Starting phenix.real_space_refine on Fri Aug 9 23:06:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voi_21265/08_2024/6voi_21265.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voi_21265/08_2024/6voi_21265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voi_21265/08_2024/6voi_21265.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voi_21265/08_2024/6voi_21265.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voi_21265/08_2024/6voi_21265.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voi_21265/08_2024/6voi_21265.cif" } resolution = 4.03 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= 0.003 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 14 5.49 5 S 105 5.16 5 C 17265 2.51 5 N 4745 2.21 5 O 5368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 14": "NH1" <-> "NH2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 366": "NH1" <-> "NH2" Residue "A PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 402": "OD1" <-> "OD2" Residue "A ARG 413": "NH1" <-> "NH2" Residue "A ASP 447": "OD1" <-> "OD2" Residue "A TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 16": "NH1" <-> "NH2" Residue "C TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 46": "OD1" <-> "OD2" Residue "C GLU 52": "OE1" <-> "OE2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C ARG 94": "NH1" <-> "NH2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C ARG 141": "NH1" <-> "NH2" Residue "C ASP 171": "OD1" <-> "OD2" Residue "C ARG 172": "NH1" <-> "NH2" Residue "C ASP 182": "OD1" <-> "OD2" Residue "C TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "C ASP 230": "OD1" <-> "OD2" Residue "C TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 279": "NH1" <-> "NH2" Residue "C GLU 300": "OE1" <-> "OE2" Residue "C ARG 301": "NH1" <-> "NH2" Residue "C PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 404": "OD1" <-> "OD2" Residue "C ARG 416": "NH1" <-> "NH2" Residue "C ASP 447": "OD1" <-> "OD2" Residue "C ASP 452": "OD1" <-> "OD2" Residue "C ARG 462": "NH1" <-> "NH2" Residue "C TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 484": "OE1" <-> "OE2" Residue "C GLU 496": "OE1" <-> "OE2" Residue "B ARG 5": "NH1" <-> "NH2" Residue "B ASP 7": "OD1" <-> "OD2" Residue "B GLU 8": "OE1" <-> "OE2" Residue "B ARG 22": "NH1" <-> "NH2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ARG 172": "NH1" <-> "NH2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 230": "OD1" <-> "OD2" Residue "B TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 366": "NH1" <-> "NH2" Residue "B GLU 386": "OE1" <-> "OE2" Residue "B GLU 394": "OE1" <-> "OE2" Residue "B TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 455": "NH1" <-> "NH2" Residue "B TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 485": "OE1" <-> "OE2" Residue "D ASP 32": "OD1" <-> "OD2" Residue "D ARG 52": "NH1" <-> "NH2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D ASP 83": "OD1" <-> "OD2" Residue "D ARG 87": "NH1" <-> "NH2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 157": "OD1" <-> "OD2" Residue "D ARG 163": "NH1" <-> "NH2" Residue "D PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 207": "NH1" <-> "NH2" Residue "D GLU 229": "OE1" <-> "OE2" Residue "D TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 284": "OE1" <-> "OE2" Residue "D GLU 311": "OE1" <-> "OE2" Residue "D ASP 333": "OD1" <-> "OD2" Residue "D TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 369": "OD1" <-> "OD2" Residue "D ARG 397": "NH1" <-> "NH2" Residue "D TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 465": "OE1" <-> "OE2" Residue "D ASP 467": "OD1" <-> "OD2" Residue "D GLU 471": "OE1" <-> "OE2" Residue "E GLU 16": "OE1" <-> "OE2" Residue "E ASP 32": "OD1" <-> "OD2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E GLU 64": "OE1" <-> "OE2" Residue "E ASP 83": "OD1" <-> "OD2" Residue "E ASP 93": "OD1" <-> "OD2" Residue "E GLU 150": "OE1" <-> "OE2" Residue "E ASP 211": "OD1" <-> "OD2" Residue "E ARG 246": "NH1" <-> "NH2" Residue "E ARG 277": "NH1" <-> "NH2" Residue "E PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 311": "OE1" <-> "OE2" Residue "E ASP 347": "OD1" <-> "OD2" Residue "E ASP 403": "OD1" <-> "OD2" Residue "E GLU 415": "OE1" <-> "OE2" Residue "E GLU 416": "OE1" <-> "OE2" Residue "E ARG 423": "NH1" <-> "NH2" Residue "E TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 453": "OE1" <-> "OE2" Residue "E ASP 467": "OD1" <-> "OD2" Residue "E PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 481": "OD1" <-> "OD2" Residue "F ARG 52": "NH1" <-> "NH2" Residue "F ARG 87": "NH1" <-> "NH2" Residue "F PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 164": "NH1" <-> "NH2" Residue "F GLU 184": "OE1" <-> "OE2" Residue "F PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 204": "OE1" <-> "OE2" Residue "F GLU 229": "OE1" <-> "OE2" Residue "F GLU 241": "OE1" <-> "OE2" Residue "F TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 273": "OD1" <-> "OD2" Residue "F TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 305": "OE1" <-> "OE2" Residue "F ASP 333": "OD1" <-> "OD2" Residue "F ASP 347": "OD1" <-> "OD2" Residue "F ASP 369": "OD1" <-> "OD2" Residue "F GLU 400": "OE1" <-> "OE2" Residue "F GLU 416": "OE1" <-> "OE2" Residue "F ARG 425": "NH1" <-> "NH2" Residue "F PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 77": "NH1" <-> "NH2" Residue "d TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 87": "OD1" <-> "OD2" Residue "d GLU 108": "OE1" <-> "OE2" Residue "d PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 208": "NH1" <-> "NH2" Residue "g ARG 48": "NH1" <-> "NH2" Residue "g ARG 