F 301 THR cc_start: 0.8898 (p) cc_final: 0.8671 (t) REVERT: F 472 GLN cc_start: 0.7289 (mp10) cc_final: 0.6760 (tm-30) REVERT: d 72 ASP cc_start: 0.7844 (t0) cc_final: 0.7551 (t70) REVERT: g 96 MET cc_start: 0.6652 (tpp) cc_final: 0.6450 (mmp) REVERT: e 50 ARG cc_start: 0.5784 (pmt170) cc_final: 0.5441 (ptt180) REVERT: e 110 ARG cc_start: 0.6711 (mtt180) cc_final: 0.5984 (mtp180) REVERT: I 105 ARG cc_start: 0.6289 (mtm-85) cc_final: 0.5098 (ttp80) REVERT: I 115 TYR cc_start: 0.4942 (m-80) cc_final: 0.4730 (m-80) REVERT: J 106 LYS cc_start: 0.4922 (ttpp) cc_final: 0.4510 (tptt) REVERT: J 182 GLU cc_start: 0.4688 (mt-10) cc_final: 0.3592 (tp30) REVERT: a 186 LEU cc_start: 0.4864 (tp) cc_final: 0.4244 (tp) REVERT: O 68 LEU cc_start: 0.3973 (tp) cc_final: 0.3769 (tt) REVERT: R 28 GLN cc_start: 0.6841 (mp10) cc_final: 0.6139 (mp10) REVERT: R 76 PHE cc_start: 0.2864 (m-10) cc_final: 0.1851 (t80) REVERT: X 28 GLN cc_start: 0.5397 (tt0) cc_final: 0.4755 (tt0) outliers start: 6 outliers final: 1 residues processed: 761 average time/residue: 0.5464 time to fit residues: 679.3411 Evaluate side-chains 578 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 577 time to evaluate : 4.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 252 optimal weight: 0.0980 chunk 140 optimal weight: 0.7980 chunk 377 optimal weight: 3.9990 chunk 309 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 chunk 454 optimal weight: 10.0000 chunk 491 optimal weight: 2.9990 chunk 405 optimal weight: 0.7980 chunk 451 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 364 optimal weight: 0.6980 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 173 GLN A 334 ASN B 443 ASN ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 HIS C 434 GLN E 120 ASN ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 ASN ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 240 GLN g 58 GLN ** g 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 97 ASN e 4 ASN e 56 GLN e 111 GLN I 133 GLN ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 145 ASN ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 34 GLN V 42 GLN ** X 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 39537 Z= 0.206 Angle : 0.640 10.275 53623 Z= 0.323 Chirality : 0.043 0.211 6417 Planarity : 0.005 0.056 6914 Dihedral : 7.745 157.248 5700 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.50 % Favored : 95.38 % Rotamer: Outliers : 0.07 % Allowed : 4.37 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.36 (0.11), residues: 5113 helix: -0.03 (0.09), residues: 2883 sheet: -1.95 (0.20), residues: 534 loop : -1.91 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP e 57 HIS 0.003 0.001 HIS g 228 PHE 0.031 0.001 PHE S 59 TYR 0.030 0.002 TYR I 100 ARG 0.008 0.000 ARG D 378 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 780 time to evaluate : 4.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7001 (mm-30) REVERT: B 321 GLU cc_start: 0.7556 (tt0) cc_final: 0.6660 (tt0) REVERT: C 321 GLU cc_start: 0.8496 (tm-30) cc_final: 0.7874 (tm-30) REVERT: C 498 MET cc_start: 0.6821 (tpp) cc_final: 0.5935 (ttp) REVERT: D 79 MET cc_start: 0.8173 (mmp) cc_final: 0.7794 (mmp) REVERT: D 305 GLU cc_start: 0.6088 (mt-10) cc_final: 0.5795 (mt-10) REVERT: D 333 ASP cc_start: 0.8671 (t0) cc_final: 0.8387 (t0) REVERT: E 273 ASP cc_start: 0.8545 (t70) cc_final: 0.8288 (t0) REVERT: E 313 ILE cc_start: 0.7992 (mt) cc_final: 0.7738 (mt) REVERT: F 311 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7204 (mm-30) REVERT: F 385 TYR cc_start: 0.7788 (t80) cc_final: 