Starting phenix.real_space_refine on Sat Mar 23 02:39:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttt_26123/03_2024/7ttt_26123_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttt_26123/03_2024/7ttt_26123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttt_26123/03_2024/7ttt_26123.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttt_26123/03_2024/7ttt_26123.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttt_26123/03_2024/7ttt_26123_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttt_26123/03_2024/7ttt_26123_updated.pdb" } resolution = 2.9 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= 1.000 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: 8 Type Number sf(0) Gaussians Al 8 5.89 5 P 16 5.49 5 Mg 8 5.21 5 S 213 5.16 5 C 21988 2.51 5 N 6103 2.21 5 O 6820 1.98 5 F 24 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 31": "OD1" <-> "OD2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A GLU 108": "OE1" <-> "OE2" Residue "A ASP 161": "OD1" <-> "OD2" Residue "A ASP 203": "OD1" <-> "OD2" Residue "A GLU 401": "OE1" <-> "OE2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "B ASP 68": "OD1" <-> "OD2" Residue "B ASP 200": "OD1" <-> "OD2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ASP 230": "OD1" <-> "OD2" Residue "B GLU 263": "OE1" <-> "OE2" Residue "B GLU 428": "OE1" <-> "OE2" Residue "B GLU 443": "OE1" <-> "OE2" Residue "C ASP 46": "OD1" <-> "OD2" Residue "C GLU 150": "OE1" <-> "OE2" Residue "C ASP 188": "OD1" <-> "OD2" Residue "C PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 413": "OE1" <-> "OE2" Residue "C GLU 492": "OE1" <-> "OE2" Residue "C ASP 493": "OD1" <-> "OD2" Residue "C GLU 499": "OE1" <-> "OE2" Residue "C ASP 527": "OD1" <-> "OD2" Residue "C GLU 528": "OE1" <-> "OE2" Residue "D ASP 73": "OD1" <-> "OD2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "D GLU 118": "OE1" <-> "OE2" Residue "D ASP 153": "OD1" <-> "OD2" Residue "D ASP 158": "OD1" <-> "OD2" Residue "D GLU 200": "OE1" <-> "OE2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "E ASP 37": "OD1" <-> "OD2" Residue "E ASP 77": "OD1" <-> "OD2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 132": "OE1" <-> "OE2" Residue "E GLU 139": "OE1" <-> "OE2" Residue "E GLU 185": "OE1" <-> "OE2" Residue "E TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 216": "OE1" <-> "OE2" Residue "E ASP 247": "OD1" <-> "OD2" Residue "E ASP 336": "OD1" <-> "OD2" Residue "E GLU 482": "OE1" <-> "OE2" Residue "E GLU 509": "OE1" <-> "OE2" Residue "F ASP 73": "OD1" <-> "OD2" Residue "F ASP 207": "OD1" <-> "OD2" Residue "F ASP 261": "OD1" <-> "OD2" Residue "F GLU 279": "OE1" <-> "OE2" Residue "F ASP 307": "OD1" <-> "OD2" Residue "F ASP 311": "OD1" <-> "OD2" Residue "F PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 402": "OE1" <-> "OE2" Residue "F ASP 533": "OD1" <-> "OD2" Residue "G PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 10": "OD1" <-> "OD2" Residue "G GLU 15": "OE1" <-> "OE2" Residue "G GLU 68": "OE1" <-> "OE2" Residue "G GLU 106": "OE1" <-> "OE2" Residue "G GLU 127": "OE1" <-> "OE2" Residue "G GLU 142": "OE1" <-> "OE2" Residue "G PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 207": "OE1" <-> "OE2" Residue "G ASP 261": "OD1" <-> "OD2" Residue "G ASP 293": "OD1" <-> "OD2" Residue "G GLU 349": "OE1" <-> "OE2" Residue "G GLU 360": "OE1" <-> "OE2" Residue "G TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 440": "OE1" <-> "OE2" Residue "H PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 251": "OE1" <-> "OE2" Residue "H ASP 255": "OD1" <-> "OD2" Residue "H GLU 262": "OE1" <-> "OE2" Residue "H TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 336": "OE1" <-> "OE2" Residue "H ASP 357": "OD1" <-> "OD2" Residue "H PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 53": "OD1" <-> "OD2" Residue "I PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 303": "OD1" <-> "OD2" Residue "I ASP 338": "OD1" <-> "OD2" Residue "I TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 357": "OE1" <-> "OE2" Residue "I GLU 420": "OE1" <-> "OE2" Residue "I PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 458": "OD1" <-> "OD2" Residue "I ASP 519": "OD1" <-> "OD2" Residue "I GLU 520": "OE1" <-> "OE2" Residue "I PHE 528": "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: 35180 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2750 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 15, 'TRANS': 335} Chain breaks: 1 Chain: "B" Number of atoms: 4029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4029 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "C" Number of atoms: 4003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4003 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 15, 'TRANS': 505} Chain breaks: 1 Chain: "D" Number of atoms: 4072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4072 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 18, 'TRANS': 509} Chain: "E" Number of atoms: 3960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3960 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 11, 'TRANS': 514} Chain: "F" Number of atoms: 3924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3924 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Chain: "G" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4063 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 14, 'TRANS': 520} Chain: "H" Number of atoms: 4064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4064 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 16, 'TRANS': 506} Chain: "I" Number of atoms: 4051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4051 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 14, 'TRANS': 513} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 18.11, per 1000 atoms: 0.51 Number of scatterers: 35180 At special positions: 0 Unit cell: (181.5, 184.8, 114.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 213 16.00 P 16 15.00 Al 8 13.00 Mg 8 11.99 F 24 9.00 O 6820 8.00 N 6103 7.00 C 21988 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.02 Conformation dependent library (CDL) restraints added in 6.9 seconds 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8488 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 166 helices and 55 sheets defined 49.8% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.15 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 removed outlier: 3.683A pdb=" N LYS A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU A 27 " --> pdb=" O VAL A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 71 through 78 removed outlier: 3.569A pdb=" N SER A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 101 through 105 Processing helix chain 'A' and resid 113 through 125 removed outlier: 3.677A pdb=" N LYS A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.573A pdb=" N HIS A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLN A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 211 removed outlier: 4.165A pdb=" N ILE A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N CYS A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 241 removed outlier: 5.306A pdb=" N CYS A 239 " --> pdb=" O GLY A 235 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LEU A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 257 removed outlier: 4.162A pdb=" N ASN A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 removed outlier: 4.044A pdb=" N PHE A 378 " --> pdb=" O GLN A 375 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A 379 " --> pdb=" O GLU A 376 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER A 382 " --> pdb=" O LYS A 379 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR A 386 " --> pdb=" O GLU A 383 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG A 390 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 401 removed outlier: 3.896A pdb=" N THR A 399 " --> pdb=" O HIS A 396 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY A 400 " --> pdb=" O TRP A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 425 removed outlier: 3.829A pdb=" N THR A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N TYR A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'B' and resid 11 through 14 No H-bonds generated for 'chain 'B' and resid 11 through 14' Processing helix chain 'B' and resid 29 through 46 removed outlier: 3.627A pdb=" N THR B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N THR B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ALA B 46 " --> pdb=" O THR B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 75 Processing helix chain 'B' and resid 81 through 96 Processing helix chain 'B' and resid 101 through 121 removed outlier: 4.200A pdb=" N LEU B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 146 Proline residue: B 144 - end of helix Processing helix chain 'B' and resid 157 through 163 removed outlier: 3.677A pdb=" N SER B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 176 through 190 removed outlier: 3.905A pdb=" N ILE B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 214 No H-bonds generated for 'chain 'B' and resid 212 through 214' Processing helix chain 'B' and resid 262 through 286 removed outlier: 4.937A pdb=" N SER B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LYS B 270 " --> pdb=" O MET B 266 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 307 Processing helix chain 'B' and resid 320 through 328 Processing helix chain 'B' and resid 341 through 343 No H-bonds generated for 'chain 'B' and resid 341 through 343' Processing helix chain 'B' and resid 382 through 404 Processing helix chain 'B' and resid 414 through 429 removed outlier: 4.092A pdb=" N THR B 429 " --> pdb=" O SER B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 456 removed outlier: 3.604A pdb=" N PHE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ILE B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Proline residue: B 449 - end of helix Processing helix chain 'B' and resid 460 through 473 removed outlier: 3.785A pdb=" N GLU B 473 " --> pdb=" O ALA B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 495 No H-bonds generated for 'chain 'B' and resid 492 