73": "NH1" <-> "NH2" Residue "g ARG 83": "NH1" <-> "NH2" Residue "g PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 91": "OE1" <-> "OE2" Residue "g ASP 106": "OD1" <-> "OD2" Residue "g ARG 127": "NH1" <-> "NH2" Residue "g ARG 144": "NH1" <-> "NH2" Residue "g ASP 154": "OD1" <-> "OD2" Residue "g ARG 170": "NH1" <-> "NH2" Residue "g ARG 171": "NH1" <-> "NH2" Residue "g TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 208": "OD1" <-> "OD2" Residue "g GLU 283": "OE1" <-> "OE2" Residue "g ASP 293": "OD1" <-> "OD2" Residue "g TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 306": "NH1" <-> "NH2" Residue "e ARG 12": "NH1" <-> "NH2" Residue "e ARG 50": "NH1" <-> "NH2" Residue "e PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 68": "NH1" <-> "NH2" Residue "e ASP 80": "OD1" <-> "OD2" Residue "e ASP 86": "OD1" <-> "OD2" Residue "e GLU 100": "OE1" <-> "OE2" Residue "e ARG 104": "NH1" <-> "NH2" Residue "e ARG 110": "NH1" <-> "NH2" Residue "e ARG 120": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 27497 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3850 Classifications: {'peptide': 501} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 483} Chain: "C" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3843 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 482} Chain: "B" Number of atoms: 3854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3854 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 17, 'TRANS': 484} Chain: "D" Number of atoms: 3619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3619 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 452} Chain: "E" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3645 Classifications: {'peptide': 481} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 455} Chain: "F" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3636 Classifications: {'peptide': 480} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 454} Chain: "d" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1384 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 4, 'TRANS': 174} Chain: "g" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2508 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 12, 'TRANS': 310} Chain: "e" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1007 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 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: "C" 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: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.14, per 1000 atoms: 0.62 Number of scatterers: 27497 At special positions: 0 Unit cell: (131.04, 145.6, 137.28, 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 105 16.00 P 14 15.00 O 5368 8.00 N 4745 7.00 C 17265 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS g 240 " - pdb=" SG CYS g 246 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.13 Conformation dependent library (CDL) restraints added in 5.0 seconds 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6572 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 32 sheets defined 46.3% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.98 Creating SS restraints... Processing helix chain 'A' and resid 10 through 25 Processing helix chain 'A' and resid 151 through 157 removed outlier: 3.766A pdb=" N MET A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 187 removed outlier: 4.026A pdb=" N GLN A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 232 through 253 removed outlier: 3.539A pdb=" N GLN A 236 " --> pdb=" O PRO A 232 " (cutoff:3.500A) Proline residue: A 240 - end of helix removed outlier: 3.821A pdb=" N PHE A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 278 removed outlier: 3.540A pdb=" N GLN A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 290 through 300 removed outlier: 3.655A pdb=" N LEU A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 339 removed outlier: 3.586A pdb=" N THR A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 338 " --> pdb=" O ASN A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 351 removed outlier: 3.503A pdb=" N PHE A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.786A pdb=" N ALA A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 371 " --> pdb=" O GLY A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 380 Processing helix chain 'A' and resid 382 through 398 removed outlier: 3.859A pdb=" N GLU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 419 removed outlier: 3.916A pdb=" N ALA A 412 " --> pdb=" O GLN A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 443 removed outlier: 4.220A pdb=" N THR A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 449 removed outlier: 4.561A pdb=" N LEU A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 468 removed outlier: 4.465A pdb=" N TYR A 457 " --> pdb=" O GLN A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 479 removed outlier: 3.793A pdb=" N GLU A 474 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 505 removed outlier: 3.881A pdb=" N ALA A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 489 " --> pdb=" O GLU A 485 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 20 removed outlier: 3.623A pdb=" N ILE C 13 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU C 15 " --> pdb=" O LYS C 11 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG C 16 " --> pdb=" O ILE C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 105 removed outlier: 3.733A pdb=" N TYR C 104 " --> pdb=" O SER C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 187 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 218 through 222 removed outlier: 3.891A