0.7513 (t80) REVERT: F 472 GLN cc_start: 0.7144 (mp10) cc_final: 0.6741 (tm-30) REVERT: d 167 ASP cc_start: 0.7864 (p0) cc_final: 0.7660 (p0) REVERT: g 121 MET cc_start: 0.6860 (ttm) cc_final: 0.6463 (ttm) REVERT: e 63 MET cc_start: 0.4877 (mmm) cc_final: 0.4507 (mmm) REVERT: e 110 ARG cc_start: 0.6542 (mtt180) cc_final: 0.6014 (mtp180) REVERT: I 105 ARG cc_start: 0.6208 (mtm-85) cc_final: 0.5147 (ttp80) REVERT: J 145 ASN cc_start: 0.4894 (OUTLIER) cc_final: 0.4494 (t0) REVERT: J 182 GLU cc_start: 0.4760 (mt-10) cc_final: 0.3713 (tp30) REVERT: a 117 TRP cc_start: 0.3250 (m-10) cc_final: 0.2452 (m-10) REVERT: a 186 LEU cc_start: 0.4596 (tp) cc_final: 0.3757 (tp) REVERT: O 68 LEU cc_start: 0.3384 (tp) cc_final: 0.3178 (tt) REVERT: P 68 LEU cc_start: 0.3579 (mp) cc_final: 0.3340 (mp) REVERT: S 60 MET cc_start: 0.3116 (tpp) cc_final: 0.1848 (tpp) REVERT: S 66 TYR cc_start: 0.5432 (m-10) cc_final: 0.5160 (m-80) REVERT: W 30 THR cc_start: 0.7232 (t) cc_final: 0.6822 (m) REVERT: X 46 GLU cc_start: 0.4560 (mt-10) cc_final: 0.4308 (mt-10) outliers start: 3 outliers final: 0 residues processed: 781 average time/residue: 0.4960 time to fit residues: 629.2949 Evaluate side-chains 567 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 566 time to evaluate : 4.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 449 optimal weight: 1.9990 chunk 341 optimal weight: 0.6980 chunk 236 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 217 optimal weight: 0.6980 chunk 305 optimal weight: 6.9990 chunk 456 optimal weight: 0.8980 chunk 483 optimal weight: 2.9990 chunk 238 optimal weight: 3.9990 chunk 432 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN B 273 GLN C 70 ASN ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 GLN C 423 GLN D 238 GLN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 266 GLN F 280 GLN d 240 GLN g 76 GLN e 4 ASN I 120 GLN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 62 GLN ** a 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 34 GLN Y 42 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 39537 Z= 0.211 Angle : 0.638 10.039 53623 Z= 0.320 Chirality : 0.043 0.242 6417 Planarity : 0.005 0.052 6914 Dihedral : 7.525 155.468 5700 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.65 % Favored : 95.23 % Rotamer: Outliers : 0.07 % Allowed : 4.25 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.08 (0.11), residues: 5113 helix: 0.18 (0.09), residues: 2870 sheet: -1.78 (0.20), residues: 559 loop : -1.76 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP a 117 HIS 0.004 0.001 HIS F 193 PHE 0.028 0.001 PHE A 390 TYR 0.038 0.002 TYR O 66 ARG 0.007 0.000 ARG D 429 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 739 time to evaluate : 4.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7569 (mt-10) cc_final: 0.6939 (mm-30) REVERT: B 182 ASP cc_start: 0.5673 (m-30) cc_final: 0.5206 (m-30) REVERT: B 321 GLU cc_start: 0.7598 (tt0) cc_final: 0.6678 (tt0) REVERT: C 248 GLU cc_start: 0.6925 (tt0) cc_final: 0.6676 (tt0) REVERT: C 251 MET cc_start: 0.8347 (ttp) cc_final: 0.8076 (ttm) REVERT: C 321 GLU cc_start: 0.8492 (tm-30) cc_final: 0.7885 (tm-30) REVERT: C 498 MET cc_start: 0.6780 (tpp) cc_final: 0.5878 (ttp) REVERT: D 79 MET cc_start: 0.8224 (mmp) cc_final: 0.7860 (mmp) REVERT: D 292 MET cc_start: 0.8145 (mtp) cc_final: 0.7922 (mtp) REVERT: D 333 ASP cc_start: 0.8686 (t0) cc_final: 0.8369 (t0) REVERT: E 273 ASP cc_start: 0.8545 (t70) cc_final: 0.8299 (t0) REVERT: F 254 LEU cc_start: 0.9085 (tp) cc_final: 0.8811 (tp) REVERT: F 472 GLN cc_start: 