through 495' Processing helix chain 'B' and resid 501 through 520 Processing helix chain 'C' and resid 19 through 36 removed outlier: 3.990A pdb=" N VAL C 36 " --> pdb=" O ILE C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 77 through 89 Processing helix chain 'C' and resid 96 through 113 removed outlier: 3.618A pdb=" N VAL C 108 " --> pdb=" O PHE C 104 " (cutoff:3.500A) Proline residue: C 110 - end of helix Processing helix chain 'C' and resid 118 through 139 Processing helix chain 'C' and resid 153 through 162 Processing helix chain 'C' and resid 169 through 184 removed outlier: 5.237A pdb=" N ALA C 173 " --> pdb=" O GLN C 170 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA C 176 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS C 177 " --> pdb=" O PHE C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 194 No H-bonds generated for 'chain 'C' and resid 192 through 194' Processing helix chain 'C' and resid 205 through 207 No H-bonds generated for 'chain 'C' and resid 205 through 207' Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 260 through 284 removed outlier: 3.827A pdb=" N GLU C 270 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TRP C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 306 removed outlier: 3.618A pdb=" N ARG C 306 " --> pdb=" O TYR C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 326 Processing helix chain 'C' and resid 339 through 341 No H-bonds generated for 'chain 'C' and resid 339 through 341' Processing helix chain 'C' and resid 379 through 401 removed outlier: 3.685A pdb=" N ASP C 391 " --> pdb=" O ARG C 387 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA C 392 " --> pdb=" O SER C 388 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS C 401 " --> pdb=" O ARG C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 426 removed outlier: 3.566A pdb=" N ARG C 425 " --> pdb=" O ARG C 421 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THR C 426 " --> pdb=" O ASP C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 453 removed outlier: 3.663A pdb=" N LEU C 442 " --> pdb=" O TYR C 438 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLU C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ILE C 444 " --> pdb=" O LYS C 440 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE C 445 " --> pdb=" O ALA C 441 " (cutoff:3.500A) Proline residue: C 446 - end of helix Processing helix chain 'C' and resid 457 through 469 Processing helix chain 'C' and resid 506 through 524 Processing helix chain 'D' and resid 31 through 51 removed outlier: 4.879A pdb=" N THR D 50 " --> pdb=" O ASN D 46 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N SER D 51 " --> pdb=" O THR D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 80 Processing helix chain 'D' and resid 86 through 101 Processing helix chain 'D' and resid 108 through 126 removed outlier: 3.626A pdb=" N GLU D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLN D 122 " --> pdb=" O GLU D 118 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 151 removed outlier: 3.726A pdb=" N ASP D 149 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS D 150 " --> pdb=" O GLU D 146 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE D 151 " --> pdb=" O HIS D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 175 removed outlier: 4.690A pdb=" N SER D 175 " --> pdb=" O THR D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 196 removed outlier: 4.174A pdb=" N SER D 180 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N HIS D 182 " --> pdb=" O ASN D 179 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG D 183 " --> pdb=" O SER D 180 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET D 185 " --> pdb=" O HIS D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 219 through 221 No H-bonds generated for 'chain 'D' and resid 219 through 221' Processing helix chain 'D' and resid 271 through 294 removed outlier: 3.821A pdb=" N LYS D 282 " --> pdb=" O GLN D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 316 Processing helix chain 'D' and resid 327 through 337 Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 392 through 414 Processing helix chain 'D' and resid 424 through 439 removed outlier: 4.110A pdb=" N LYS D 439 " --> pdb=" O GLN D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 466 removed outlier: 3.734A pdb=" N GLU D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL D 457 " --> pdb=" O ASP D 453 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ILE D 458 " --> pdb=" O ALA D 454 " (cutoff:3.500A) Proline residue: D 459 - end of helix Processing helix chain 'D' and resid 470 through 483 Processing helix chain 'D' and resid 510 through 529 Processing helix chain 'E' and resid 21 through 42 removed outlier: 3.652A pdb=" N VAL E 39 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N SER E 41 " --> pdb=" O ASP E 37 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N THR E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 71 Processing helix chain 'E' and resid 79 through 94 removed outlier: 3.857A pdb=" N VAL E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU E 84 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 118 removed outlier: 3.977A pdb=" N THR E 103 " --> pdb=" O THR E 99 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER E 115 " --> pdb=" O ARG E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 144 Processing helix chain 'E' and resid 152 through 166 Processing helix chain 'E' and resid 171 through 190 removed outlier: 3.572A pdb=" N LYS E 176 " --> pdb=" O THR E 173 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASP E 177 " --> pdb=" O HIS E 174 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE E 179 " --> pdb=" O LYS E 176 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL E 184 " --> pdb=" O LYS E 181 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU E 185 " --> pdb=" O LEU E 182 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA E 186 " --> pdb=" O ALA E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 198 No H-bonds generated for 'chain 'E' and resid 196 through 198' Processing helix chain 'E' and resid 209 through 211 No H-bonds generated for 'chain 'E' and resid 209 through 211' Processing helix chain 'E' and resid 261 through 285 removed outlier: 3.545A pdb=" N MET E 275 " --> pdb=" O GLU E 271 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N HIS E 285 " --> pdb=" O ARG E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 306 Processing helix chain 'E' and resid 317 through 327 Processing helix chain 'E' and resid 338 through 340 No H-bonds generated for 'chain 'E' and resid 338 through 340' Processing helix chain 'E' and resid 380 through 402 removed outlier: 3.750A pdb=" N ASP E 392 " --> pdb=" O ARG E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 427 removed outlier: 3.769A pdb=" N ARG E 427 " --> pdb=" O GLN E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 454 removed outlier: 3.903A pdb=" N MET E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU E 446 " --> pdb=" O ALA E 442 " (cutoff:3.500A) Proline residue: E 447 - end of helix removed outlier: 3.614A pdb=" N ALA E 454 " --> pdb=" O ILE E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 470 Processing helix chain 'E' and resid 488 through 491 No H-bonds generated for 'chain 'E' and resid 488 through 491' Processing helix chain 'E' and resid 497 through 516 removed outlier: 3.613A pdb=" N ARG E 516 " --> pdb=" O GLU E 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 51 removed outlier: 4.647A pdb=" N THR F 50 " --> pdb=" O ASP F 46 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N SER F 51 " --> pdb=" O ALA F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 80 Processing helix chain 'F' and resid 88 through 101 removed outlier: 3.867A pdb=" N VAL F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU F 93 " --> pdb=" O ARG F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 126 removed outlier: 4.042A pdb=" N VAL F 110 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR F 121 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LYS F 122 " --> pdb=" O ASP F 118 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU F 123 " --> pdb=" O SER F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 151 removed outlier: 3.638A pdb=" N GLU F 146 " --> pdb=" O GLU F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 171 Processing helix chain 'F' and resid 180 through 192 Proline residue: F 185 - end of helix removed outlier: 3.583A pdb=" N VAL F 188 " --> pdb=" O SER F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 207 No H-bonds generated for 'chain 'F' and resid 205 through 207' Processing helix chain 'F' and resid 218 through 220 No H-bonds generated for 'chain 'F' and resid 218 through 220' Processing helix chain 'F' and resid 269 through 293 removed outlier: 4.093A pdb=" N ASP F 273 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU F 276 " --> pdb=" O MET F 272 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR F 293 " --> pdb=" O GLN F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 319 Processing helix chain 'F' and resid 333 through 340 Processing helix chain 'F' and resid 348 through 350 No H-bonds generated for 'chain 'F' and resid 348 through 350' Processing helix chain 'F' and resid 353 through 355 No H-bonds generated for 'chain 'F' and resid 353 through 355' Processing helix chain 'F' and resid 395 through 417 Processing helix chain 'F' and resid 427 through 442 removed outlier: 3.762A pdb=" N ARG F 441 " --> pdb=" O THR F 437 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR F 442 " --> pdb=" O GLU F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 457 Processing helix chain 'F' and resid 460 through 468 Processing helix chain 'F' and resid 473 through 486 removed outlier: 3.668A pdb=" N GLN F 486 " --> pdb=" O ASN F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 504 through 506 No H-bonds generated for 'chain 'F' and resid 504 through 506' Processing helix chain 'F' and resid 512 through 531 removed outlier: 3.804A pdb=" N LYS F 531 " --> pdb=" O ARG F 527 