pdb=" N TYR C 221 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR C 222 " --> pdb=" O MET C 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 218 through 222' Processing helix chain 'C' and resid 232 through 253 Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 263 through 278 Processing helix chain 'C' and resid 283 through 287 removed outlier: 3.506A pdb=" N ALA C 286 " --> pdb=" O GLY C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 300 Processing helix chain 'C' and resid 329 through 339 Processing helix chain 'C' and resid 346 through 352 Processing helix chain 'C' and resid 367 through 371 removed outlier: 3.978A pdb=" N ALA C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 393 removed outlier: 4.386A pdb=" N GLY C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS C 382 " --> pdb=" O LYS C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 422 removed outlier: 3.732A pdb=" N GLU C 419 " --> pdb=" O GLN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 443 removed outlier: 4.200A pdb=" N MET C 436 " --> pdb=" O GLU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 469 Processing helix chain 'C' and resid 470 through 479 Processing helix chain 'C' and resid 483 through 503 Processing helix chain 'B' and resid 9 through 19 removed outlier: 4.344A pdb=" N GLY B 19 " --> pdb=" O GLU B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 176 through 186 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 218 through 221 Processing helix chain 'B' and resid 232 through 252 Proline residue: B 240 - end of helix removed outlier: 3.938A pdb=" N PHE B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 277 Processing helix chain 'B' and resid 283 through 287 removed outlier: 3.591A pdb=" N ALA B 286 " --> pdb=" O GLY B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 300 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'B' and resid 346 through 353 removed outlier: 3.600A pdb=" N PHE B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 removed outlier: 3.622A pdb=" N ALA B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 396 removed outlier: 4.536A pdb=" N VAL B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 421 Processing helix chain 'B' and resid 430 through 443 removed outlier: 3.840A pdb=" N GLY B 441 " --> pdb=" O THR B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 452 No H-bonds generated for 'chain 'B' and resid 450 through 452' Processing helix chain 'B' and resid 453 through 469 removed outlier: 4.299A pdb=" N GLU B 460 " --> pdb=" O LYS B 456 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS B 466 " --> pdb=" O ARG B 462 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR B 467 " --> pdb=" O THR B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 479 removed outlier: 4.242A pdb=" N GLN B 473 " --> pdb=" O LYS B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 503 Processing helix chain 'D' and resid 153 through 159 Processing helix chain 'D' and resid 179 through 189 Processing helix chain 'D' and resid 205 through 219 Processing helix chain 'D' and resid 227 through 231 removed outlier: 4.310A pdb=" N LYS D 231 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 264 removed outlier: 3.875A pdb=" N PHE D 260 " --> pdb=" O MET D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 289 removed outlier: 3.587A pdb=" N PHE D 278 " --> pdb=" O ASN D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 311 Processing helix chain 'D' and resid 329 through 333 removed outlier: 3.891A pdb=" N ASP D 332 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP D 333 " --> pdb=" O PRO D 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 329 through 333' Processing helix chain 'D' and resid 336 through 344 removed outlier: 4.164A pdb=" N THR D 342 " --> pdb=" O ALA D 338 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA D 344 " --> pdb=" O ALA D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 359 removed outlier: 4.155A pdb=" N ALA D 357 " --> pdb=" O SER D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 401 removed outlier: 3.523A pdb=" N VAL D 380 " --> pdb=" O GLN D 376 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLU D 382 " --> pdb=" O ARG D 378 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N GLU D 383 " --> pdb=" O ILE D 379 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N HIS D 384 " --> pdb=" O VAL D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 406 Processing helix chain 'D' and resid 409 through 413 removed outlier: 3.547A pdb=" N LEU D 413 " --> pdb=" O LEU D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 431 Processing helix chain 'D' and resid 450 through 463 removed outlier: 4.186A pdb=" N ARG D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 475 removed outlier: 4.130A pdb=" N PHE D 474 " --> pdb=" O PRO D 470 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR D 475 " --> pdb=" O GLU D 471 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 470 through 475' Processing helix chain 'D' and resid 479 through 494 Processing helix chain 'E' and resid 153 through 159 Processing helix chain 'E' and resid 177 through 192 Processing helix chain 'E' and resid 205 through 219 Processing helix chain 'E' and resid 242 through 265 removed outlier: 3.520A pdb=" N ARG E 248 " --> pdb=" O GLY E 244 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLY E 250 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU E 251 " --> pdb=" O MET E 247 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE E 260 " --> pdb=" O MET E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 290 