0.7156 (mp10) cc_final: 0.6780 (tm-30) REVERT: g 121 MET cc_start: 0.6964 (ttm) cc_final: 0.6498 (ttm) REVERT: g 284 PHE cc_start: 0.5124 (p90) cc_final: 0.4915 (p90) REVERT: e 63 MET cc_start: 0.4944 (mmm) cc_final: 0.4443 (mmm) REVERT: e 110 ARG cc_start: 0.6603 (mtt180) cc_final: 0.6028 (mtp180) REVERT: I 105 ARG cc_start: 0.6131 (mtm-85) cc_final: 0.5208 (ttp80) REVERT: I 160 LEU cc_start: 0.5841 (mt) cc_final: 0.5114 (pp) REVERT: J 182 GLU cc_start: 0.4621 (mt-10) cc_final: 0.3696 (tp30) REVERT: a 186 LEU cc_start: 0.4730 (tp) cc_final: 0.4178 (tp) REVERT: P 60 MET cc_start: 0.1185 (mmm) cc_final: -0.0025 (mtt) REVERT: P 68 LEU cc_start: 0.3708 (mp) cc_final: 0.3393 (mp) REVERT: S 60 MET cc_start: 0.3020 (tpp) cc_final: 0.2326 (tpp) REVERT: W 30 THR cc_start: 0.7054 (t) cc_final: 0.6718 (m) outliers start: 3 outliers final: 0 residues processed: 740 average time/residue: 0.5057 time to fit residues: 613.6748 Evaluate side-chains 557 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 557 time to evaluate : 4.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 402 optimal weight: 6.9990 chunk 274 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 359 optimal weight: 1.9990 chunk 199 optimal weight: 7.9990 chunk 412 optimal weight: 0.6980 chunk 334 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 246 optimal weight: 0.3980 chunk 433 optimal weight: 6.9990 chunk 121 optimal weight: 0.0670 overall best weight: 1.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 ASN ** D 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 4 ASN e 56 GLN I 133 GLN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 39537 Z= 0.266 Angle : 0.663 10.677 53623 Z= 0.332 Chirality : 0.044 0.331 6417 Planarity : 0.005 0.053 6914 Dihedral : 7.482 158.609 5700 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.18 % Favored : 94.72 % Rotamer: Outliers : 0.05 % Allowed : 2.94 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.01 (0.11), residues: 5113 helix: 0.19 (0.09), residues: 2871 sheet: -1.66 (0.21), residues: 548 loop : -1.67 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP a 44 HIS 0.005 0.001 HIS d 141 PHE 0.027 0.002 PHE a 222 TYR 0.030 0.002 TYR A 330 ARG 0.008 0.000 ARG C 216 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 716 time to evaluate : 4.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.6673 (pmt170) cc_final: 0.5358 (ttp80) REVERT: B 269 GLN cc_start: 0.7121 (mt0) cc_final: 0.6818 (mt0) REVERT: B 436 MET cc_start: 0.6815 (ttm) cc_final: 0.6572 (tmm) REVERT: C 251 MET cc_start: 0.8445 (ttp) cc_final: 0.8152 (ttm) REVERT: C 321 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8119 (tm-30) REVERT: C 498 MET cc_start: 0.6809 (tpp) cc_final: 0.5955 (ttp) REVERT: D 79 MET cc_start: 0.8241 (mmp) cc_final: 0.7901 (mmp) REVERT: D 306 MET cc_start: 0.8163 (tpt) cc_final: 0.7954 (mmm) REVERT: D 333 ASP cc_start: 0.8675 (t0) cc_final: 0.8315 (t0) REVERT: E 273 ASP cc_start: 0.8530 (t70) cc_final: 0.8251 (t0) REVERT: E 313 ILE cc_start: 0.7979 (mt) cc_final: 0.7765 (mt) REVERT: E 335 THR cc_start: 0.7520 (p) cc_final: 0.7306 (p) REVERT: E 490 LEU cc_start: 0.8108 (pp) cc_final: 0.7389 (tt) REVERT: F 33 VAL cc_start: 0.8706 (p) cc_final: 0.8440 (m) REVERT: F 254 LEU cc_start: 0.9145 (tp) cc_final: 0.8865 (tp) REVERT: d 238 LYS cc_start: 0.6287 (tptt) cc_final: 0.5826 (mtpt) REVERT: g 121 MET cc_start: 0.6825 (ttm) cc_final: 0.6354 (ttm) REVERT: g 284 PHE cc_start: 0.5318 (p90) cc_final: 0.5026 (p90) REVERT: g 286 GLN cc_start: 0.7232 (tt0) cc_final: 0.6898 (tt0) REVERT: e 63 MET cc_start: 0.5052 (mmm) cc_final: 0.4577 (mmm) REVERT: e 110 ARG cc_start: 0.6635 (mtt180) cc_final: 0.6045 (mtp180) REVERT: I 56 ARG cc_start: 0.2625 (ttp80) cc_final: 0.2325 (ttp-110) REVERT: I 104 GLU cc_start: 0.7503 (pt0) cc_final: 0.7237 (pt0) REVERT: I 105 ARG cc_start: 0.6174 (mtm-85) cc_final: 0.5242 (ttp80) REVERT: I 160 LEU cc_start: 0.5940 (mt) cc_final: 0.5232 (pp) REVERT: J 182 GLU cc_start: 0.4790 (mt-10) cc_final: 0.3753 (tp30) REVERT: a 186 LEU cc_start: 0.4524 (tp) cc_final: 0.4271 (tp) REVERT: O 60 MET cc_start: 0.1984 (mmm) cc_final: 0.1767 (mmt) REVERT: P 60 MET cc_start: 0.1058 (mmm) cc_final: 0.0032 (mtt) REVERT: S 60 MET cc_start: 0.3050 (tpp) cc_final: 0.2565 (tpp) REVERT: W 30 THR cc_start: 0.7018 (t) cc_final: 0.6749 (m) REVERT: X 44 GLU cc_start: 0.4674 (pm20) cc_final: 0.4260 (pm20) REVERT: X 60 MET cc_start: 0.5493 (tpp) cc_final: 0.5250 (tpp) outliers start: 2 outliers final: 2 residues processed: 718 average time/residue: 0.5171 time to fit residues: 615.6300 Evaluate side-chains 551 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 549 time to evaluate : 4.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 162 optimal weight: 0.8980 chunk 435 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 283 optimal weight: 6.9990 chunk 119 optimal weight: 0.6980 chunk 483 optimal weight: 2.9990 chunk 401 optimal weight: 6.9990 chunk 223 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 253 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN C 351 ASN ** D 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 GLN E 60 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 GLN ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 396 GLN e 4 ASN ** I 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 39537 Z= 0.242 Angle : 0.652 10.056 53623 Z= 0.325 Chirality : 0.044 0.279 6417 Planarity : 0.005 0.053 6914 Dihedral : 7.429 162.699 5700 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.30 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.92 (0.12), residues: 5113 helix: 0.25 (0.10), residues: 2868 sheet: -1.62 (0.21), residues: 555 loop : -1.60 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP e 57 HIS 0.003 0.001 HIS d 141 PHE 0.032 0.002 PHE A 390 TYR 0.023 0.002 TYR A 330 ARG 0.009 0.000 ARG A 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10226 Ramachandran restraints generated. 5113 Oldfield, 0 Emsley, 5113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 703 time to evaluate : 3.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.6662 (pmt170) cc_final: 0.5456 (ttp80) REVERT: A 334 ASN cc_start: 0.8159 (m-40) cc_final: 0.7471 (m110) REVERT: B 138 MET cc_start: 0.6529 (tpp) cc_final: 0.6292 (tpp) REVERT: B 269 GLN cc_start: 0.7153 (mt0) cc_final: 0.6737 (mt0) REVERT: B 436 MET cc_start: 0.6900 (ttm) cc_final: 0.6653 (tmm) REVERT: C 57 GLU cc_start: 0.7194 (pm20) cc_final: 0.6956 (pm20) REVERT: C 251 MET cc_start: 0.8480 (ttp) cc_final: 0.8160 (ttm) REVERT: C 321 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8041 (tm-30) REVERT: C 498 MET cc_start: 0.6901 (tpp) cc_final: 0.5980 (ttp) REVERT: D 79 MET cc_start: 0.8218 (mmp) cc_final: 0.7879 (mmp) REVERT: D 333 ASP cc_start: 0.8688 (t0) cc_final: 0.8312 (t0) REVERT: E 273 ASP cc_start: 0.8487 (t70) cc_final: 0.8174 (t0) REVERT: E 335 THR cc_start: 0.7565 (p) cc_final: 0.7327 (p) REVERT: E 490 LEU cc_start: 0.8075 (pp) cc_final: 0.7285 (tt) REVERT: F 254 LEU cc_start: 0.9123 (tp) cc_final: 0.8873 (tp) REVERT: g 121 MET cc_start: 0.6841 (ttm) cc_final: 