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 32 removed outlier: 3.623A pdb=" N VAL G 32 " --> pdb=" O ILE G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 64 Processing helix chain 'G' and resid 70 through 85 removed outlier: 4.217A pdb=" N LEU G 75 " --> pdb=" O ALA G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 109 Processing helix chain 'G' and resid 114 through 134 removed outlier: 3.932A pdb=" N ASN G 133 " --> pdb=" O VAL G 129 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLU G 134 " --> pdb=" O ARG G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 156 Processing helix chain 'G' and resid 165 through 179 removed outlier: 3.706A pdb=" N ILE G 179 " --> pdb=" O ALA G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 207 No H-bonds generated for 'chain 'G' and resid 205 through 207' Processing helix chain 'G' and resid 257 through 281 removed outlier: 4.488A pdb=" N ASP G 261 " --> pdb=" O GLU G 258 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN G 262 " --> pdb=" O LYS G 259 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN G 265 " --> pdb=" O GLN G 262 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU G 267 " --> pdb=" O ARG G 264 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE G 270 " --> pdb=" O GLU G 267 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N THR G 271 " --> pdb=" O SER G 268 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN G 276 " --> pdb=" O GLU G 273 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA G 280 " --> pdb=" O LYS G 277 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR G 281 " --> pdb=" O ILE G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 303 removed outlier: 3.788A pdb=" N LYS G 298 " --> pdb=" O ASP G 294 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N TYR G 299 " --> pdb=" O MET G 295 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE G 300 " --> pdb=" O CYS G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 323 Processing helix chain 'G' and resid 342 through 344 No H-bonds generated for 'chain 'G' and resid 342 through 344' Processing helix chain 'G' and resid 382 through 404 removed outlier: 3.710A pdb=" N ASP G 394 " --> pdb=" O ARG G 390 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 429 removed outlier: 4.275A pdb=" N THR G 428 " --> pdb=" O GLU G 424 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N SER G 429 " --> pdb=" O ASN G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 434 through 455 removed outlier: 3.969A pdb=" N LEU G 446 " --> pdb=" O ALA G 442 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL G 447 " --> pdb=" O ARG G 443 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ILE G 448 " --> pdb=" O SER G 444 " (cutoff:3.500A) Proline residue: G 449 - end of helix Processing helix chain 'G' and resid 460 through 475 Processing helix chain 'G' and resid 478 through 483 removed outlier: 5.317A pdb=" N ASN G 482 " --> pdb=" O GLU G 479 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 501 No H-bonds generated for 'chain 'G' and resid 498 through 501' Processing helix chain 'G' and resid 507 through 524 Processing helix chain 'H' and resid 20 through 37 removed outlier: 3.564A pdb=" N ILE H 36 " --> pdb=" O THR H 32 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE H 37 " --> pdb=" O ILE H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 69 removed outlier: 4.306A pdb=" N GLU H 69 " --> pdb=" O ALA H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 90 Processing helix chain 'H' and resid 97 through 115 removed outlier: 4.085A pdb=" N ALA H 109 " --> pdb=" O MET H 105 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLU H 110 " --> pdb=" O LEU H 106 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N HIS H 111 " --> pdb=" O SER H 107 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N PHE H 112 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN H 115 " --> pdb=" O HIS H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 139 removed outlier: 3.769A pdb=" N ASP H 131 " --> pdb=" O ARG H 127 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP H 132 " --> pdb=" O LYS H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 160 Processing helix chain 'H' and resid 164 through 183 removed outlier: 4.292A pdb=" N ARG H 167 " --> pdb=" O ALA H 164 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N SER H 170 " --> pdb=" O ARG H 167 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N CYS H 173 " --> pdb=" O SER H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 211 No H-bonds generated for 'chain 'H' and resid 209 through 211' Processing helix chain 'H' and resid 261 through 285 removed outlier: 4.836A pdb=" N THR H 265 " --> pdb=" O GLU H 261 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU H 271 " --> pdb=" O ILE H 267 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU H 272 " --> pdb=" O LEU H 268 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU H 285 " --> pdb=" O ASP H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 306 Processing helix chain 'H' and resid 317 through 327 Processing helix chain 'H' and resid 335 through 337 No H-bonds generated for 'chain 'H' and resid 335 through 337' Processing helix chain 'H' and resid 381 through 403 Processing helix chain 'H' and resid 413 through 428 removed outlier: 3.868A pdb=" N LYS H 427 " --> pdb=" O THR H 423 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ALA H 428 " --> pdb=" O GLU H 424 " (cutoff:3.500A) Processing helix chain 'H' and resid 432 through 455 Proline residue: H 436 - end of helix removed outlier: 3.993A pdb=" N VAL H 440 " --> pdb=" O TYR H 437 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU H 445 " --> pdb=" O GLN H 442 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL H 446 " --> pdb=" O ALA H 443 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE H 447 " --> pdb=" O LEU H 444 " (cutoff:3.500A) Proline residue: H 448 - end of helix Processing helix chain 'H' and resid 459 through 470 removed outlier: 3.886A pdb=" N THR H 464 " --> pdb=" O ILE H 460 " (cutoff:3.500A) Processing helix chain 'H' and resid 490 through 493 No H-bonds generated for 'chain 'H' and resid 490 through 493' Processing helix chain 'H' and resid 499 through 518 removed outlier: 3.823A pdb=" N ARG H 518 " --> pdb=" O VAL H 514 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 36 removed outlier: 3.805A pdb=" N LEU I 20 " --> pdb=" O ALA I 16 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA I 21 " --> pdb=" O GLN I 17 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL I 33 " --> pdb=" O GLY I 29 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N THR I 36 " --> pdb=" O ASP I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 66 Processing helix chain 'I' and resid 72 through 87 removed outlier: 3.567A pdb=" N ILE I 87 " --> pdb=" O ALA I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 112 removed outlier: 3.605A pdb=" N TYR I 109 " --> pdb=" O GLN I 105 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLU I 112 " --> pdb=" O LEU I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 137 removed outlier: 3.630A pdb=" N GLU I 136 " --> pdb=" O GLN I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 156 Processing helix chain 'I' and resid 162 through 178 removed outlier: 3.636A pdb=" N VAL I 167 " --> pdb=" O GLU I 163 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU I 170 " --> pdb=" O ASP I 166 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA I 171 " --> pdb=" O VAL I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 203 No H-bonds generated for 'chain 'I' and resid 201 through 203' Processing helix chain 'I' and resid 253 through 281 removed outlier: 4.496A pdb=" N ARG I 264 " --> pdb=" O VAL I 260 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LYS I 265 " --> pdb=" O LYS I 261 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N PHE I 266 " --> pdb=" O ALA I 262 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE I 267 " --> pdb=" O GLU I 263 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG I 270 " --> pdb=" O PHE I 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 299 through 306 Processing helix chain 'I' and resid 319 through 327 removed outlier: 4.628A pdb=" N LEU I 324 " --> pdb=" O MET I 321 " (cutoff:3.500A) Processing helix chain 'I' and resid 381 through 403 Processing helix chain 'I' and resid 413 through 423 Processing helix chain 'I' and resid 431 through 455 removed outlier: 4.005A pdb=" N GLN I 434 " --> pdb=" O GLY I 431 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE I 447 " --> pdb=" O LEU I 444 " (cutoff:3.500A) Proline residue: I 448 - end of helix Processing helix chain 'I' and resid 459 through 468 Processing helix chain 'I' and resid 489 through 492 No H-bonds generated for 'chain 'I' and resid 489 through 492' Processing helix chain 'I' and resid 498 through 516 Processing sheet with id= A, first strand: chain 'A' and resid 90 through 92 removed outlier: 8.682A pdb=" N VAL A 91 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU A 65 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N ILE A 64 " --> pdb=" O ILE A 4 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N HIS A 6 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL A 66 " --> pdb=" O HIS A 6 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN A 8 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N VAL A 5 " --> pdb=" O GLN A 131 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE A 133 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ILE A 7 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU A 135 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ALA A 9 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N HIS A 137 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE A 163 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N LEU A 135 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASN A 165 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N HIS A 137 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHE A 167 " --> pdb=" O HIS A 137 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 