removed outlier: 3.960A pdb=" N PHE E 278 " --> pdb=" O ASN E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 311 Processing helix chain 'E' and resid 329 through 333 removed outlier: 3.703A pdb=" N ASP E 332 " --> pdb=" O VAL E 329 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP E 333 " --> pdb=" O PRO E 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 329 through 333' Processing helix chain 'E' and resid 336 through 344 Processing helix chain 'E' and resid 353 through 360 Processing helix chain 'E' and resid 376 through 381 Processing helix chain 'E' and resid 381 through 402 Processing helix chain 'E' and resid 408 through 413 removed outlier: 4.118A pdb=" N GLU E 412 " --> pdb=" O LEU E 408 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU E 413 " --> pdb=" O GLY E 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 408 through 413' Processing helix chain 'E' and resid 417 through 431 Processing helix chain 'E' and resid 450 through 464 removed outlier: 3.771A pdb=" N GLY E 464 " --> pdb=" O LEU E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 474 Processing helix chain 'E' and resid 479 through 495 removed outlier: 4.246A pdb=" N LYS E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 159 Processing helix chain 'F' and resid 179 through 193 removed outlier: 4.988A pdb=" N LYS F 191 " --> pdb=" O ASN F 187 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA F 192 " --> pdb=" O ASN F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 219 Processing helix chain 'F' and resid 226 through 230 removed outlier: 3.784A pdb=" N SER F 230 " --> pdb=" O ILE F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 247 removed outlier: 3.540A pdb=" N ARG F 246 " --> pdb=" O PRO F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 263 Processing helix chain 'F' and resid 276 through 290 removed outlier: 4.065A pdb=" N GLY F 282 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY F 290 " --> pdb=" O SER F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 311 Processing helix chain 'F' and resid 329 through 333 Processing helix chain 'F' and resid 336 through 341 Processing helix chain 'F' and resid 341 through 346 removed outlier: 4.025A pdb=" N HIS F 345 " --> pdb=" O THR F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 359 removed outlier: 4.116A pdb=" N LYS F 359 " --> pdb=" O GLY F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'F' and resid 381 through 409 removed outlier: 4.750A pdb=" N ASP F 403 " --> pdb=" O LYS F 399 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE F 404 " --> pdb=" O GLU F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 413 removed outlier: 4.070A pdb=" N LEU F 413 " --> pdb=" O LEU F 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 410 through 413' Processing helix chain 'F' and resid 416 through 431 Processing helix chain 'F' and resid 438 through 443 Processing helix chain 'F' and resid 450 through 463 removed outlier: 3.565A pdb=" N LEU F 460 " --> pdb=" O ARG F 456 " (cutoff:3.500A) Processing helix chain 'F' and resid 470 through 475 Processing helix chain 'F' and resid 479 through 496 removed outlier: 3.776A pdb=" N LYS F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Processing helix chain 'd' and resid 73 through 89 Processing helix chain 'd' and resid 91 through 107 Processing helix chain 'd' and resid 108 through 116 removed outlier: 4.211A pdb=" N TYR d 112 " --> pdb=" O GLU d 108 " (cutoff:3.500A) Processing helix chain 'd' and resid 121 through 137 Processing helix chain 'd' and resid 139 through 152 Processing helix chain 'd' and resid 154 through 156 No H-bonds generated for 'chain 'd' and resid 154 through 156' Processing helix chain 'd' and resid 157 through 174 removed outlier: 4.033A pdb=" N GLU d 166 " --> pdb=" O LEU d 162 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASP d 167 " --> pdb=" O ASN d 163 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 203 Processing helix chain 'd' and resid 236 through 249 removed outlier: 4.279A pdb=" N GLN d 240 " --> pdb=" O SER d 236 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU d 249 " --> pdb=" O ALA d 245 " (cutoff:3.500A) Processing helix chain 'g' and resid 43 through 100 Proline residue: g 84 - end of helix removed outlier: 3.691A pdb=" N TYR g 94 " --> pdb=" O VAL g 90 " (cutoff:3.500A) Processing helix chain 'g' and resid 107 through 111 removed outlier: 3.953A pdb=" N LYS g 111 " --> pdb=" O PRO g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 151 removed outlier: 4.042A pdb=" N MET g 136 " --> pdb=" O GLY g 132 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU g 151 " --> pdb=" O GLU g 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 161 through 169 Processing helix chain 'g' and resid 187 through 204 removed outlier: 3.693A pdb=" N SER g 204 " --> pdb=" O SER g 200 " (cutoff:3.500A) Processing helix chain 'g' and resid 287 through 362 removed outlier: 3.715A pdb=" N ILE g 291 " --> pdb=" O ASP g 287 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU g 292 " --> pdb=" O PRO g 288 " (cutoff:3.500A) Proline residue: g 297 - end of helix removed outlier: 3.736A pdb=" N SER g 311 " --> pdb=" O ALA g 307 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN g 361 " --> pdb=" O VAL g 357 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA g 362 " --> pdb=" O ALA g 358 " (cutoff:3.500A) Processing helix chain 'e' and resid 88 through 104 removed outlier: 4.032A pdb=" N ARG e 104 " --> pdb=" O GLU e 100 " (cutoff:3.500A) Processing helix chain 'e' and resid 107 through 131 removed outlier: 3.909A pdb=" N ILE e 113 " --> pdb=" O