0.6438 (ttm) REVERT: g 284 PHE cc_start: 0.5289 (p90) cc_final: 0.5052 (p90) REVERT: g 286 GLN cc_start: 0.7171 (tt0) cc_final: 0.6847 (tt0) REVERT: e 63 MET cc_start: 0.5125 (mmm) cc_final: 0.4665 (mmm) REVERT: e 110 ARG cc_start: 0.6631 (mtt180) cc_final: 0.6165 (mtp180) REVERT: I 56 ARG cc_start: 0.2638 (ttp80) cc_final: 0.2304 (ttp-170) REVERT: I 104 GLU cc_start: 0.7570 (pt0) cc_final: 0.7311 (pt0) REVERT: I 105 ARG cc_start: 0.6097 (mtm-85) cc_final: 0.5230 (ttp80) REVERT: I 160 LEU cc_start: 0.5723 (mt) cc_final: 0.5154 (pp) REVERT: J 182 GLU cc_start: 0.4898 (mt-10) cc_final: 0.3885 (tp30) REVERT: a 186 LEU cc_start: 0.4664 (tp) cc_final: 0.4036 (tp) REVERT: N 4 LEU cc_start: 0.4969 (tp) cc_final: 0.4573 (mp) REVERT: P 60 MET cc_start: 0.1024 (mmm) cc_final: -0.0090 (mtt) REVERT: S 63 LEU cc_start: 0.3249 (mm) cc_final: 0.2958 (tp) REVERT: W 30 THR cc_start: 0.7152 (t) cc_final: 0.6840 (m) outliers start: 0 outliers final: 0 residues processed: 703 average time/residue: 0.4896 time to fit residues: 564.1760 Evaluate side-chains 556 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 556 time to evaluate : 4.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.6682 > 50: distance: 82 - 87: 7.436 distance: 88 - 89: 10.853 distance: 89 - 90: 7.526 distance: 89 - 98: 3.768 distance: 90 - 127: 16.026 distance: 92 - 94: 9.068 distance: 93 - 95: 10.477 distance: 94 - 96: 5.642 distance: 95 - 97: 9.082 distance: 96 - 97: 6.472 distance: 98 - 99: 9.034 distance: 99 - 100: 12.709 distance: 99 - 102: 11.729 distance: 100 - 101: 11.656 distance: 100 - 109: 3.640 distance: 101 - 136: 23.293 distance: 102 - 103: 15.083 distance: 103 - 104: 10.566 distance: 104 - 105: 9.268 distance: 105 - 106: 19.824 distance: 106 - 107: 16.757 distance: 106 - 108: 10.190 distance: 110 - 111: 7.065 distance: 110 - 113: 10.855 distance: 111 - 112: 9.819 distance: 111 - 120: 9.253 distance: 112 - 141: 23.126 distance: 113 - 114: 5.928 distance: 114 - 115: 6.053 distance: 114 - 116: 15.459 distance: 115 - 117: 9.016 distance: 116 - 118: 5.386 distance: 117 - 119: 8.379 distance: 118 - 119: 17.358 distance: 120 - 121: 9.869 distance: 121 - 122: 8.420 distance: 121 - 124: 7.644 distance: 122 - 123: 6.630 distance: 122 - 127: 6.053 distance: 123 - 145: 26.286 distance: 124 - 125: 24.788 distance: 124 - 126: 18.483 distance: 127 - 128: 11.993 distance: 128 - 129: 16.296 distance: 128 - 131: 10.116 distance: 129 - 130: 26.091 distance: 129 - 136: 11.384 distance: 130 - 151: 11.612 distance: 131 - 132: 17.847 distance: 132 - 133: 7.543 distance: 133 - 134: 13.009 distance: 133 - 135: 9.466 distance: 136 - 137: 8.970 distance: 137 - 138: 4.346 distance: 137 - 140: 8.371 distance: 138 - 139: 10.894 distance: 138 - 141: 3.246 distance: 139 - 160: 35.330 distance: 141 - 142: 13.170 distance: 142 - 143: 16.183 distance: 143 - 144: 10.015 distance: 143 - 145: 16.045 distance: 144 - 167: 14.102 distance: 145 - 146: 9.611 distance: 146 - 147: 18.259 distance: 146 - 149: 9.034 distance: 147 - 148: 25.843 distance: 147 - 151: 28.129 distance: 149 - 150: 9.752 distance: 151 - 152: 21.862 distance: 152 - 153: 25.226 distance: 152 - 155: 17.640 distance: 153 - 154: 7.538 distance: 153 - 160: 39.972 distance: 155 - 156: 22.974 distance: 156 - 157: 15.439 distance: 157 - 158: 13.419 distance: 157 - 159: 12.952 distance: 160 - 161: 22.805 distance: 161 - 162: 29.180 distance: 161 - 164: 15.793 distance: 162 - 163: 22.923 distance: 162 - 167: 8.643 distance: 163 - 183: 32.383 distance: 164 - 165: 15.949 distance: 164 - 166: 15.222