51 through 53 Processing sheet with id= C, first strand: chain 'A' and resid 199 through 201 removed outlier: 3.569A pdb=" N CYS A 201 " --> pdb=" O PHE A 266 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 20 through 22 Processing sheet with id= E, first strand: chain 'B' and resid 54 through 57 Processing sheet with id= F, first strand: chain 'B' and resid 202 through 208 removed outlier: 6.781A pdb=" N SER B 373 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N CYS B 205 " --> pdb=" O SER B 373 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE B 375 " --> pdb=" O CYS B 205 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE B 207 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LEU B 377 " --> pdb=" O ILE B 207 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 220 through 223 Processing sheet with id= H, first strand: chain 'B' and resid 345 through 347 removed outlier: 6.641A pdb=" N VAL B 290 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N TYR B 242 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL B 292 " --> pdb=" O TYR B 242 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N MET B 311 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N THR B 293 " --> pdb=" O MET B 311 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL B 313 " --> pdb=" O THR B 293 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 408 through 410 Processing sheet with id= J, first strand: chain 'B' and resid 478 through 480 Processing sheet with id= K, first strand: chain 'C' and resid 14 through 17 Processing sheet with id= L, first strand: chain 'C' and resid 47 through 50 Processing sheet with id= M, first strand: chain 'C' and resid 195 through 201 removed outlier: 7.106A pdb=" N CYS C 370 " --> pdb=" O GLY C 196 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N LYS C 198 " --> pdb=" O CYS C 370 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N PHE C 372 " --> pdb=" O LYS C 198 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL C 200 " --> pdb=" O PHE C 372 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU C 374 " --> pdb=" O VAL C 200 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 213 through 217 Processing sheet with id= O, first strand: chain 'C' and resid 237 through 240 removed outlier: 6.695A pdb=" N VAL C 288 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N LEU C 240 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU C 290 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE C 309 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N SER C 291 " --> pdb=" O PHE C 309 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA C 311 " --> pdb=" O SER C 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'C' and resid 405 through 407 Processing sheet with id= Q, first strand: chain 'C' and resid 485 through 488 Processing sheet with id= R, first strand: chain 'D' and resid 26 through 29 removed outlier: 3.775A pdb=" N LYS D 535 " --> pdb=" O SER D 26 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 59 through 62 Processing sheet with id= T, first strand: chain 'D' and resid 209 through 213 removed outlier: 6.611A pdb=" N VAL D 383 " --> pdb=" O LYS D 210 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N GLU D 212 " --> pdb=" O VAL D 383 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ILE D 385 " --> pdb=" O GLU D 212 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 228 through 230 Processing sheet with id= V, first strand: chain 'D' and resid 354 through 356 removed outlier: 6.758A pdb=" N LEU D 299 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N LEU D 251 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE D 301 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N CYS D 302 " --> pdb=" O PRO D 320 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL D 322 " --> pdb=" O CYS D 302 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 418 through 420 Processing sheet with id= X, first strand: chain 'E' and resid 17 through 19 Processing sheet with id= Y, first strand: chain 'E' and resid 50 through 53 Processing sheet with id= Z, first strand: chain 'E' and resid 199 through 205 removed outlier: 6.634A pdb=" N CYS E 371 " --> pdb=" O HIS E 200 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ILE E 202 " --> pdb=" O CYS E 371 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ILE E 373 " --> pdb=" O ILE E 202 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LYS E 204 " --> pdb=" O ILE E 373 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU E 375 " --> pdb=" O LYS E 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'E' and resid 218 through 220 Processing sheet with id= AB, first strand: chain 'E' and resid 344 through 346 removed outlier: 3.641A pdb=" N CYS E 346 " --> pdb=" O ALA E 235 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N CYS E 289 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ALA E 240 " --> pdb=" O CYS E 289 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE E 291 " --> pdb=" O ALA E 240 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N MET E 310 " --> pdb=" O PHE E 290 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASN E 292 " --> pdb=" O MET E 310 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE E 312 " --> pdb=" O ASN E 292 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 406 through 408 Processing sheet with id= AD, first strand: chain 'E' and resid 476 through 479 Processing sheet with id= AE, first strand: chain 'F' and resid 59 through 62 Processing sheet with id= AF, first strand: chain 'F' and resid 208 through 214 removed outlier: 6.902A pdb=" N VAL F 386 " --> pdb=" O LYS F 209 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N VAL F 211 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE F 388 " --> pdb=" O VAL F 211 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LYS F 213 " --> pdb=" O ILE F 388 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL F 390 " --> pdb=" O LYS F 213 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 226 through 229 removed outlier: 4.041A pdb=" N GLY F 371 " --> pdb=" O LEU F 367 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 357 through 359 removed outlier: 6.768A pdb=" N VAL F 297 " --> pdb=" O GLY F 247 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE F 249 " --> pdb=" O VAL F 297 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU F 299 " --> pdb=" O ILE F 249 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N MET F 323 " --> pdb=" O LEU F 298 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILE F 300 " --> pdb=" O MET F 323 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE F 325 " --> pdb=" O ILE F 300 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 421 through 423 Processing sheet with id= AJ, first strand: chain 'F' and resid 491 through 494 Processing sheet with id= AK, first strand: chain 'G' and resid 9 through 13 Processing sheet with id= AL, first strand: chain 'G' and resid 43 through 46 Processing sheet with id= AM, first strand: chain 'G' and resid 196 through 199 removed outlier: 3.907A pdb=" N ASN G 196 " --> pdb=" O ALA G 373 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'G' and resid 213 through 216 Processing sheet with id= AO, first strand: chain 'G' and resid 346 through 348 removed outlier: 6.589A pdb=" N VAL G 285 " --> pdb=" O ALA G 235 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU G 237 " --> pdb=" O VAL G 285 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU G 287 " --> pdb=" O LEU G 237 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N MET G 306 " --> pdb=" O ILE G 286 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N THR G 288 " --> pdb=" O MET G 306 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL G 308 " --> pdb=" O THR G 288 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'G' and resid 408 through 410 Processing sheet with id= AQ, first strand: chain 'H' and resid 15 through 18 Processing sheet with id= AR, first strand: chain 'H' and resid 48 through 51 Processing sheet with id= AS, first strand: chain 'H' and resid 199 through 205 removed outlier: 6.832A pdb=" N CYS H 372 " --> pdb=" O ARG H 200 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N GLU H 202 " --> pdb=" O CYS H 372 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ILE H 374 " --> pdb=" O GLU H 202 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ILE H 204 " --> pdb=" O ILE H 374 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU H 376 " --> pdb=" O ILE H 204 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR H 373 " --> pdb=" O LEU H 215 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'H' and resid 218 through 220 Processing sheet with id= AU, first strand: chain 'H' and resid 238 through 241 removed outlier: 6.472A pdb=" N VAL H 289 " --> pdb=" O VAL H 239 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LEU H 241 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE H 291 " --> pdb=" O LEU H 241 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR H 310 " --> pdb=" O VAL H 290 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N THR H 292 " --> pdb=" O THR H 310 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE H 312 " --> pdb=" O THR H 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= AU Processing sheet with id= AV, first strand: chain 'H' and resid 407 through 409 Processing sheet with id= AW, first strand: chain 'H' and resid 478 through 481 removed outlier: 4.002A pdb=" N THR H 486 " --> pdb=" O ASN H 481 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'I' and resid 12 through 14 Processing sheet with id= AY, first strand: chain 'I' and resid 45 through 48 Processing sheet with id= AZ, first strand: chain 'I' and resid 191 through 196 removed outlier: 7.054A pdb=" N VAL I 372 " --> pdb=" O GLU I 192 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N MET I 194 " --> pdb=" O VAL I 372 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU I 374 " --> pdb=" O MET I 194 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N MET I 196 " --> pdb=" O LEU I 374 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE I 376 " --> pdb=" O MET I 196 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'I' and resid 210 through 212 Processing sheet with id= BB, first strand: chain 'I' and resid 345 through 347 removed outlier: 6.743A pdb=" N GLY I 288 " --> pdb=" O TYR I 229 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N LEU I 231 " --> pdb=" O GLY I 288 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL I 290 " --> pdb=" O LEU I 231 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N CYS I 233 " --> pdb=" O VAL I 290 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE I 292 " --> pdb=" O CYS I 233 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL I 311 " --> pdb=" O VAL I 291 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ASN I 293 " --> pdb=" O VAL I 311 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU I 313 " --> pdb=" O ASN I 293 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'I' and resid 477 through 479 1678 hydrogen bonds defined for protein. 