LYS e 109 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU e 114 " --> pdb=" O ARG e 110 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU e 127 " --> pdb=" O ARG e 123 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ALA e 128 " --> pdb=" O THR e 124 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER e 129 " --> pdb=" O ARG e 125 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN e 130 " --> pdb=" O VAL e 126 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR e 131 " --> pdb=" O GLU e 127 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 5.958A pdb=" N VAL A 32 " --> pdb=" O HIS A 43 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N HIS A 43 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ASN A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LEU A 67 " --> pdb=" O ASN A 71 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLY A 73 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 55 removed outlier: 7.380A pdb=" N LEU A 53 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 167 Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 227 removed outlier: 7.415A pdb=" N GLU A 227 " --> pdb=" O TYR A 196 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ALA A 198 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 29 through 35 removed outlier: 6.655A pdb=" N ARG C 41 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 97 through 100 removed outlier: 4.084A pdb=" N GLU C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 319 through 321 removed outlier: 3.547A pdb=" N GLY C 170 " --> pdb=" O VAL C 320 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 193 through 196 removed outlier: 6.231A pdb=" N ILE C 193 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ILE C 260 " --> pdb=" O ILE C 193 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL C 195 " --> pdb=" O ILE C 260 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 198 through 199 removed outlier: 6.519A pdb=" N ALA C 198 " --> pdb=" O GLU C 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 62 through 67 removed outlier: 4.239A pdb=" N GLU B 52 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LEU B 53 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR B 31 " --> pdb=" O HIS B 43 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ASN B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU B 67 " --> pdb=" O ASN B 71 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N GLY B 73 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU B 65 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE D 92 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ALA D 46 " --> pdb=" O THR D 94 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASN D 45 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL D 61 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N VAL D 65 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL D 77 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN D 67 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ALA D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ILE D 23 " --> pdb=" O ALA D 34 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 97 through 98 removed outlier: 4.053A pdb=" N ARG B 128 " --> pdb=" O ILE B 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 108 through 109 removed outlier: 5.759A pdb=" N ILE B 109 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N THR B 228 " --> pdb=" O ILE B 109 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL B 225 " --> pdb=" O CYS B 194 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TYR B 196 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLU B 227 " --> pdb=" O TYR B 196 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ALA B 198 " --> pdb=" O GLU B 227 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE B 193 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE B 260 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL B 195 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ASP B 262 " --> pdb=" O VAL B 195 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL B 197 " --> pdb=" O ASP B 262 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR B 315 " --> pdb=" O THR B 257 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 341 through 342 Processing sheet with id=AB5, first strand: chain 'D' and resid 99 through 101 Processing sheet with id=AB6, first strand: chain 'E' and resid 25 through 27 removed outlier: 6.660A pdb=" N VAL E 77 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N VAL E 65 " --> pdb=" O VAL E 77 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 99 through 100 Processing sheet with id=AB8, first strand: chain 'E' and resid 148 through 149 removed outlier: 4.383A pdb=" N TYR E 162 " --> pdb=" O PHE E 149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AC1, first strand: chain 'E' and resid 197 through 200 Processing sheet with id=AC2, first strand: chain 'E' and resid 202 through 204 removed outlier: 6.640A pdb=" N GLY E 237 " --> pdb=" O VAL E 202 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 23 through 27 removed outlier: 5.928A pdb=" N ILE F 23 " --> pdb=" O ALA F 34 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ALA F 34 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ARG F 73 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU F 68 " --> pdb=" O ARG F 73 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ARG F 75 " --> pdb=" O GLN F 66 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 100 through 101 Processing sheet with id=AC5, first strand: chain 'F' and resid 148 through 149 removed outlier: 4.324A pdb=" N TYR F 162 " --> pdb=" O PHE F 149 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 269 through 273 removed outlier: 7.144A pdb=" N LEU F 270 " --> pdb=" O ILE F 324 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ALA F 326 " --> pdb=" O LEU F 270 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE F 272 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LYS F 167 " --> pdb=" O ALA F 348 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N THR F 350 " --> pdb=" O LYS F 167 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLY F 169 " --> pdb=" O THR F 350 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU F 352 " --> pdb=" O GLY F 169 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE F 171 " --> pdb=" O LEU F 352 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 200 through 202 Processing sheet with id=AC8, first strand: chain 'd' and resid 177 through 178 Processing sheet with id=AC9, first strand: chain 'd' and resid 212 through 213 removed outlier: 6.572A pdb=" N VAL d 180 " --> pdb=" O VAL d 212 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'g' and resid 156 through 159 removed outlier: 3.581A pdb=" N ILE g 158 " --> pdb=" O LEU g 120 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ALA g 119 " --> pdb=" O GLU g 211 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU g 213 " --> pdb=" O ALA g 119 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N MET g 121 " --> pdb=" O LEU g 213 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL g 226 " --> pdb=" O TYR g 214 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'g' and resid 254 through 259 removed outlier: 3.555A pdb=" N THR g 265 " --> pdb=" O THR g 258 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'e' and resid 12 through 19 removed outlier: 7.104A pdb=" N VAL e 7 " --> pdb=" O ILE e 14 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ASN e 16 " --> pdb=" O LEU e 5 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU e 5 " --> pdb=" O ASN e 16 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU e 18 " --> pdb=" O LEU e 3 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LEU e 3 " --> pdb=" O GLU e 18 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE e 74 " --> pdb=" O ASN e 4 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'e' and resid 21 through 23 removed outlier: 3.565A pdb=" N GLU e 21 " --> pdb=" O ARG e 52 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG e 50 " --> pdb=" O ILE e 23 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'e' and resid 47 through 48 removed outlier: 3.909A pdb=" N GLY e 47 " --> pdb=" O LEU e 62 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU e 62 " --> pdb=" O GLY e 47 " (cutoff:3.500A) 1206 hydrogen bonds defined for protein. 3486 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.95 Time building geometry restraints manager: 12.18 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: 9313 1.34 - 1.46: 5491 1.46 - 1.58: 12854 1.58 - 1.71: 23 1.71 - 1.83: 198 Bond restraints: 27879 Sorted by residual: bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.04e+01 bond pdb=" C4 ATP D 601 " pdb=" C5 ATP D 601 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.91e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.65e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.14e+01 bond pdb=" C5 ATP D 601 " pdb=" C6 ATP D 601 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.26e+01 ... (remaining 27874 not shown) Histogram of bond angle deviations from ideal: 97.03 - 104.85: 526 104.85 - 112.67: 14990 112.67 - 120.49: 11971 120.49 - 128.31: 10212 128.31 - 136.13: 82 Bond angle restraints: 37781 Sorted by residual: angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 117.30 22.57 1.00e+00 1.00e+00 5.09e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 118.15 21.72 1.00e+00 1.00e+00 4.72e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 120.44 19.43 1.00e+00 1.00e+00 3.78e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 118.33 18.50 1.00e+00 1.00e+00 3.42e+02 angle pdb=" PB ATP D 601 " pdb=" O3B ATP D 601 " pdb=" PG ATP D 601 " ideal model delta sigma weight residual 139.87 121.51 18.36 1.00e+00 1.00e+00 3.37e+02 ... (remaining 37776 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.14: 16290 27.14 - 54.29: 805 54.29 - 81.43: 67 81.43 - 108.57: 14 108.57 - 135.71: 3 Dihedral angle restraints: 17179 sinusoidal: 6940 harmonic: 10239 Sorted by residual: 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 -130.96 -49.04 0 5.00e+00 4.00e-02 9.62e+01 dihedral pdb=" CA ALA E 295 " pdb=" C ALA E 295 " pdb=" N VAL E 296 " pdb=" CA VAL E 296 " ideal model delta harmonic sigma weight residual 180.00 -133.84 -46.16 0 5.00e+00 4.00e-02 8.52e+01 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 -139.18 -40.82 0 5.00e+00 4.00e-02 6.67e+01 ... (remaining 17176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3461 0.054 - 0.108: 835 0.108 - 0.161: 130 0.161 - 0.215: 16 0.215 - 0.269: 4 Chirality restraints: 4446 Sorted by residual: chirality pdb=" CB ILE g 239 " pdb=" CA ILE g 239 " pdb=" CG1 ILE g 239 " pdb=" CG2 ILE g 239 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE e 31 " pdb=" CA ILE e 31 " pdb=" CG1 ILE e 31 " pdb=" CG2 ILE e 31 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CB ILE e 69 " pdb=" CA ILE e 69 " pdb=" CG1 ILE e 69 " pdb=" CG2 ILE e 69 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 4443 not shown) Planarity restraints: 4912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 176 " -0.015 2.00e-02 2.50e+03 3.08e-02 9.48e+00 pdb=" C LYS B 176 " 0.053 