4530 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: 13.71 Time building geometry restraints manager: 15.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 6136 1.28 - 1.42: 7656 1.42 - 1.55: 21406 1.55 - 1.68: 37 1.68 - 1.82: 370 Bond restraints: 35605 Sorted by residual: bond pdb=" F1 AF3 B 603 " pdb="AL AF3 B 603 " ideal model delta sigma weight residual 1.637 1.801 -0.164 2.00e-02 2.50e+03 6.70e+01 bond pdb=" F3 AF3 I 603 " pdb="AL AF3 I 603 " ideal model delta sigma weight residual 1.637 1.801 -0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" F3 AF3 H 603 " pdb="AL AF3 H 603 " ideal model delta sigma weight residual 1.637 1.801 -0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" F3 AF3 E 603 " pdb="AL AF3 E 603 " ideal model delta sigma weight residual 1.637 1.801 -0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" F1 AF3 E 603 " pdb="AL AF3 E 603 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.68e+01 ... (remaining 35600 not shown) Histogram of bond angle deviations from ideal: 98.36 - 106.01: 660 106.01 - 113.65: 20894 113.65 - 121.30: 17744 121.30 - 128.94: 8635 128.94 - 136.58: 161 Bond angle restraints: 48094 Sorted by residual: angle pdb=" CA ASP G 528 " pdb=" CB ASP G 528 " pdb=" CG ASP G 528 " ideal model delta sigma weight residual 112.60 119.21 -6.61 1.00e+00 1.00e+00 4.36e+01 angle pdb=" CA PHE B 191 " pdb=" CB PHE B 191 " pdb=" CG PHE B 191 " ideal model delta sigma weight residual 113.80 120.00 -6.20 1.00e+00 1.00e+00 3.84e+01 angle pdb=" C GLY C 41 " pdb=" N PRO C 42 " pdb=" CA PRO C 42 " ideal model delta sigma weight residual 119.56 125.71 -6.15 1.01e+00 9.80e-01 3.71e+01 angle pdb=" CA ASP B 230 " pdb=" CB ASP B 230 " pdb=" CG ASP B 230 " ideal model delta sigma weight residual 112.60 118.47 -5.87 1.00e+00 1.00e+00 3.45e+01 angle pdb=" CA ALA A 271 " pdb=" C ALA A 271 " pdb=" N PRO A 272 " ideal model delta sigma weight residual 118.44 127.49 -9.05 1.59e+00 3.96e-01 3.24e+01 ... (remaining 48089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.50: 21339 35.50 - 71.00: 556 71.00 - 106.49: 45 106.49 - 141.99: 6 141.99 - 177.49: 6 Dihedral angle restraints: 21952 sinusoidal: 8835 harmonic: 13117 Sorted by residual: dihedral pdb=" C5' ADP E 602 " pdb=" O5' ADP E 602 " pdb=" PA ADP E 602 " pdb=" O2A ADP E 602 " ideal model delta sinusoidal sigma weight residual -60.00 117.49 -177.49 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP C 602 " pdb=" O3A ADP C 602 " pdb=" PA ADP C 602 " pdb=" PB ADP C 602 " ideal model delta sinusoidal sigma weight residual -60.00 113.95 -173.94 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP B 602 " pdb=" O3A ADP B 602 " pdb=" PA ADP B 602 " pdb=" PB ADP B 602 " ideal model delta sinusoidal sigma weight residual 300.00 127.11 172.89 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 21949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 4999 0.067 - 0.133: 650 0.133 - 0.200: 39 0.200 - 0.267: 5 0.267 - 0.333: 5 Chirality restraints: 5698 Sorted by residual: chirality pdb=" CB VAL C 406 " pdb=" CA VAL C 406 " pdb=" CG1 VAL C 406 " pdb=" CG2 VAL C 406 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA ALA A 271 " pdb=" N ALA A 271 " pdb=" C ALA A 271 " pdb=" CB ALA A 271 " both_signs ideal model delta sigma weight residual False 2.48 2.17 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA LYS C 401 " pdb=" N LYS C 401 " pdb=" C LYS C 401 " pdb=" CB LYS C 401 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 5695 not shown) Planarity restraints: 6157 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 269 " 0.027 2.00e-02 2.50e+03 5.48e-02 3.00e+01 pdb=" C GLY A 269 " -0.095 2.00e-02 2.50e+03 pdb=" O GLY A 269 " 0.036 2.00e-02 2.50e+03 pdb=" N PHE A 270 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 189 " 0.025 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" C SER B 189 " -0.085 2.00e-02 2.50e+03 pdb=" O SER B 189 " 0.031 2.00e-02 2.50e+03 pdb=" N ILE B 190 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 197 " -0.016 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C PHE B 197 " 0.058 2.00e-02 2.50e+03 pdb=" O PHE B 197 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN B 198 " -0.020 2.00e-02 2.50e+03 ... (remaining 6154 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 139 2.50 - 3.10: 24675 3.10 - 3.70: 49494 3.70 - 4.30: 72238 4.30 - 4.90: 126007 Nonbonded interactions: 272553 Sorted by model distance: nonbonded pdb="MG MG B 601 " pdb=" O1A ADP B 602 " model vdw 1.898 2.170 nonbonded pdb="MG MG G 601 " pdb=" F1 AF3 G 603 " model vdw 1.906 2.120 nonbonded pdb="MG MG B 601 " pdb=" O1B ADP B 602 " model vdw 1.938 2.170 nonbonded pdb="MG MG C 601 " pdb=" O1A ADP C 602 " model vdw 1.958 2.170 nonbonded pdb="MG MG H 601 " pdb=" O1B ADP H 602 " model vdw 1.978 2.170 ... (remaining 272548 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.180 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: 9.350 Check model and map are aligned: 0.530 Set scattering table: 0.280 Process input model: 94.350 Find NCS groups from input model: 2.300 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 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 : 0.006 0.164 35605 Z= 0.361 Angle : 0.706 9.589 48094 Z= 0.401 Chirality : 0.046 0.333 5698 Planarity : 0.005 0.079 6157 Dihedral : 16.274 177.491 13464 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.92 % Favored : 95.95 % Rotamer: Outliers : 1.10 % Allowed : 13.07 % Favored : 85.83 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.13), residues: 4539 helix: 1.21 (0.11), residues: 2282 sheet: 0.65 (0.22), residues: 587 loop : -1.37 (0.14), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 435 HIS 0.007 0.001 HIS A 37 PHE 0.029 0.002 PHE G 8 TYR 0.016 0.001 TYR I 351 ARG 0.005 0.000 ARG H 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 236 time to evaluate : 4.009 Fit side-chains revert: symmetry clash REVERT: B 68 ASP cc_start: 0.7870 (t0) cc_final: 0.7458 (t0) REVERT: D 24 ARG cc_start: 0.7546 (ttt180) cc_final: 0.7293 (mtp180) REVERT: E 170 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.7162 (mtpp) outliers start: 42 outliers final: 24 residues processed: 270 average time/residue: 1.5646 time to fit residues: 503.7871 Evaluate side-chains 252 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 227 time to evaluate : 4.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain H residue 20 ARG Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 342 ASP Chi-restraints excluded: chain I residue 391 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 381 optimal weight: 7.9990 chunk 342 optimal weight: 4.9990 chunk 190 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 chunk 231 optimal weight: 1.9990 chunk 183 optimal weight: 9.9990 chunk 354 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 215 optimal weight: 10.0000 chunk 263 optimal weight: 5.9990 chunk 410 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS A 370 ASN A 375 GLN B 175 ASN ** D 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 ASN I 84 GLN I 514 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.0427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 35605 Z= 0.276 Angle : 0.587 9.316 48094 Z= 0.296 Chirality : 0.044 0.173 5698 Planarity : 0.004 0.070 6157 Dihedral : 9.548 178.128 4979 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.08 % Favored : 95.90 % Rotamer: Outliers : 2.57 % Allowed : 12.34 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.13), residues: 4539 helix: 1.51 (0.11), residues: 2277 sheet: 0.61 (0.22), residues: 600 loop : -1.37 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 435 HIS 0.006 0.001 HIS A 37 PHE 0.019 0.001 PHE A 367 TYR 0.012 0.001 TYR F 282 ARG 0.003 0.000 ARG C 375 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 241 time to evaluate : 4.207 Fit side-chains REVERT: A 375 GLN cc_start: 0.8131 (pt0) cc_final: 0.7528 (pt0) REVERT: B 68 ASP cc_start: 0.8016 (t0) cc_final: 0.7539 (t0) REVERT: B 133 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.6654 (mp0) REVERT: B 230 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7858 (t0) REVERT: B 315 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7607 (pp) REVERT: D 158 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7907 (t70) REVERT: E 116 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8636 (mt) REVERT: E 170 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8330 (mmtm) REVERT: E 247 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.8069 (p0) REVERT: E 353 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8148 (tpt) REVERT: H 270 MET cc_start: 0.8210 (mtm) cc_final: 0.7983 (mtp) REVERT: H 476 GLU cc_start: 0.9235 (OUTLIER) cc_final: 0.8672 (mt-10) outliers start: 98 outliers final: 41 residues processed: 307 average time/residue: 1.4907 time to fit residues: 549.1189 Evaluate side-chains 276 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 226 time to evaluate : 3.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 196 HIS Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 468 MET Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain E residue 247 ASP Chi-restraints excluded: chain E residue 353 MET Chi-restraints excluded: chain E residue 509 GLU Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 446 MET Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 209 MET Chi-restraints excluded: chain G residue 366 ASN Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 258 ILE Chi-restraints excluded: chain H residue 463 LEU Chi-restraints excluded: chain H residue 476 GLU Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain I residue 482 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 228 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 341 optimal weight: 0.9990 chunk 279 optimal weight: 6.9990 chunk 113 optimal weight: 0.7980 chunk 411 optimal weight: 0.0170 chunk 444 optimal weight: 3.9990 chunk 366 optimal weight: 9.9990 chunk 407 optimal weight: 4.9990 chunk 140 optimal weight: 8.9990 chunk 329 optimal weight: 7.9990 overall best weight: 1.7624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS A 190 HIS C 30 GLN ** D 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 10 ASN ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 GLN I 514 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.0693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35605 Z= 0.173 Angle : 0.530 9.689 48094 Z= 0.264 Chirality : 0.042 0.167 5698 Planarity : 0.004 0.063 6157 Dihedral : 8.867 175.494 4960 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.46 % Favored : 96.52 % Rotamer: Outliers : 2.39 % Allowed : 13.46 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.13), residues: 4539 helix: 1.76 (0.11), residues: 2273 sheet: 0.64 (0.22), residues: 606 loop : -1.27 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 435 HIS 0.004 0.001 HIS H 111 PHE 0.016 0.001 PHE A 20 TYR 0.012 0.001 TYR F 282 ARG 0.002 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 248 time to evaluate : 4.080 Fit side-chains REVERT: A 375 GLN cc_start: 0.8148 (pt0) cc_final: 0.7480 (pt0) REVERT: B 133 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6567 (mp0) REVERT: B 196 HIS cc_start: 0.7322 (OUTLIER) cc_final: 0.7024 (m-70) REVERT: B 230 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7879 (t0) REVERT: B 249 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7989 (ppp) REVERT: B 315 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7743 (pp) REVERT: B 372 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.7982 (pt) REVERT: D 96 LYS cc_start: 0.7835 (tppt) cc_final: 0.7575 (tppt) REVERT: D 158 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7807 (t70) REVERT: E 170 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8435 (mmtm) REVERT: E 353 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8197 (tpt) REVERT: E 416 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8276 (mt) REVERT: F 231 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7444 (pt0) REVERT: F 402 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7840 (tm-30) REVERT: F 446 MET cc_start: 0.6864 (OUTLIER) cc_final: 0.6008 (mmm) REVERT: H 270 MET cc_start: 0.8212 (mtm) cc_final: 0.7907 (mtp) outliers start: 91 outliers final: 42 residues processed: 309 average time/residue: 1.4725 time to fit residues: 546.8410 Evaluate side-chains 280 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 226 time to evaluate : 4.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 196 HIS Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 468 MET Chi-restraints excluded: chain E residue 10 ASN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain E residue 353 MET Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 509 GLU Chi-restraints excluded: chain F residue 231 GLN Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 272 MET Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 446 MET Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 132 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 258 ILE Chi-restraints excluded: chain H residue 463 LEU Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 482 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 406 optimal weight: 4.9990 chunk 309 optimal weight: 9.9990 chunk 213 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 196 optimal weight: 10.0000 chunk 276 optimal weight: 0.1980 chunk 412 optimal weight: 8.9990 chunk 436 optimal weight: 0.5980 chunk 215 optimal weight: 0.6980 chunk 391 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS A 190 HIS C 252 ASN D 515 GLN ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 GLN I 514 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35605 Z= 0.209 Angle : 0.537 11.350 48094 Z= 0.267 Chirality : 0.042 0.165 5698 Planarity : 0.004 0.063 6157 Dihedral : 8.704 172.164 4955 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.88 % Favored : 96.10 % Rotamer: Outliers : 2.57 % Allowed : 14.12 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.13), residues: 4539 helix: 1.79 (0.11), residues: 2276 sheet: 0.65 (0.22), residues: 599 loop : -1.25 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 435 HIS 0.005 0.001 HIS A 37 PHE 0.014 0.001 PHE A 20 TYR 0.013 0.001 TYR F 282 ARG 0.005 0.000 ARG G 480 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 238 time to evaluate : 4.654 Fit side-chains REVERT: A 375 GLN cc_start: 0.8128 (pt0) cc_final: 0.7447 (pt0) REVERT: B 133 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6590 (mp0) REVERT: B 196 HIS cc_start: 0.7198 (OUTLIER) cc_final: 0.6949 (m-70) REVERT: B 315 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7756 (pp) REVERT: C 413 GLU cc_start: 0.8074 (mp0) cc_final: 0.7836 (mp0) REVERT: D 96 LYS cc_start: 0.7928 (tppt) cc_final: 0.7595 (tppt) REVERT: D 158 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7867 (t70) REVERT: E 353 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8153 (tpt) REVERT: F 231 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7508 (pt0) REVERT: F 402 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7812 (tm-30) REVERT: H 270 MET cc_start: 0.8221 (mtm) cc_final: 0.7964 (mtp) REVERT: I 333 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8338 (pp) REVERT: I 415 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: I 520 GLU cc_start: 0.7883 (pt0) cc_final: 0.7521 (pt0) outliers start: 98 outliers final: 53 residues processed: 308 average time/residue: 1.5113 time to fit residues: 559.2096 Evaluate side-chains 292 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 231 time to evaluate : 3.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 196 HIS Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 468 MET Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 353 MET Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 509 GLU Chi-restraints excluded: chain F residue 231 GLN Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 446 MET Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 366 ASN Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 258 ILE Chi-restraints excluded: chain H residue 463 LEU Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 415 GLU Chi-restraints excluded: chain I residue 482 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 363 optimal weight: 9.9990 chunk 248 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 325 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 372 optimal weight: 7.9990 chunk 302 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 223 optimal weight: 2.9990 chunk 392 optimal weight: 2.9990 chunk 110 optimal weight: 0.4980 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS A 190 HIS D 515 GLN E 73 ASN ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 GLN I 514 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35605 Z= 0.180 Angle : 0.522 9.481 48094 Z= 0.258 Chirality : 0.041 0.159 5698 Planarity : 0.004 0.064 6157 Dihedral : 8.266 163.845 4951 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.55 % Allowed : 14.67 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.13), residues: 4539 helix: 1.85 (0.11), residues: 2281 sheet: 0.71 (0.22), residues: 597 loop : -1.18 (0.14), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 435 HIS 0.004 0.001 HIS A 37 PHE 0.013 0.001 PHE A 20 TYR 0.013 0.001 TYR F 282 ARG 0.007 0.000 ARG G 480 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 246 time to evaluate : 4.283 Fit side-chains REVERT: A 205 GLU cc_start: 0.4284 (mm-30) cc_final: 0.3931 (mt-10) REVERT: A 375 GLN cc_start: 0.8140 (pt0) cc_final: 0.7442 (pt0) REVERT: B 133 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.6584 (mp0) REVERT: B 196 HIS cc_start: 0.7001 (OUTLIER) cc_final: 0.6771 (m-70) REVERT: B 249 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7991 (ppp) REVERT: B 315 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7779 (pp) REVERT: D 96 LYS cc_start: 0.7981 (tppt) cc_final: 0.7656 (tppt) REVERT: D 158 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7859 (t70) REVERT: E 353 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8191 (tpt) REVERT: E 416 LEU cc_start: 0.8617 (tp) cc_final: 0.8263 (mt) REVERT: E 481 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8502 (ptt-90) REVERT: F 231 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7460 (pt0) REVERT: F 402 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7895 (tm-30) REVERT: F 446 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.6036 (mmm) REVERT: G 182 THR cc_start: 0.7379 (OUTLIER) cc_final: 0.6817 (p) REVERT: G 480 ARG cc_start: 0.7284 (mmm-85) cc_final: 0.6664 (mmp-170) REVERT: H 270 MET cc_start: 0.8135 (mtm) cc_final: 0.7904 (mtp) REVERT: I 63 LEU cc_start: 0.8479 (tp) cc_final: 0.8217 (tt) REVERT: I 333 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8315 (pp) REVERT: I 520 GLU cc_start: 0.7911 (pt0) cc_final: 0.7526 (pt0) outliers start: 97 outliers final: 54 residues processed: 316 average time/residue: 1.4861 time to fit residues: 565.1381 Evaluate side-chains 298 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 233 time to evaluate : 4.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 196 HIS Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 249 MET Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 468 MET Chi-restraints excluded: chain D residue 515 GLN Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 353 MET Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 481 ARG Chi-restraints excluded: chain E residue 509 GLU Chi-restraints excluded: chain F residue 231 GLN Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 446 MET Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 132 ILE Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 366 ASN Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 258 ILE Chi-restraints excluded: chain H residue 459 THR Chi-restraints excluded: chain H residue 463 LEU Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 482 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 146 optimal weight: 5.9990 chunk 393 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 256 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 437 optimal weight: 4.9990 chunk 363 optimal weight: 10.0000 chunk 202 optimal weight: 2.9990 chunk 36 optimal weight: 0.0370 chunk 144 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS A 190 HIS E 294 GLN H 188 ASN I 84 GLN I 514 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 35605 Z= 0.284 Angle : 0.571 9.562 48094 Z= 0.285 Chirality : 0.044 0.167 5698 Planarity : 0.004 0.068 6157 Dihedral : 8.310 163.247 4951 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.34 % Favored : 95.64 % Rotamer: Outliers : 2.78 % Allowed : 14.99 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.13), residues: 4539 helix: 1.73 (0.11), residues: 2275 sheet: 0.65 (0.22), residues: 586 loop : -1.24 (0.14), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 484 HIS 0.005 0.001 HIS A 37 PHE 0.013 0.001 PHE E 497 TYR 0.012 0.001 TYR F 282 ARG 0.005 0.000 ARG G 480 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 244 time to evaluate : 3.914 Fit side-chains REVERT: A 73 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.7196 (mpm) REVERT: A 205 GLU cc_start: 0.4305 (mm-30) cc_final: 0.3945 (mt-10) REVERT: A 375 GLN cc_start: 0.8174 (pt0) cc_final: 0.7416 (pt0) REVERT: A 379 LYS cc_start: 0.8721 (mtpp) cc_final: 0.8496 (mtpt) REVERT: B 68 ASP cc_start: 0.8009 (t0) cc_final: 0.7583 (t0) REVERT: B 133 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.6681 (mp0) REVERT: B 315 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7877 (pp) REVERT: D 96 LYS cc_start: 0.8065 (tppt) cc_final: 0.7710 (tppt) REVERT: D 158 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.7915 (t70) REVERT: D 457 VAL cc_start: 0.8871 (OUTLIER) cc_final: 0.8640 (t) REVERT: E 66 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.7861 (t0) REVERT: E 86 ASP cc_start: 0.8267 (t70) cc_final: 0.8043 (t70) REVERT: E 353 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8477 (ttt) REVERT: E 481 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8504 (ptt-90) REVERT: F 128 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8392 (mm) REVERT: F 402 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7886 (tm-30) REVERT: F 446 MET cc_start: 0.7057 (OUTLIER) cc_final: 0.6199 (mmm) REVERT: G 182 THR cc_start: 0.7382 (OUTLIER) cc_final: 0.6850 (p) REVERT: G 480 ARG cc_start: 0.7307 (mmm-85) cc_final: 0.6765 (mmp-170) REVERT: H 270 MET cc_start: 0.8276 (mtm) cc_final: 0.8010 (mtp) REVERT: I 339 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8585 (mp) REVERT: I 415 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7680 (mp0) REVERT: I 487 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7773 (ppp) REVERT: I 520 GLU cc_start: 0.7928 (pt0) cc_final: 0.7516 (pt0) outliers start: 106 outliers final: 55 residues processed: 320 average time/residue: 1.5224 time to fit residues: 583.2881 Evaluate side-chains 303 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 234 time to evaluate : 4.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 468 MET Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 353 MET Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 481 ARG Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 446 MET Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 132 ILE Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 366 ASN Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 258 ILE Chi-restraints excluded: chain H residue 459 THR Chi-restraints excluded: chain H residue 463 LEU Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 339 LEU Chi-restraints excluded: chain I residue 415 GLU Chi-restraints excluded: chain I residue 482 ASN Chi-restraints excluded: chain I residue 487 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 421 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 249 optimal weight: 2.9990 chunk 319 optimal weight: 0.9990 chunk 247 optimal weight: 1.9990 chunk 368 optimal weight: 8.9990 chunk 244 optimal weight: 4.9990 chunk 435 optimal weight: 4.9990 chunk 272 optimal weight: 0.8980 chunk 265 optimal weight: 9.9990 chunk 201 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS A 190 HIS ** D 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN I 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 35605 Z= 0.160 Angle : 0.519 9.140 48094 Z= 0.258 Chirality : 0.041 0.153 5698 Planarity : 0.003 0.064 6157 Dihedral : 7.746 156.799 4948 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.61 % Favored : 96.36 % Rotamer: Outliers : 2.41 % Allowed : 15.75 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.13), residues: 4539 helix: 1.89 (0.11), residues: 2275 sheet: 0.68 (0.22), residues: 588 loop : -1.17 (0.14), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 435 HIS 0.004 0.001 HIS A 37 PHE 0.027 0.001 PHE G 8 TYR 0.013 0.001 TYR F 282 ARG 0.005 0.000 ARG G 480 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 248 time to evaluate : 4.349 Fit side-chains REVERT: A 205 GLU cc_start: 0.4275 (mm-30) cc_final: 0.3940 (mt-10) REVERT: A 375 GLN cc_start: 0.8187 (pt0) cc_final: 0.7509 (pt0) REVERT: B 133 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6575 (mp0) REVERT: B 372 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.7975 (pt) REVERT: D 93 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7727 (mp0) REVERT: D 96 LYS cc_start: 0.8047 (tppt) cc_final: 0.7723 (tppt) REVERT: D 158 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.7959 (t70) REVERT: D 393 MET cc_start: 0.7914 (mtm) cc_final: 0.7602 (mpt) REVERT: D 457 VAL cc_start: 0.8806 (OUTLIER) cc_final: 0.8568 (t) REVERT: E 353 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8199 (tpt) REVERT: E 416 LEU cc_start: 0.8604 (tp) cc_final: 0.8264 (mt) REVERT: E 481 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8513 (ptt-90) REVERT: F 231 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7395 (pt0) REVERT: F 446 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6092 (mmm) REVERT: G 182 THR cc_start: 0.7329 (OUTLIER) cc_final: 0.6807 (p) REVERT: G 480 ARG cc_start: 0.7279 (mmm-85) cc_final: 0.6763 (mmp-170) REVERT: H 270 MET cc_start: 0.8122 (mtm) cc_final: 0.7875 (mtp) REVERT: I 63 LEU cc_start: 0.8490 (tp) cc_final: 0.8245 (tt) REVERT: I 66 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.6543 (mp0) REVERT: I 333 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8316 (pp) REVERT: I 520 GLU cc_start: 0.7849 (pt0) cc_final: 0.7418 (pt0) outliers start: 92 outliers final: 56 residues processed: 315 average time/residue: 1.4698 time to fit residues: 559.2687 Evaluate side-chains 305 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 238 time to evaluate : 4.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 468 MET Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 353 MET Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 389 SER Chi-restraints excluded: chain E residue 481 ARG Chi-restraints excluded: chain E residue 509 GLU Chi-restraints excluded: chain F residue 231 GLN Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain F residue 446 MET Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 132 ILE Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 366 ASN Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 258 ILE Chi-restraints excluded: chain H residue 459 THR Chi-restraints excluded: chain H residue 463 LEU Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 66 GLU Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 482 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 269 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 260 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 276 optimal weight: 9.9990 chunk 296 optimal weight: 3.9990 chunk 215 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 342 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS A 190 HIS ** D 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 GLN I 514 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35605 Z= 0.210 Angle : 0.533 8.464 48094 Z= 0.265 Chirality : 0.042 0.154 5698 Planarity : 0.004 0.066 6157 Dihedral : 7.628 159.271 4948 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.41 % Allowed : 15.96 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.13), residues: 4539 helix: 1.87 (0.11), residues: 2273 sheet: 0.69 (0.22), residues: 588 loop : -1.18 (0.14), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 435 HIS 0.006 0.001 HIS A 37 PHE 0.025 0.001 PHE G 8 TYR 0.012 0.001 TYR F 282 ARG 0.004 0.000 ARG G 480 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 237 time to evaluate : 4.316 Fit side-chains REVERT: A 73 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.7173 (mpm) REVERT: A 205 GLU cc_start: 0.4261 (mm-30) cc_final: 0.3923 (mt-10) REVERT: A 375 GLN cc_start: 0.8227 (pt0) cc_final: 0.7509 (pt0) REVERT: B 133 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.6649 (mp0) REVERT: D 93 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7723 (mp0) REVERT: D 96 LYS cc_start: 0.8070 (tppt) cc_final: 0.7739 (tppt) REVERT: D 457 VAL cc_start: 0.8819 (OUTLIER) cc_final: 0.8581 (t) REVERT: E 353 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8159 (tpt) REVERT: E 416 LEU cc_start: 0.8626 (tp) cc_final: 0.8274 (mt) REVERT: E 481 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8521 (ptt-90) REVERT: F 231 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7459 (pt0) REVERT: G 182 THR cc_start: 0.7327 (OUTLIER) cc_final: 0.6890 (p) REVERT: H 10 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7549 (tt) REVERT: H 270 MET cc_start: 0.8166 (mtm) cc_final: 0.7894 (mtp) REVERT: I 63 LEU cc_start: 0.8492 (tp) cc_final: 0.8241 (tt) REVERT: I 338 ASP cc_start: 0.7960 (p0) cc_final: 0.7662 (p0) REVERT: I 339 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8618 (mp) REVERT: I 415 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7597 (mp0) REVERT: I 520 GLU cc_start: 0.7920 (pt0) cc_final: 0.7477 (pt0) outliers start: 92 outliers final: 58 residues processed: 308 average time/residue: 1.4548 time to fit residues: 541.8549 Evaluate side-chains 299 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 231 time to evaluate : 4.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 468 MET Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 353 MET Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 481 ARG Chi-restraints excluded: chain E residue 509 GLU Chi-restraints excluded: chain F residue 231 GLN Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain F residue 446 MET Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 132 ILE Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 366 ASN Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 258 ILE Chi-restraints excluded: chain H residue 459 THR Chi-restraints excluded: chain H residue 463 LEU Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 339 LEU Chi-restraints excluded: chain I residue 415 GLU Chi-restraints excluded: chain I residue 482 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 396 optimal weight: 10.0000 chunk 417 optimal weight: 4.9990 chunk 380 optimal weight: 0.1980 chunk 405 optimal weight: 9.9990 chunk 244 optimal weight: 3.9990 chunk 176 optimal weight: 0.5980 chunk 318 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 366 optimal weight: 1.9990 chunk 383 optimal weight: 1.9990 chunk 404 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS A 190 HIS ** D 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 35605 Z= 0.144 Angle : 0.507 8.137 48094 Z= 0.251 Chirality : 0.041 0.153 5698 Planarity : 0.003 0.065 6157 Dihedral : 7.214 154.210 4946 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.92 % Allowed : 16.59 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.13), residues: 4539 helix: 2.00 (0.11), residues: 2268 sheet: 0.77 (0.22), residues: 601 loop : -1.08 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 21 HIS 0.005 0.001 HIS A 37 PHE 0.012 0.001 PHE A 20 TYR 0.012 0.001 TYR F 282 ARG 0.007 0.000 ARG G 480 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 248 time to evaluate : 4.236 Fit side-chains REVERT: A 73 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.7055 (mpm) REVERT: A 205 GLU cc_start: 0.4169 (mm-30) cc_final: 0.3883 (mt-10) REVERT: A 375 GLN cc_start: 0.8209 (pt0) cc_final: 0.7493 (pt0) REVERT: B 133 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6617 (mp0) REVERT: B 315 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7905 (pp) REVERT: B 372 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.7950 (pt) REVERT: C 113 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7600 (mt-10) REVERT: D 93 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7711 (mp0) REVERT: D 96 LYS cc_start: 0.7922 (tppt) cc_final: 0.7628 (tppt) REVERT: D 457 VAL cc_start: 0.8784 (OUTLIER) cc_final: 0.8556 (t) REVERT: E 251 ILE cc_start: 0.2991 (OUTLIER) cc_final: 0.2717 (pt) REVERT: E 416 LEU cc_start: 0.8552 (tp) cc_final: 0.8249 (mt) REVERT: F 231 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7463 (pt0) REVERT: F 446 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6254 (mmm) REVERT: G 182 THR cc_start: 0.7342 (OUTLIER) cc_final: 0.6871 (p) REVERT: H 270 MET cc_start: 0.8091 (mtm) cc_final: 0.7848 (mtp) REVERT: I 63 LEU cc_start: 0.8472 (tp) cc_final: 0.8232 (tt) REVERT: I 66 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.6567 (mp0) REVERT: I 338 ASP cc_start: 0.7876 (p0) cc_final: 0.7637 (p0) REVERT: I 339 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8608 (mp) REVERT: I 487 MET cc_start: 0.7932 (ppp) cc_final: 0.7706 (ppp) REVERT: I 520 GLU cc_start: 0.7885 (pt0) cc_final: 0.7474 (pt0) outliers start: 73 outliers final: 48 residues processed: 302 average time/residue: 1.4067 time to fit residues: 514.9285 Evaluate side-chains 292 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 233 time to evaluate : 4.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 468 MET Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 509 GLU Chi-restraints excluded: chain F residue 231 GLN Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain F residue 446 MET Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 132 ILE Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 366 ASN Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 258 ILE Chi-restraints excluded: chain H residue 459 THR Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 66 GLU Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 339 LEU Chi-restraints excluded: chain I residue 482 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 266 optimal weight: 7.9990 chunk 429 optimal weight: 0.7980 chunk 262 optimal weight: 10.0000 chunk 203 optimal weight: 4.9990 chunk 298 optimal weight: 0.3980 chunk 450 optimal weight: 2.9990 chunk 414 optimal weight: 9.9990 chunk 358 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 276 optimal weight: 8.9990 chunk 219 optimal weight: 8.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS A 190 HIS ** D 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 GLN I 514 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35605 Z= 0.215 Angle : 0.541 11.826 48094 Z= 0.268 Chirality : 0.042 0.157 5698 Planarity : 0.004 0.067 6157 Dihedral : 7.271 158.875 4945 Min Nonbonded Distance : 1.576 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.78 % Allowed : 16.90 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.13), residues: 4539 helix: 1.92 (0.11), residues: 2268 sheet: 0.74 (0.22), residues: 590 loop : -1.09 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 435 HIS 0.006 0.001 HIS A 37 PHE 0.023 0.001 PHE G 8 TYR 0.012 0.001 TYR F 282 ARG 0.007 0.000 ARG G 480 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9078 Ramachandran restraints generated. 4539 Oldfield, 0 Emsley, 4539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 235 time to evaluate : 3.951 Fit side-chains REVERT: A 73 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.7026 (mpm) REVERT: A 205 GLU cc_start: 0.4166 (mm-30) cc_final: 0.3944 (mt-10) REVERT: A 375 GLN cc_start: 0.8212 (pt0) cc_final: 0.7499 (pt0) REVERT: B 133 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6598 (mp0) REVERT: B 315 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7877 (pp) REVERT: C 113 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7689 (mt-10) REVERT: D 93 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7764 (mp0) REVERT: D 96 LYS cc_start: 0.8038 (tppt) cc_final: 0.7723 (tppt) REVERT: D 457 VAL cc_start: 0.8835 (OUTLIER) cc_final: 0.8595 (t) REVERT: D 460 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8104 (mtp) REVERT: E 416 LEU cc_start: 0.8596 (tp) cc_final: 0.8280 (mt) REVERT: F 231 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7472 (pt0) REVERT: G 182 THR cc_start: 0.7397 (OUTLIER) cc_final: 0.6920 (p) REVERT: H 270 MET cc_start: 0.8162 (mtm) cc_final: 0.7902 (mtp) REVERT: I 63 LEU cc_start: 0.8502 (tp) cc_final: 0.8256 (tt) REVERT: I 261 LYS cc_start: 0.8164 (mppt) cc_final: 0.7913 (mptt) REVERT: I 338 ASP cc_start: 0.7911 (p0) cc_final: 0.7666 (p0) REVERT: I 339 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8605 (mp) REVERT: I 487 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7727 (ppp) REVERT: I 520 GLU cc_start: 0.7922 (pt0) cc_final: 0.7478 (pt0) outliers start: 68 outliers final: 49 residues processed: 285 average time/residue: 1.4660 time to fit residues: 506.1324 Evaluate side-chains 289 residues out of total 3810 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 231 time to evaluate : 4.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 509 GLU Chi-restraints excluded: chain F residue 231 GLN Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 414 CYS Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 132 ILE Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 366 ASN Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 258 ILE Chi-restraints excluded: chain H residue 459 THR Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 339 LEU Chi-restraints excluded: chain I residue 482 ASN Chi-restraints excluded: chain I residue 487 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 284 optimal weight: 0.7980 chunk 381 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 330 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 359 optimal weight: 0.7980 chunk 150 optimal weight: 0.7980 chunk 368 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS A 190 HIS B 67 ASN ** D 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.104447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.087947 restraints weight = 55601.094| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.40 r_work: 0.3058 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 35605 Z= 0.144 Angle : 0.508 11.899 48094 Z= 0.251 Chirality : 0.041 0.155 5698 Planarity : 0.003 0.065 6157 Dihedral : 6.958 152.946 4945 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.52 % Allowed : 17.43 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.13), residues: 4539 helix: 2.05 (0.11), residues: 2267 sheet: 0.84 (0.22), residues: 611 loop : -1.03 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 21 HIS 0.005 0.001 HIS A 37 PHE 0.011 0.001 PHE A 20 TYR 0.013 0.001 TYR F 282 ARG 0.007 0.000 ARG G 480 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9784.12 seconds wall clock time: 174 minutes 53.85 seconds (10493.85 seconds total)