2.00e-02 2.50e+03 pdb=" O LYS B 176 " -0.020 2.00e-02 2.50e+03 pdb=" N THR B 177 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG g 83 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.42e+00 pdb=" N PRO g 84 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO g 84 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO g 84 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 241 " 0.041 5.00e-02 4.00e+02 6.15e-02 6.06e+00 pdb=" N PRO D 242 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO D 242 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 242 " 0.033 5.00e-02 4.00e+02 ... (remaining 4909 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 792 2.69 - 3.25: 29148 3.25 - 3.80: 44571 3.80 - 4.35: 58526 4.35 - 4.90: 96912 Nonbonded interactions: 229949 Sorted by model distance: nonbonded pdb=" O ALA F 295 " pdb=" N GLY F 297 " model vdw 2.142 3.120 nonbonded pdb=" O ILE A 193 " pdb=" OG1 THR A 257 " model vdw 2.153 3.040 nonbonded pdb=" O LEU A 53 " pdb=" OG1 THR A 92 " model vdw 2.159 3.040 nonbonded pdb=" O ALA E 295 " pdb=" N GLY E 297 " model vdw 2.199 3.120 nonbonded pdb=" OG1 THR d 181 " pdb=" OG1 THR d 222 " model vdw 2.203 3.040 ... (remaining 229944 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 503 or resid 600)) selection = (chain 'B' and (resid 6 through 503 or resid 600)) selection = (chain 'C' and (resid 6 through 503 or resid 600)) } ncs_group { reference = (chain 'D' and resid 17 through 494) selection = (chain 'E' and resid 17 through 494) selection = (chain 'F' and resid 17 through 494) } 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: 2.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.120 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 74.110 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 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 0.084 27879 Z= 0.331 Angle : 0.946 22.569 37781 Z= 0.602 Chirality : 0.048 0.269 4446 Planarity : 0.005 0.063 4912 Dihedral : 15.346 135.715 10604 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.73 % Favored : 91.96 % Rotamer: Outliers : 0.24 % Allowed : 7.68 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.86 (0.12), residues: 3557 helix: -1.75 (0.11), residues: 1421 sheet: -3.82 (0.18), residues: 451 loop : -2.90 (0.13), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP e 15 HIS 0.004 0.001 HIS F 345 PHE 0.019 0.002 PHE B 472 TYR 0.013 0.001 TYR g 94 ARG 0.022 0.001 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 752 time to evaluate : 3.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7794 (mm-30) REVERT: A 191 ASN cc_start: 0.7230 (t0) cc_final: 0.6834 (t0) REVERT: A 237 TYR cc_start: 0.8916 (t80) cc_final: 0.8713 (t80) REVERT: A 389 GLN cc_start: 0.8620 (tp-100) cc_final: 0.8405 (tm-30) REVERT: C 14 ARG cc_start: 0.5852 (mmm160) cc_final: 0.5234 (mpt-90) REVERT: C 237 TYR cc_start: 0.8766 (t80) cc_final: 0.8528 (t80) REVERT: C 251 MET cc_start: 0.7923 (ttp) cc_final: 0.7510 (ttp) REVERT: C 300 GLU cc_start: 0.8592 (tt0) cc_final: 0.8382 (tp30) REVERT: C 314 MET cc_start: 0.8597 (ttp) cc_final: 0.8374 (ttt) REVERT: C 348 ASP cc_start: 0.7481 (m-30) cc_final: 0.6956 (m-30) REVERT: C 449 LEU cc_start: 0.7993 (mt) cc_final: 0.7690 (tp) REVERT: B 110 ASN cc_start: 0.8522 (t0) cc_final: 0.8224 (t0) REVERT: B 157 MET cc_start: 0.7650 (mpp) cc_final: 0.7324 (mpp) REVERT: B 164 GLN cc_start: 0.8717 (tm-30) cc_final: 0.8217 (tm-30) REVERT: B 422 LYS cc_start: 0.7436 (pttp) cc_final: 0.7058 (ptmt) REVERT: B 489 LEU cc_start: 0.6955 (pp) cc_final: 0.6638 (pp) REVERT: B 495 GLN cc_start: 0.5786 (mm110) cc_final: 0.5583 (tm-30) REVERT: D 79 MET cc_start: 0.8966 (mmp) cc_final: 0.8256 (mmm) REVERT: D 121 LEU cc_start: 0.8598 (pp) cc_final: 0.7917 (pt) REVERT: D 178 LYS cc_start: 0.7819 (ttpp) cc_final: 0.7618 (ttpp) REVERT: D 256 MET cc_start: 0.8153 (ttm) cc_final: 0.7709 (mtt) REVERT: D 283 SER cc_start: 0.8492 (t) cc_final: 0.8091 (p) REVERT: E 20 LEU cc_start: 0.7291 (mt) cc_final: 0.6940 (tt) REVERT: E 39 LYS cc_start: 0.8259 (mmtm) cc_final: 0.7786 (mmmm) REVERT: E 64 GLU cc_start: 0.8248 (pp20) cc_final: 0.7816 (pp20) REVERT: E 89 MET cc_start: 0.8639 (mtt) cc_final: 0.8164 (mtp) REVERT: E 155 VAL cc_start: 0.9199 (t) cc_final: 0.8996 (t) REVERT: E 191 LYS cc_start: 0.8361 (tptm) cc_final: 0.8122 (ttpt) REVERT: E 206 THR cc_start: 0.8679 (m) cc_final: 0.7904 (m) REVERT: E 214 MET cc_start: 0.7840 (mmt) cc_final: 0.7278 (tpp) REVERT: E 218 GLU cc_start: 0.6611 (pt0) cc_final: 0.6285 (pt0) REVERT: E 238 GLN cc_start: 0.7035 (mt0) cc_final: 0.6536 (mp10) REVERT: E 306 MET cc_start: 0.8478 (tmm) cc_final: 0.7235 (tmm) REVERT: E 310 GLN cc_start: 0.8005 (mt0) cc_final: 0.7620 (mt0) REVERT: E 313 ILE cc_start: 0.8542 (mm) cc_final: 0.8221 (mt) REVERT: F 63 CYS cc_start: 0.8227 (m) cc_final: 0.7905 (m) REVERT: F 184 GLU cc_start: 0.7232 (tm-30) cc_final: 0.6679 (tm-30) REVERT: F 386 GLU cc_start: 0.7870 (tp30) cc_final: 0.7650 (tp30) REVERT: F 399 LYS cc_start: 0.8193 (ttpp) cc_final: 0.7934 (ttmm) REVERT: d 72 ASP cc_start: 0.6324 (m-30) cc_final: 0.6064 (m-30) REVERT: d 92 LEU cc_start: 0.5172 (tp) cc_final: 0.4858 (pt) REVERT: d 169 PHE cc_start: 0.7366 (t80) cc_final: 0.7087 (t80) REVERT: d 171 LYS cc_start: 0.8578 (ttpp) cc_final: 0.8340 (ttmm) REVERT: d 208 ARG cc_start: 0.7942 (ttp-110) cc_final: 0.7717 (ttp-110) REVERT: d 239 LYS cc_start: 0.5689 (mttt) cc_final: 0.4945 (ttpt) REVERT: g 100 LEU cc_start: 0.7092 (pp) cc_final: 0.6828 (pp) REVERT: g 136 MET cc_start: 0.8050 (tpt) cc_final: 0.7603 (ttp) REVERT: g 139 LYS cc_start: 0.7186 (ttpt) cc_final: 0.6494 (mptt) REVERT: g 144 ARG cc_start: 0.6377 (mmm160) cc_final: 0.5665 (tpp80) REVERT: g 263 LYS cc_start: 0.7803 (mtpt) cc_final: 0.7198 (ttmt) REVERT: e 20 LYS cc_start: 0.6083 (tptp) cc_final: 0.5697 (ttpt) REVERT: e 37 HIS cc_start: 0.7308 (t-90) cc_final: 0.6910 (t-90) REVERT: e 63 MET cc_start: 0.4653 (mmm) cc_final: 0.4279 (mmp) REVERT: e 91 GLU cc_start: 0.6898 (tp30) cc_final: 0.5947 (pm20) outliers start: 7 outliers final: 3 residues processed: 757 average time/residue: 0.4224 time to fit residues: 484.5367 Evaluate side-chains 523 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 520 time to evaluate : 3.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 299 optimal weight: 10.0000 chunk 269 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 181 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 278 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 169 optimal weight: 0.4980 chunk 207 optimal weight: 2.9990 chunk 322 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 GLN A 504 GLN C 186 ASN C 273 GLN B 34 GLN B 201 GLN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN ** d 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 342 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 27879 Z= 0.340 Angle : 0.753 9.482 37781 Z= 0.389 Chirality : 0.048 0.240 4446 Planarity : 0.005 0.071 4912 Dihedral : 8.871 123.775 4022 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.02 % Favored : 90.75 % Rotamer: Outliers : 0.10 % Allowed : 6.97 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.13), residues: 3557 helix: -0.67 (0.13), residues: 1424 sheet: -3.46 (0.20), residues: 438 loop : -2.46 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP e 15 HIS 0.005 0.001 HIS F 345 PHE 0.031 0.002 PHE B 292 TYR 0.022 0.002 TYR B 445 ARG 0.008 0.001 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7114 Ramachandran restraints generated. 3557 Oldfield, 0 Emsley, 3557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 642 time to evaluate : 3.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.6871 (m-80) cc_final: 0.6631 (m-80) REVERT: A 107 ARG cc_start: 0.8255 (mmt-90) cc_final: 0.8025 (mmt-90) REVERT: A 131 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7755 (mm-30) REVERT: A 191 ASN cc_start: 0.7226 (t0) cc_final: 0.6792 (t0) REVERT: A 447 ASP cc_start: 0.7334 (t0) cc_final: 0.6907 (t0) REVERT: C 14 ARG cc_start: 0.5679 (mmm160) cc_final: 0.5094 (mpt-90) REVERT: C 49 MET cc_start: 0.8252 (mtm) cc_final: 0.7947 (mtt) REVERT: C 52 GLU cc_start: 0.8219 (mt-10) cc_final: 0.8006 (mt-10) REVERT: C 251 MET cc_start: 0.7979 (ttp) cc_final: 0.7579 (ttp) REVERT: C 314 MET cc_start: 0.8658 (ttp) cc_final: 0.8457 (ttt) REVERT: C 348 ASP cc_start: 0.7460 (m-30) cc_final: 0.6943 (m-30) REVERT: C 386 GLU cc_start: 0.7876 (tp30) cc_final: 0.7524 (tp30) REVERT: B 34 GLN cc_start: 0.8557 (tt0) cc_final: 0.8267 (tt0) REVERT: B 110 ASN cc_start: 0.8422 (t0) cc_final: 0.8214 (p0) REVERT: B 157 MET cc_start: 0.7504 (mpp) cc_final: 0.7230 (mpp) REVERT: B 164 GLN cc_start: 0.8709 (tm-30) cc_final: 0.8336 (tm-30) REVERT: B 251 MET cc_start: 0.8693 (ttp) cc_final: 0.8279 (ttp) REVERT: D 83 ASP cc_start: 0.7628 (m-30) cc_final: 0.7380 (m-30) REVERT: D 247 MET cc_start: 0.8095 (ttp) cc_final: 0.7708 (ttp) REVERT: E 20 LEU cc_start: 0.7259 (mt) cc_final: 0.6914 (tp) REVERT: E 39 LYS cc_start: 0.8422 (mmtm) cc_final: 0.7912 (mmmm) REVERT: E 64 GLU cc_start: 0.8386 (pp20) cc_final: 0.8095 (pp20) REVERT: E 89 MET cc_start: 0.8590 (mtt) cc_final: 0.8175 (mtp) REVERT: E 155 VAL cc_start: 0.9154 (t) cc_final: 0.8855 (t) REVERT: E 191 LYS cc_start: 0.8298 (tptm) cc_final: 0.8074 (ttpt) REVERT: E 206 THR cc_start: 0.8626 (m) cc_final: 0.7995 (m) REVERT: E 218 GLU cc_start: 0.6532 (pt0) cc_final: 0.6218 (pt0) REVERT: E 247 MET cc_start: 0.8210 (ttp) cc_final: 0.7846 (ttp) REVERT: E 313 ILE cc_start: 0.8463 (mm) cc_final: 0.8109 (mt) REVERT: F 43 ILE cc_start: 0.9034 (mt) cc_final: 0.8681 (mt) REVERT: F 71 ASN cc_start: 0.7832 (t0) cc_final: 0.7625 (t0) REVERT: F 184 GLU cc_start: 0.7447 (tm-30) cc_final: 0.6854 (tm-30) REVERT: F 216 MET cc_start: 0.8021 (mmp) cc_final: 0.7444 (mmm) REVERT: F 399 LYS cc_start: 0.8185 (ttpp) cc_final: 0.7905 (ttmm) REVERT: F 475 TYR cc_start: 0.8796 (t80) cc_final: 0.8517 (t80) REVERT: d 92 LEU cc_start: 0.5104 (tp) cc_final: 0.4753 (pt) REVERT: d 169 PHE cc_start: 0.7261 (t80) cc_final: 0.7031 (t80) REVERT: d 171 LYS cc_start: 0.8628 (ttpp) cc_final: 0.8332 (ttmm) REVERT: d 239 LYS cc_start: 0.5541 (mttt) cc_final: 0.4830 (ttpt) REVERT: g 136 MET cc_start: 0.8012 (tpt) cc_final: 0.7619 (ttp) REVERT: g 139 LYS cc_start: 0.7293 (ttpt) cc_final: 0.6570 (mptt) REVERT: g 155 TYR cc_start: 0.6330 (p90) cc_final: 0.5774 (p90) REVERT: g 187 THR cc_start: 0.7235 (m) cc_final: 0.7002 (p) REVERT: e 20 LYS cc_start: 0.6048 (tptp) cc_final: 0.5796 (mtpt) REVERT: e 37 HIS cc_start: 0.7435 (t-90) cc_final: 0.6978 (t-90) outliers start: 3 outliers final: 2 residues processed: 645 average time/residue: 0.3788 time to fit residues: 386.2733 Evaluate side-chains 506 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 504 time to evaluate : 2.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 179 optimal weight: 1.9990 chunk 100 optimal weight: 0.0020 chunk 268 optimal weight: 0.7980 chunk 219 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 322 optimal weight: 5.9990 chunk 348 optimal weight: 1.9990 chunk 287 optimal weight: 0.0980 chunk 320 optimal weight: 0.8980 chunk 110 optimal weight: 0.0470 chunk 259 optimal weight: 0.7980 overall best weight: 0.3486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: