Starting phenix.real_space_refine on Sat Mar 23 23:59:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voj_21266/03_2024/6voj_21266_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voj_21266/03_2024/6voj_21266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voj_21266/03_2024/6voj_21266.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voj_21266/03_2024/6voj_21266.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voj_21266/03_2024/6voj_21266_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6voj_21266/03_2024/6voj_21266_updated.pdb" } resolution = 4.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 129 5.16 5 C 24849 2.51 5 N 6674 2.21 5 O 7487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 15": "OE1" <-> "OE2" Residue "A TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 386": "OE1" <-> "OE2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "B ARG 5": "NH1" <-> "NH2" Residue "B GLU 8": "OE1" <-> "OE2" Residue "B ARG 14": "NH1" <-> "NH2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B GLU 285": "OE1" <-> "OE2" Residue "B GLU 386": "OE1" <-> "OE2" Residue "B GLU 433": "OE1" <-> "OE2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B GLU 492": "OE1" <-> "OE2" Residue "C GLU 8": "OE1" <-> "OE2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C ARG 107": "NH1" <-> "NH2" Residue "C ARG 216": "NH1" <-> "NH2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "C ARG 297": "NH1" <-> "NH2" Residue "C ARG 455": "NH1" <-> "NH2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C GLU 492": "OE1" <-> "OE2" Residue "D ARG 52": "NH1" <-> "NH2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D GLU 305": "OE1" <-> "OE2" Residue "D GLU 412": "OE1" <-> "OE2" Residue "D GLU 491": "OE1" <-> "OE2" Residue "E GLU 64": "OE1" <-> "OE2" Residue "E GLU 150": "OE1" <-> "OE2" Residue "E ARG 163": "NH1" <-> "NH2" Residue "E GLU 265": "OE1" <-> "OE2" Residue "E GLU 284": "OE1" <-> "OE2" Residue "E GLU 382": "OE1" <-> "OE2" Residue "E GLU 383": "OE1" <-> "OE2" Residue "E GLU 400": "OE1" <-> "OE2" Residue "E GLU 415": "OE1" <-> "OE2" Residue "E GLU 428": "OE1" <-> "OE2" Residue "F GLU 64": "OE1" <-> "OE2" Residue "F ARG 87": "NH1" <-> "NH2" Residue "F ARG 127": "NH1" <-> "NH2" Residue "F ARG 164": "NH1" <-> "NH2" Residue "F GLU 184": "OE1" <-> "OE2" Residue "F GLU 284": "OE1" <-> "OE2" Residue "d ARG 77": "NH1" <-> "NH2" Residue "d GLU 93": "OE1" <-> "OE2" Residue "d GLU 164": "OE1" <-> "OE2" Residue "d ARG 208": "NH1" <-> "NH2" Residue "e ARG 12": "NH1" <-> "NH2" Residue "e ARG 68": "NH1" <-> "NH2" Residue "e GLU 97": "OE1" <-> "OE2" Residue "e GLU 100": "OE1" <-> "OE2" Residue "e GLU 107": "OE1" <-> "OE2" Residue "e ARG 110": "NH1" <-> "NH2" Residue "e GLU 127": "OE1" <-> "OE2" Residue "g GLU 46": "OE1" <-> "OE2" Residue "g ARG 48": "NH1" <-> "NH2" Residue "g ARG 73": "NH1" <-> "NH2" Residue "g ARG 83": "NH1" <-> "NH2" Residue "g ARG 127": "NH1" <-> "NH2" Residue "g PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 144": "NH1" <-> "NH2" Residue "g ARG 170": "NH1" <-> "NH2" Residue "g GLU 190": "OE1" <-> "OE2" Residue "g GLU 206": "OE1" <-> "OE2" Residue "g GLU 251": "OE1" <-> "OE2" Residue "g ARG 256": "NH1" <-> "NH2" Residue "g PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 306": "NH1" <-> "NH2" Residue "I ARG 59": "NH1" <-> "NH2" Residue "I GLU 68": "OE1" <-> "OE2" Residue "I ARG 71": "NH1" <-> "NH2" Residue "I ARG 82": "NH1" <-> "NH2" Residue "I GLU 127": "OE1" <-> "OE2" Residue "J GLU 96": "OE1" <-> "OE2" Residue "J GLU 136": "OE1" <-> "OE2" Residue "J GLU 182": "OE1" <-> "OE2" Residue "a TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 59": "NH1" <-> "NH2" Residue "a GLU 89": "OE1" <-> "OE2" Residue "a GLU 126": "OE1" <-> "OE2" Residue "a GLU 241": "OE1" <-> "OE2" Residue "M GLU 44": "OE1" <-> "OE2" Residue "N GLU 37": "OE1" <-> "OE2" Residue "P GLU 37": "OE1" <-> "OE2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "V GLU 37": "OE1" <-> "OE2" Residue "X GLU 37": "OE1" <-> "OE2" Residue "Y GLU 44": "OE1" <-> "OE2" Residue "Z GLU 44": "OE1" <-> "OE2" 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: 39155 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 3827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3827 Classifications: {'peptide': 498} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 479} Chain: "B" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3851 Classifications: {'peptide': 501} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 482} Chain: "C" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3849 Classifications: {'peptide': 501} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 482} Chain: "D" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3636 Classifications: {'peptide': 480} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 453} Chain: "E" Number of atoms: 3619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3619 Classifications: {'peptide': 478} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 451} Chain: "F" Number of atoms: 3627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3627 Classifications: {'peptide': 479} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 452} Chain: "d" Number of atoms: 1383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1383 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 4, 'TRANS': 174} Chain: "e" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1010 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "g" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2502 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 12, 'TRANS': 309} Chain: "I" Number of atoms: 1244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1244 Classifications: {'peptide': 154} Link IDs: {'TRANS': 153} Chain: "J" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1049 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "a" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1734 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 14, 'TRANS': 207} Chain: "M" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "N" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "O" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "P" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "Q" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "R" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "S" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "T" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "U" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "V" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "W" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "X" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "Y" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "Z" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'ATP': 1, 'TTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 19.70, per 1000 atoms: 0.50 Number of scatterers: 39155 At special positions: 0 Unit cell: (169.533, 174.798, 210.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 129 16.00 P 16 15.00 O 7487 8.00 N 6674 7.00 C 24849 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.78 Conformation dependent library (CDL) restraints added in 7.1 seconds 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9420 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 172 helices and 26 sheets defined 54.6% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.06 Creating SS restraints... Processing helix chain 'A' and resid 11 through 24 Processing helix chain 'A' and resid 57 through 59 No H-bonds generated for 'chain 'A' and resid 57 through 59' Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 176 through 186 removed outlier: 3.960A pdb=" N ILE A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 215 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 233 through 252 Proline residue: A 240 - end of helix Processing helix chain 'A' and resid 264 through 277 Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 291 through 299 removed outlier: 3.809A pdb=" N LEU A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 338 Processing helix chain 'A' and resid 347 through 350 No H-bonds generated for 'chain 'A' and resid 347 through 350' Processing helix chain 'A' and resid 368 through 371 removed outlier: 3.661A pdb=" N ALA A 371 " --> pdb=" O GLY A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 368 through 371' Processing helix chain 'A' and resid 374 through 392 removed outlier: 4.122A pdb=" N LYS A 378 " --> pdb=" O LYS A 374 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 400 No H-bonds generated for 'chain 'A' and resid 398 through 400' Processing helix chain 'A' and resid 405 through 421 Processing helix chain 'A' and resid 431 through 442 Processing helix chain 'A' and resid 454 through 468 Processing helix chain 'A' and resid 471 through 479 Processing helix chain 'A' and resid 484 through 502 Processing helix chain 'B' and resid 12 through 18 Processing helix chain 'B' and resid 152 through 156 Processing helix chain 'B' and resid 176 through 187 removed outlier: 4.207A pdb=" N GLN B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 233 through 252 Proline residue: B 240 - end of helix Processing helix chain 'B' and resid 265 through 277 removed outlier: 3.775A pdb=" N MET B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 286 No H-bonds generated for 'chain 'B' and resid 284 through 286' Processing helix chain 'B' and resid 289 through 301 removed outlier: 3.848A pdb=" N PHE B 292 " --> pdb=" O GLY B 289 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLU B 300 " --> pdb=" O ARG B 297 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG B 301 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 330 through 338 Processing helix chain 'B' and resid 347 through 350 No H-bonds generated for 'chain 'B' and resid 347 through 350' Processing helix chain 'B' and resid 368 through 371 Processing helix chain 'B' and resid 374 through 379 Processing helix chain 'B' and resid 383 through 398 removed outlier: 3.863A pdb=" N PHE B 396 " --> pdb=" O GLU B 392 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN B 398 " --> pdb=" O GLU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 421 removed outlier: 4.136A pdb=" N LEU B 421 " --> pdb=" O LEU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 442 Processing helix chain 'B' and resid 453 through 468 removed outlier: 3.855A pdb=" N GLU B 460 " --> pdb=" O LYS B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 478 Processing helix chain 'B' and resid 484 through 503 Processing helix chain 'C' and resid 6 through 17 removed outlier: 4.203A pdb=" N SER C 10 " --> pdb=" O ALA C 6 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LYS C 11 " --> pdb=" O ASP C 7 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ARG C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE C 17 " --> pdb=" O ILE C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 137 through 139 No H-bonds generated for 'chain 'C' and resid 137 through 139' Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'C' and resid 176 through 185 Processing helix chain 'C' and resid 203 through 215 Processing helix chain 'C' and resid 219 through 221 No H-bonds generated for 'chain 'C' and resid 219 through 221' Processing helix chain 'C' and resid 233 through 252 Proline residue: C 240 - end of helix removed outlier: 4.262A pdb=" N PHE C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 277 Processing helix chain 'C' and resid 284 through 286 No H-bonds generated for 'chain 'C' and resid 284 through 286' Processing helix chain 'C' and resid 289 through 301 removed outlier: 4.110A pdb=" N PHE C 292 " --> pdb=" O GLY C 289 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG C 297 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU C 300 " --> pdb=" O ARG C 297 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG C 301 " --> pdb=" O LEU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 325 No H-bonds generated for 'chain 'C' and resid 323 through 325' Processing helix chain 'C' and resid 330 through 338 removed outlier: 3.575A pdb=" N SER C 337 " --> pdb=" O THR C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 351 Processing helix chain 'C' and resid 374 through 394 removed outlier: 5.711A pdb=" N LYS C 382 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU C 383 " --> pdb=" O VAL C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 412 Processing helix chain 'C' and resid 415 through 421 Processing helix chain 'C' and resid 431 through 443 removed outlier: 3.527A pdb=" N GLY C 441 " --> pdb=" O THR C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 467 Processing helix chain 'C' and resid 471 through 479 Processing helix chain 'C' and resid 484 through 502 Processing helix chain 'D' and resid 139 through 141 No H-bonds generated for 'chain 'D' and resid 139 through 141' Processing helix chain 'D' and resid 154 through 158 Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 206 through 218 Processing helix chain 'D' and resid 243 through 262 removed outlier: 4.798A pdb=" N GLY D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LEU D 251 " --> pdb=" O MET D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 288 removed outlier: 4.002A pdb=" N LEU D 288 " --> pdb=" O GLU D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 310 Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 337 through 345 removed outlier: 4.366A pdb=" N ALA D 344 " --> pdb=" O ALA D 340 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N HIS D 345 " --> pdb=" O THR D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 359 Processing helix chain 'D' and resid 377 through 380 No H-bonds generated for 'chain 'D' and resid 377 through 380' Processing helix chain 'D' and resid 382 through 405 removed outlier: 4.696A pdb=" N ASP D 403 " --> pdb=" O LYS D 399 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 430 removed outlier: 4.413A pdb=" N ARG D 429 " --> pdb=" O ARG D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 442 removed outlier: 4.191A pdb=" N VAL D 440 " --> pdb=" O VAL D 437 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR D 442 " --> pdb=" O GLU D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 462 Processing helix chain 'D' and resid 471 through 474 removed outlier: 4.035A pdb=" N PHE D 474 " --> pdb=" O GLU D 471 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 471 through 474' Processing helix chain 'D' and resid 480 through 495 Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 154 through 158 Processing helix chain 'E' and resid 178 through 189 Processing helix chain 'E' and resid 206 through 219 removed outlier: 3.586A pdb=" N TYR E 213 " --> pdb=" O GLY E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 230 No H-bonds generated for 'chain 'E' and resid 228 through 230' Processing helix chain 'E' and resid 243 through 264 removed outlier: 5.105A pdb=" N GLY E 250 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU E 251 " --> pdb=" O MET E 247 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE E 260 " --> pdb=" O MET E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 286 removed outlier: 3.584A pdb=" N GLY E 282 " --> pdb=" O PHE E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 313 removed outlier: 3.786A pdb=" N LEU E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG E 312 " --> pdb=" O SER E 308 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE E 313 " --> pdb=" O LEU E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 332 No H-bonds generated for 'chain 'E' and resid 330 through 332' Processing helix chain 'E' and resid 337 through 345 removed outlier: 4.447A pdb=" N ALA E 344 " --> pdb=" O ALA E 340 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N HIS E 345 " --> pdb=" O THR E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 358 Processing helix chain 'E' and resid 377 through 407 removed outlier: 7.730A pdb=" N GLU E 382 " --> pdb=" O ARG E 378 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N GLU E 383 " --> pdb=" O ILE E 379 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N HIS E 384 " --> pdb=" O VAL E 380 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR E 385 " --> pdb=" O GLY E 381 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASP E 403 " --> pdb=" O LYS E 399 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ILE E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 430 removed outlier: 3.918A pdb=" N THR E 420 " --> pdb=" O GLU E 416 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 440 No H-bonds generated for 'chain 'E' and resid 438 through 440' Processing helix chain 'E' and resid 451 through 463 removed outlier: 4.138A pdb=" N ARG E 456 " --> pdb=" O ALA E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 471 through 473 No H-bonds generated for 'chain 'E' and resid 471 through 473' Processing helix chain 'E' and resid 480 through 490 Processing helix chain 'F' and resid 154 through 158 Processing helix chain 'F' and resid 178 through 192 Processing helix chain 'F' and resid 206 through 218 Processing helix chain 'F' and resid 243 through 263 removed outlier: 3.884A pdb=" N MET F 247 " --> pdb=" O PRO F 243 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLY F 250 " --> pdb=" O ARG F 246 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU F 251 " --> pdb=" O MET F 247 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE F 260 " --> pdb=" O MET F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 289 Processing helix chain 'F' and resid 302 through 312 removed outlier: 3.765A pdb=" N LEU F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ARG F 312 " --> pdb=" O SER F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 332 No H-bonds generated for 'chain 'F' and resid 330 through 332' Processing helix chain 'F' and resid 337 through 345 removed outlier: 3.536A pdb=" N ALA F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N HIS F 345 " --> pdb=" O THR F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 359 Processing helix chain 'F' and resid 377 through 380 No H-bonds generated for 'chain 'F' and resid 377 through 380' Processing helix chain 'F' and resid 382 through 400 removed outlier: 3.522A pdb=" N GLU F 400 " --> pdb=" O GLN F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 431 Processing helix chain 'F' and resid 439 through 442 No H-bonds generated for 'chain 'F' and resid 439 through 442' Processing helix chain 'F' and resid 451 through 462 Processing helix chain 'F' and resid 471 through 473 No H-bonds generated for 'chain 'F' and resid 471 through 473' Processing helix chain 'F' and resid 480 through 494 Processing helix chain 'd' and resid 76 through 89 Processing helix chain 'd' and resid 92 through 105 removed outlier: 3.703A pdb=" N SER d 97 " --> pdb=" O GLU d 93 " (cutoff:3.500A) Processing helix chain 'd' and resid 109 through 116 Processing helix chain 'd' and resid 122 through 136 Processing helix chain 'd' and resid 140 through 151 removed outlier: 4.540A pdb=" N PHE d 145 " --> pdb=" O HIS d 141 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE d 146 " --> pdb=" O THR d 142 " (cutoff:3.500A) Processing helix chain 'd' and resid 155 through 173 removed outlier: 3.504A pdb=" N VAL d 158 " --> pdb=" O ILE d 155 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LYS d 159 " --> pdb=" O ASN d 156 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU d 162 " --> pdb=" O LYS d 159 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE d 165 " --> pdb=" O LEU d 162 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU d 166 " --> pdb=" O ASN d 163 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR d 173 " --> pdb=" O ASN d 170 " (cutoff:3.500A) Processing helix chain 'd' and resid 188 through 202 Processing helix chain 'd' and resid 238 through 246 Processing helix chain 'e' and resid 89 through 105 removed outlier: 4.420A pdb=" N ARG e 104 " --> pdb=" O GLU e 100 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LYS e 105 " --> pdb=" O ALA e 101 " (cutoff:3.500A) Processing helix chain 'e' and resid 109 through 130 removed outlier: 4.030A pdb=" N ILE e 113 " --> pdb=" O LYS e 109 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU e 114 " --> pdb=" O ARG e 110 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA e 118 " --> pdb=" O GLU e 114 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA e 128 " --> pdb=" O THR e 124 " (cutoff:3.500A) Processing helix chain 'g' and resid 43 through 99 removed outlier: 3.596A pdb=" N GLU g 77 " --> pdb=" O ARG g 73 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL g 80 " --> pdb=" O GLN g 76 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY g 82 " --> pdb=" O ALA g 78 " (cutoff:3.500A) Proline residue: g 84 - end of helix removed outlier: 3.730A pdb=" N VAL g 92 " --> pdb=" O THR g 88 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASN g 97 " --> pdb=" O LEU g 93 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLU g 98 " --> pdb=" O TYR g 94 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLN g 99 " --> pdb=" O ASN g 95 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 147 Processing helix chain 'g' and resid 162 through 169 Processing helix chain 'g' and resid 189 through 203 Processing helix chain 'g' and resid 247 through 249 No H-bonds generated for 'chain 'g' and resid 247 through 249' Processing helix chain 'g' and resid 288 through 362 Proline residue: g 297 - end of helix Processing helix chain 'I' and resid 32 through 157 removed outlier: 4.070A pdb=" N VAL I 36 " --> pdb=" O ILE I 32 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE I 145 " --> pdb=" O ARG I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 179 Processing helix chain 'J' and resid 89 through 201 removed outlier: 4.925A pdb=" N THR J 110 " --> pdb=" O LYS J 106 " (cutoff:3.500A) Proline residue: J 111 - end of helix Processing helix chain 'J' and resid 204 through 218 removed outlier: 3.562A pdb=" N ILE J 214 " --> pdb=" O LEU J 210 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N VAL J 215 " --> pdb=" O SER J 211 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS J 216 " --> pdb=" O ASP J 212 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS J 217 " --> pdb=" O ASP J 213 " (cutoff:3.500A) Processing helix chain 'a' and resid 37 through 58 Processing helix chain 'a' and resid 70 through 87 Processing helix chain 'a' and resid 92 through 114 Proline residue: a 96 - end of helix removed outlier: 3.641A pdb=" N PHE a 102 " --> pdb=" O GLY a 99 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N PHE a 104 " --> pdb=" O MET a 101 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL a 107 " --> pdb=" O PHE a 104 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP a 110 " --> pdb=" O VAL a 107 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU a 114 " --> pdb=" O SER a 111 " (cutoff:3.500A) Processing helix chain 'a' and resid 134 through 154 Processing helix chain 'a' and resid 169 through 206 removed outlier: 3.864A pdb=" N LEU a 172 " --> pdb=" O PRO a 169 " (cutoff:3.500A) Proline residue: a 173 - end of helix removed outlier: 3.555A pdb=" N ASP a 179 " --> pdb=" O ILE a 176 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS a 182 " --> pdb=" O ASP a 179 " (cutoff:3.500A) Proline residue: a 183 - end of helix removed outlier: 4.385A pdb=" N ARG a 189 " --> pdb=" O LEU a 186 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU a 190 " --> pdb=" O SER a 187 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE a 191 " --> pdb=" O PHE a 188 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU a 195 " --> pdb=" O GLY a 192 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL a 203 " --> pdb=" O VAL a 200 " (cutoff:3.500A) Processing helix chain 'a' and resid 214 through 243 removed outlier: 3.587A pdb=" N GLY a 225 " --> pdb=" O LEU a 221 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 19 Processing helix chain 'M' and resid 22 through 41 Processing helix chain 'M' and resid 43 through 75 removed outlier: 4.270A pdb=" N GLY M 47 " --> pdb=" O GLU M 44 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ARG M 50 " --> pdb=" O GLY M 47 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N GLY M 51 " --> pdb=" O LYS M 48 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA M 62 " --> pdb=" O PHE M 59 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU M 63 " --> pdb=" O MET M 60 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR M 66 " --> pdb=" O LEU M 63 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL M 70 " --> pdb=" O GLY M 67 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU M 72 " --> pdb=" O VAL M 69 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU M 75 " --> pdb=" O LEU M 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 20 removed outlier: 3.858A pdb=" N VAL N 17 " --> pdb=" O ALA N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 41 removed outlier: 3.873A pdb=" N GLY N 29 " --> pdb=" O GLY N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 75 removed outlier: 5.183A pdb=" N GLY N 51 " --> pdb=" O GLY N 47 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N THR N 52 " --> pdb=" O LYS N 48 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU N 63 " --> pdb=" O PHE N 59 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR N 64 " --> pdb=" O MET N 60 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY N 67 " --> pdb=" O LEU N 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 19 removed outlier: 3.690A pdb=" N VAL O 17 " --> pdb=" O ALA O 13 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 41 removed outlier: 3.599A pdb=" N GLY O 29 " --> pdb=" O GLY O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 75 removed outlier: 4.189A pdb=" N GLY O 51 " --> pdb=" O GLY O 47 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N THR O 52 " --> pdb=" O LYS O 48 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU O 63 " --> pdb=" O PHE O 59 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR O 64 " --> pdb=" O MET O 60 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY O 67 " --> pdb=" O LEU O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 20 removed outlier: 4.076A pdb=" N VAL P 17 " --> pdb=" O ALA P 13 " (cutoff:3.500A) Processing helix chain 'P' and resid 23 through 41 removed outlier: 3.858A pdb=" N GLY P 38 " --> pdb=" O GLN P 34 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE P 39 " --> pdb=" O ALA P 35 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 75 removed outlier: 4.591A pdb=" N GLY P 47 " --> pdb=" O GLU P 44 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ARG P 50 " --> pdb=" O GLY P 47 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY P 51 " --> pdb=" O LYS P 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR P 52 " --> pdb=" O ILE P 49 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA P 62 " --> pdb=" O PHE P 59 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU P 63 " --> pdb=" O MET P 60 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N TYR P 66 " --> pdb=" O LEU P 63 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY P 67 " --> pdb=" O THR P 64 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA P 73 " --> pdb=" O VAL P 70 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 41 removed outlier: 4.207A pdb=" N VAL Q 17 " --> pdb=" O ALA Q 13 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N SER Q 21 " --> pdb=" O VAL Q 17 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ILE Q 22 " --> pdb=" O GLY Q 18 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N GLY Q 23 " --> pdb=" O LEU Q 19 " (cutoff:3.500A) Proline residue: Q 24 - end of helix removed outlier: 3.552A pdb=" N GLY Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY Q 38 " --> pdb=" O GLN Q 34 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA Q 40 " --> pdb=" O VAL Q 36 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG Q 41 " --> pdb=" O GLU Q 37 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 75 removed outlier: 4.082A pdb=" N THR Q 52 " --> pdb=" O LYS Q 48 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU Q 63 " --> pdb=" O PHE Q 59 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR Q 64 " --> pdb=" O MET Q 60 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY Q 67 " --> pdb=" O LEU Q 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 41 removed outlier: 3.537A pdb=" N VAL R 17 " --> pdb=" O ALA R 13 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER R 21 " --> pdb=" O VAL R 17 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ILE R 22 " --> pdb=" O GLY R 18 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N GLY R 23 " --> pdb=" O LEU R 19 " (cutoff:3.500A) Proline residue: R 24 - end of helix removed outlier: 3.767A pdb=" N GLY R 29 " --> pdb=" O GLY R 25 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY R 38 " --> pdb=" O GLN R 34 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA R 40 " --> pdb=" O VAL R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 75 removed outlier: 3.677A pdb=" N ARG R 50 " --> pdb=" O GLU R 46 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR R 52 " --> pdb=" O LYS R 48 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU R 63 " --> pdb=" O PHE R 59 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR R 64 " --> pdb=" O MET R 60 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY R 67 " --> pdb=" O LEU R 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 21 removed outlier: 3.543A pdb=" N VAL S 17 " --> pdb=" O ALA S 13 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER S 21 " --> pdb=" O VAL S 17 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 41 removed outlier: 4.055A pdb=" N GLY S 38 " --> pdb=" O GLN S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 75 removed outlier: 4.305A pdb=" N GLY S 47 " --> pdb=" O GLU S 44 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG S 50 " --> pdb=" O GLY S 47 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY S 51 " --> pdb=" O LYS S 48 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU S 55 " --> pdb=" O THR S 52 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA S 62 " --> pdb=" O PHE S 59 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU S 63 " --> pdb=" O MET S 60 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR S 66 " --> pdb=" O LEU S 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 19 Processing helix chain 'T' and resid 21 through 41 removed outlier: 3.629A pdb=" N VAL T 26 " --> pdb=" O ILE T 22 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY T 29 " --> pdb=" O GLY T 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 47 through 75 removed outlier: 4.118A pdb=" N GLY T 51 " --> pdb=" O GLY T 47 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N THR T 52 " --> pdb=" O LYS T 48 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU T 63 " --> pdb=" O PHE T 59 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR T 64 " --> pdb=" O MET T 60 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY T 67 " --> pdb=" O LEU T 63 " (cutoff:3.500A) Processing helix chain 'U' and resid 4 through 41 removed outlier: 3.662A pdb=" N VAL U 17 " --> pdb=" O ALA U 13 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER U 21 " --> pdb=" O VAL U 17 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE U 22 " --> pdb=" O GLY U 18 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLY U 23 " --> pdb=" O LEU U 19 " (cutoff:3.500A) Proline residue: U 24 - end of helix removed outlier: 3.571A pdb=" N GLY U 29 " --> pdb=" O GLY U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 43 through 75 removed outlier: 3.695A pdb=" N GLU U 46 " --> pdb=" O PRO U 43 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLY U 47 " --> pdb=" O GLU U 44 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG U 50 " --> pdb=" O GLY U 47 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY U 51 " --> pdb=" O LYS U 48 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU U 63 " --> pdb=" O MET U 60 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU U 72 " --> pdb=" O VAL U 69 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 41 removed outlier: 4.009A pdb=" N VAL V 17 " --> pdb=" O ALA V 13 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER V 21 " --> pdb=" O VAL V 17 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE V 22 " --> pdb=" O GLY V 18 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLY V 23 " --> pdb=" O LEU V 19 " (cutoff:3.500A) Proline residue: V 24 - end of helix removed outlier: 3.631A pdb=" N GLY V 38 " --> pdb=" O GLN V 34 " (cutoff:3.500A) Processing helix chain 'V' and resid 46 through 75 removed outlier: 4.250A pdb=" N GLY V 51 " --> pdb=" O GLY V 47 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR V 52 " --> pdb=" O LYS V 48 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU V 63 " --> pdb=" O PHE V 59 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR V 64 " --> pdb=" O MET V 60 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY V 67 " --> pdb=" O LEU V 63 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 19 removed outlier: 3.905A pdb=" N VAL W 17 " --> pdb=" O ALA W 13 " (cutoff:3.500A) Processing helix chain 'W' and resid 22 through 36 removed outlier: 3.737A pdb=" N GLY W 29 " --> pdb=" O GLY W 25 " (cutoff:3.500A) Processing helix chain 'W' and resid 38 through 41 No H-bonds generated for 'chain 'W' and resid 38 through 41' Processing helix chain 'W' and resid 46 through 75 removed outlier: 5.641A pdb=" N GLY W 51 " --> pdb=" O GLY W 47 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR W 52 " --> pdb=" O LYS W 48 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU W 63 " --> pdb=" O PHE W 59 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR W 64 " --> pdb=" O MET W 60 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY W 67 " --> pdb=" O LEU W 63 " (cutoff:3.500A) Processing helix chain 'X' and resid 4 through 41 removed outlier: 3.622A pdb=" N VAL X 17 " --> pdb=" O ALA X 13 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER X 21 " --> pdb=" O VAL X 17 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE X 22 " --> pdb=" O GLY X 18 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLY X 23 " --> pdb=" O LEU X 19 " (cutoff:3.500A) Proline residue: X 24 - end of helix removed outlier: 3.619A pdb=" N GLY X 38 " --> pdb=" O GLN X 34 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE X 39 " --> pdb=" O ALA X 35 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA X 40 " --> pdb=" O VAL X 36 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG X 41 " --> pdb=" O GLU X 37 " (cutoff:3.500A) Processing helix chain 'X' and resid 43 through 75 removed outlier: 3.919A pdb=" N GLU X 46 " --> pdb=" O PRO X 43 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLY X 47 " --> pdb=" O GLU X 44 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG X 50 " --> pdb=" O GLY X 47 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY X 51 " --> pdb=" O LYS X 48 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER X 56 " --> pdb=" O LEU X 53 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA X 62 " --> pdb=" O PHE X 59 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR X 66 " --> pdb=" O LEU X 63 " (cutoff:3.500A) Processing helix chain 'Y' and resid 5 through 40 removed outlier: 4.122A pdb=" N VAL Y 17 " --> pdb=" O ALA Y 13 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER Y 21 " --> pdb=" O VAL Y 17 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE Y 22 " --> pdb=" O GLY Y 18 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLY Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) Proline residue: Y 24 - end of helix removed outlier: 4.227A pdb=" N GLY Y 29 " --> pdb=" O GLY Y 25 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY Y 38 " --> pdb=" O GLN Y 34 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE Y 39 " --> pdb=" O ALA Y 35 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ALA Y 40 " --> pdb=" O VAL Y 36 " (cutoff:3.500A) Processing helix chain 'Y' and resid 46 through 75 removed outlier: 4.081A pdb=" N GLY Y 51 " --> pdb=" O GLY Y 47 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR Y 52 " --> pdb=" O LYS Y 48 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU Y 63 " --> pdb=" O PHE Y 59 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR Y 64 " --> pdb=" O MET Y 60 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY Y 67 " --> pdb=" O LEU Y 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 4 through 40 removed outlier: 3.651A pdb=" N VAL Z 17 " --> pdb=" O ALA Z 13 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER Z 21 " --> pdb=" O VAL Z 17 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE Z 22 " --> pdb=" O GLY Z 18 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLY Z 23 " --> pdb=" O LEU Z 19 " (cutoff:3.500A) Proline residue: Z 24 - end of helix removed outlier: 3.844A pdb=" N ILE Z 39 " --> pdb=" O ALA Z 35 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ALA Z 40 " --> pdb=" O VAL Z 36 " (cutoff:3.500A) Processing helix chain 'Z' and resid 44 through 75 removed outlier: 4.139A pdb=" N GLY Z 47 " --> pdb=" O GLU Z 44 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY Z 51 " --> pdb=" O LYS Z 48 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR Z 52 " --> pdb=" O ILE Z 49 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA Z 62 " --> pdb=" O PHE Z 59 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR Z 66 " --> pdb=" O LEU Z 63 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA Z 73 " --> pdb=" O VAL Z 70 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 30 through 34 removed outlier: 6.835A pdb=" N ARG A 41 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 341 through 344 removed outlier: 3.629A pdb=" N VAL A 320 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 170 " --> pdb=" O VAL A 320 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 223 through 226 removed outlier: 3.533A pdb=" N THR A 315 " --> pdb=" O THR A 257 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 30 through 35 removed outlier: 6.364A pdb=" N ARG B 41 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL B 75 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ALA B 64 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 97 through 99 Processing sheet with id= F, first strand: chain 'B' and resid 168 through 170 removed outlier: 3.554A pdb=" N VAL B 320 " --> pdb=" O ILE B 168 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 257 through 262 removed outlier: 6.550A pdb=" N ILE B 193 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N ILE B 260 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL B 195 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ASP B 262 " --> pdb=" O VAL B 195 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL B 197 " --> pdb=" O ASP B 262 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 39 through 42 removed outlier: 6.355A pdb=" N VAL C 75 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ALA C 64 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 54 through 56 Processing sheet with id= J, first strand: chain 'C' and resid 97 through 99 Processing sheet with id= K, first strand: chain 'C' and resid 341 through 345 Processing sheet with id= L, first strand: chain 'C' and resid 313 through 316 removed outlier: 3.565A pdb=" N LEU C 258 " --> pdb=" O ILE C 193 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 22 through 27 removed outlier: 6.367A pdb=" N ASP D 32 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE D 26 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL D 30 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN D 67 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL D 77 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N VAL D 65 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL D 61 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL D 49 " --> pdb=" O VAL D 61 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 167 through 172 removed outlier: 6.113A pdb=" N SER D 323 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEU D 170 " --> pdb=" O SER D 323 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N GLN D 325 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N GLY D 172 " --> pdb=" O GLN D 325 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL D 327 " --> pdb=" O GLY D 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 268 through 273 removed outlier: 7.145A pdb=" N VAL D 196 " --> pdb=" O LEU D 269 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N PHE D 271 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL D 198 " --> pdb=" O PHE D 271 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ASP D 273 " --> pdb=" O VAL D 198 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLY D 200 " --> pdb=" O ASP D 273 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 20 through 22 removed outlier: 6.862A pdb=" N ARG E 75 " --> pdb=" O GLN E 66 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N LEU E 68 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ARG E 73 " --> pdb=" O LEU E 68 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ALA E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILE E 23 " --> pdb=" O ALA E 34 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 99 through 101 Processing sheet with id= R, first strand: chain 'E' and resid 167 through 172 removed outlier: 7.815A pdb=" N ILE E 168 " --> pdb=" O ILE E 321 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N SER E 323 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU E 170 " --> pdb=" O SER E 323 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLN E 325 " --> pdb=" O LEU E 170 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N GLY E 172 " --> pdb=" O GLN E 325 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL E 327 " --> pdb=" O GLY E 172 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 20 through 22 removed outlier: 4.980A pdb=" N GLU F 90 " --> pdb=" O LYS F 50 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS F 50 " --> pdb=" O GLU F 90 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ARG F 75 " --> pdb=" O GLN F 66 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ALA F 34 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ILE F 23 " --> pdb=" O ALA F 34 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 99 through 101 Processing sheet with id= U, first strand: chain 'F' and resid 348 through 350 removed outlier: 3.530A pdb=" N ALA F 348 " --> pdb=" O LYS F 167 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N ILE F 168 " --> pdb=" O ILE F 321 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N SER F 323 " --> pdb=" O ILE F 168 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N LEU F 170 " --> pdb=" O SER F 323 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N GLN F 325 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE F 272 " --> pdb=" O ILE F 324 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL F 196 " --> pdb=" O ASP F 267 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'd' and resid 206 through 213 removed outlier: 3.670A pdb=" N GLU d 176 " --> pdb=" O ASN d 206 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE d 223 " --> pdb=" O VAL d 233 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL d 233 " --> pdb=" O ILE d 223 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'e' and resid 4 through 8 Processing sheet with id= X, first strand: chain 'e' and resid 30 through 34 removed outlier: 3.516A pdb=" N LEU e 24 " --> pdb=" O ILE e 31 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL e 33 " --> pdb=" O ILE e 22 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE e 22 " --> pdb=" O VAL e 33 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'g' and resid 156 through 159 Processing sheet with id= Z, first strand: chain 'a' and resid 28 through 30 2082 hydrogen bonds defined for protein. 5637 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: 13.19 Time building geometry restraints manager: 17.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13037 1.34 - 1.46: 6886 1.46 - 1.58: 19512 1.58 - 1.70: 26 1.70 - 1.82: 246 Bond restraints: 39707 Sorted by residual: bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.32e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.14e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.13e+01 bond pdb=" C4 ATP E 601 " pdb=" C5 ATP E 601 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.77e+01 bond pdb=" C5 ATP A 600 " pdb=" C6 ATP A 600 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.88e+01 ... (remaining 39702 not shown) Histogram of bond angle deviations from ideal: 95.29 - 103.52: 551 103.52 - 111.75: 18415 111.75 - 119.98: 17445 119.98 - 128.21: 17312 128.21 - 136.44: 132 Bond angle restraints: 53855 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 120.51 19.36 1.00e+00 1.00e+00 3.75e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 120.63 19.24 1.00e+00 1.00e+00 3.70e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 118.02 18.81 1.00e+00 1.00e+00 3.54e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 121.16 18.71 1.00e+00 1.00e+00 3.50e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 118.26 18.57 1.00e+00 1.00e+00 3.45e+02 ... (remaining 53850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.09: 23169 30.09 - 60.19: 902 60.19 - 90.28: 118 90.28 - 120.37: 1 120.37 - 150.46: 2 Dihedral angle restraints: 24192 sinusoidal: 9485 harmonic: 14707 Sorted by residual: dihedral pdb=" CA ALA E 295 " pdb=" C ALA E 295 " pdb=" N VAL E 296 " pdb=" CA VAL E 296 " ideal model delta harmonic sigma weight residual -180.00 -128.09 -51.91 0 5.00e+00 4.00e-02 1.08e+02 dihedral pdb=" CA ALA D 295 " pdb=" C ALA D 295 " pdb=" N VAL D 296 " pdb=" CA VAL D 296 " ideal model delta harmonic sigma weight residual -180.00 -129.87 -50.13 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CA PRO g 276 " pdb=" C PRO g 276 " pdb=" N ALA g 277 " pdb=" CA ALA g 277 " ideal model delta harmonic sigma weight residual 180.00 141.85 38.15 0 5.00e+00 4.00e-02 5.82e+01 ... (remaining 24189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 5315 0.066 - 0.132: 1035 0.132 - 0.197: 82 0.197 - 0.263: 7 0.263 - 0.329: 1 Chirality restraints: 6440 Sorted by residual: chirality pdb=" C9 TTX C 602 " pdb=" C10 TTX C 602 " pdb=" C8 TTX C 602 " pdb=" N3 TTX C 602 " both_signs ideal model delta sigma weight residual False -2.28 -2.61 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CB ILE g 227 " pdb=" CA ILE g 227 " pdb=" CG1 ILE g 227 " pdb=" CG2 ILE g 227 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C1' ATP E 601 " pdb=" C2' ATP E 601 " pdb=" N9 ATP E 601 " pdb=" O4' ATP E 601 " both_signs ideal model delta sigma weight residual False 2.41 2.65 -0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 6437 not shown) Planarity restraints: 6944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 TTX C 602 " -0.411 2.00e-02 2.50e+03 3.54e-01 1.88e+03 pdb=" C12 TTX C 602 " -0.051 2.00e-02 2.50e+03 pdb=" C13 TTX C 602 " 0.467 2.00e-02 2.50e+03 pdb=" C9 TTX C 602 " 0.434 2.00e-02 2.50e+03 pdb=" N3 TTX C 602 " -0.020 2.00e-02 2.50e+03 pdb=" O3 TTX C 602 " -0.419 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C15 TTX C 602 " -0.183 2.00e-02 2.50e+03 1.70e-01 4.32e+02 pdb=" C5 TTX C 602 " 0.220 2.00e-02 2.50e+03 pdb=" C6 TTX C 602 " -0.039 2.00e-02 2.50e+03 pdb=" C7 TTX C 602 " 0.227 2.00e-02 2.50e+03 pdb=" N1 TTX C 602 " -0.033 2.00e-02 2.50e+03 pdb=" O1 TTX C 602 " -0.193 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5 TTX C 602 " -0.170 2.00e-02 2.50e+03 1.40e-01 2.44e+02 pdb=" C8 TTX C 602 " 0.062 2.00e-02 2.50e+03 pdb=" C9 TTX C 602 " -0.129 2.00e-02 2.50e+03 pdb=" N2 TTX C 602 " 0.219 2.00e-02 2.50e+03 pdb=" O2 TTX C 602 " 0.018 2.00e-02 2.50e+03 ... (remaining 6941 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 5668 2.75 - 3.29: 40790 3.29 - 3.83: 68523 3.83 - 4.36: 79374 4.36 - 4.90: 133699 Nonbonded interactions: 328054 Sorted by model distance: nonbonded pdb=" O THR C 228 " pdb=" OG SER C 231 " model vdw 2.217 2.440 nonbonded pdb=" O ALA D 438 " pdb=" OG1 THR D 442 " model vdw 2.223 2.440 nonbonded pdb=" O GLY D 360 " pdb=" OH TYR D 475 " model vdw 2.233 2.440 nonbonded pdb=" O VAL d 198 " pdb=" OG1 THR d 202 " model vdw 2.234 2.440 nonbonded pdb=" O PRO F 337 " pdb=" OG1 THR F 341 " model vdw 2.265 2.440 ... (remaining 328049 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 503) selection = (chain 'B' and resid 7 through 503) selection = (chain 'C' and resid 7 through 503) } ncs_group { reference = (chain 'D' and resid 18 through 494) selection = (chain 'E' and resid 18 through 494) selection = (chain 'F' and resid 18 through 494) } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 17.540 Check model and map are aligned: 0.580 Set scattering table: 0.330 Process input model: 99.900 Find NCS groups from input model: 2.600 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 39707 Z= 0.330 Angle : 0.932 19.357 53855 Z= 0.554 Chirality : 0.050 0.329 6440 Planarity : 0.008 0.354 6944 Dihedral : 16.097 150.465 14772 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.88 % Favored : 94.04 % Rotamer: Outliers : 0.39 % Allowed : 10.66 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.12 % Twisted Proline : 0.49 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.10), residues: 5133 helix: -1.87 (0.08), residues: 2811 sheet: -2.71 (0.20), residues: 510 loop : -2.85 (0.12), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP e 57 HIS 0.006 0.001 HIS d 141 PHE 0.021 0.002 PHE S 59 TYR 0.028 0.002 TYR a 148 ARG 0.006 0.001 ARG D 312 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 941 time to evaluate : 4.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7278 (mm-30) cc_final: 0.6778 (mm-30) REVERT: A 82 MET cc_start: 0.7734 (mmt) cc_final: 0.7450 (mmm) REVERT: A 172 ARG cc_start: 0.7946 (tmm160) cc_final: 0.6826 (ptt90) REVERT: A 219 MET cc_start: 0.8458 (tpt) cc_final: 0.8257 (tpp) REVERT: A 251 MET cc_start: 0.7486 (ttp) cc_final: 0.7237 (ttm) REVERT: A 473 GLN cc_start: 0.8332 (tt0) cc_final: 0.7641 (tp40) REVERT: A 501 PHE cc_start: 0.5586 (t80) cc_final: 0.5354 (t80) REVERT: B 387 LEU cc_start: 0.8548 (mt) cc_final: 0.8190 (tt) REVERT: B 429 LEU cc_start: 0.7990 (mt) cc_final: 0.7679 (mt) REVERT: B 433 GLU cc_start: 0.7590 (mt-10) cc_final: 0.6885 (tt0) REVERT: B 466 LYS cc_start: 0.6625 (mttm) cc_final: 0.6172 (tppt) REVERT: C 58 GLU cc_start: 0.5731 (mp0) cc_final: 0.5467 (mp0) REVERT: C 81 LEU cc_start: 0.7278 (mt) cc_final: 0.7062 (mp) REVERT: C 90 LYS cc_start: 0.7491 (mttt) cc_final: 0.7072 (mttm) REVERT: C 154 ILE cc_start: 0.9064 (mm) cc_final: 0.8826 (mm) REVERT: C 272 ARG cc_start: 0.7417 (ttp-110) cc_final: 0.7068 (ttm170) REVERT: C 290 ASP cc_start: 0.7557 (m-30) cc_final: 0.6049 (m-30) REVERT: C 358 ILE cc_start: 0.8894 (mm) cc_final: 0.8692 (tt) REVERT: C 364 VAL cc_start: 0.7900 (t) cc_final: 0.7697 (t) REVERT: C 452 ASP cc_start: 0.7353 (m-30) cc_final: 0.7004 (m-30) REVERT: C 470 PRO cc_start: 0.7095 (Cg_endo) cc_final: 0.6762 (Cg_exo) REVERT: D 102 VAL cc_start: 0.7022 (m) cc_final: 0.6657 (m) REVERT: D 110 ILE cc_start: 0.8080 (mm) cc_final: 0.7823 (mt) REVERT: D 247 MET cc_start: 0.7874 (ttp) cc_final: 0.7321 (ttp) REVERT: D 335 THR cc_start: 0.7947 (m) cc_final: 0.7744 (m) REVERT: D 343 PHE cc_start: 0.7283 (m-80) cc_final: 0.6957 (m-80) REVERT: D 404 ILE cc_start: 0.6136 (mp) cc_final: 0.5754 (mp) REVERT: D 479 ASN cc_start: 0.6406 (t0) cc_final: 0.5749 (m110) REVERT: E 85 LEU cc_start: 0.9050 (mm) cc_final: 0.8628 (mm) REVERT: E 306 MET cc_start: 0.8116 (tpp) cc_final: 0.7802 (tpp) REVERT: E 428 GLU cc_start: 0.6678 (pp20) cc_final: 0.6363 (pp20) REVERT: F 57 GLN cc_start: 0.6388 (pm20) cc_final: 0.5454 (tm-30) REVERT: F 269 LEU cc_start: 0.8312 (tp) cc_final: 0.7982 (tp) REVERT: F 288 LEU cc_start: 0.7633 (mt) cc_final: 0.7338 (mt) REVERT: F 462 LEU cc_start: 0.6416 (mt) cc_final: 0.6090 (pp) REVERT: F 492 MET cc_start: 0.6631 (mmm) cc_final: 0.6377 (mmm) REVERT: d 234 ASP cc_start: 0.5961 (p0) cc_final: 0.5556 (p0) REVERT: d 243 GLU cc_start: 0.6441 (tp30) cc_final: 0.6222 (mm-30) REVERT: e 105 LYS cc_start: 0.7120 (mtmt) cc_final: 0.6786 (mtmm) REVERT: g 74 ARG cc_start: 0.6380 (mmt180) cc_final: 0.5990 (ttp80) REVERT: g 130 CYS cc_start: 0.7382 (m) cc_final: 0.7109 (t) REVERT: g 135 ASN cc_start: 0.6569 (m-40) cc_final: 0.5439 (t0) REVERT: g 138 LEU cc_start: 0.7828 (mt) cc_final: 0.7408 (mm) REVERT: g 227 ILE cc_start: 0.7263 (tp) cc_final: 0.7020 (mt) REVERT: g 236 LYS cc_start: 0.5686 (mmtm) cc_final: 0.5284 (ttmm) REVERT: g 343 ARG cc_start: 0.6682 (mtm110) cc_final: 0.5998 (mtm180) REVERT: g 353 ILE cc_start: 0.8820 (mt) cc_final: 0.8569 (tp) REVERT: I 134 GLN cc_start: 0.6486 (mm-40) cc_final: 0.5826 (tp40) REVERT: I 153 LEU cc_start: 0.7160 (tt) cc_final: 0.6835 (mt) REVERT: J 116 MET cc_start: 0.3641 (mmt) cc_final: 0.2789 (mmt) REVERT: J 181 ILE cc_start: 0.6516 (mm) cc_final: 0.6044 (mm) REVERT: J 185 LEU cc_start: 0.7392 (tp) cc_final: 0.7126 (tt) REVERT: J 198 ASP cc_start: 0.3759 (m-30) cc_final: 0.3442 (m-30) REVERT: a 178 GLU cc_start: 0.4337 (tt0) cc_final: 0.4089 (tm-30) REVERT: a 184 LEU cc_start: 0.8191 (tt) cc_final: 0.7477 (tp) REVERT: a 190 LEU cc_start: 0.5413 (mt) cc_final: 0.5202 (mt) REVERT: a 195 LEU cc_start: 0.5749 (tp) cc_final: 0.5546 (tt) REVERT: a 223 THR cc_start: 0.6687 (p) cc_final: 0.6318 (m) REVERT: M 28 GLN cc_start: 0.4277 (mt0) cc_final: 0.3870 (mt0) REVERT: M 60 MET cc_start: 0.3061 (mtm) cc_final: 0.2423 (mmt) REVERT: N 46 GLU cc_start: 0.4890 (tt0) cc_final: 0.4438 (pp20) REVERT: N 57 LEU cc_start: 0.7722 (mt) cc_final: 0.7395 (mt) REVERT: P 61 GLU cc_start: 0.5474 (tp30) cc_final: 0.5236 (mm-30) REVERT: Q 50 ARG cc_start: 0.3903 (mmm-85) cc_final: 0.3595 (ttt180) REVERT: R 75 LEU cc_start: 0.5993 (mt) cc_final: 0.5714 (tp) REVERT: S 60 MET cc_start: 0.4456 (mtm) cc_final: 0.3997 (tpp) REVERT: T 60 MET cc_start: 0.3942 (mtm) cc_final: 0.3265 (ttm) REVERT: W 37 GLU cc_start: 0.5878 (tt0) cc_final: 0.5149 (tp30) REVERT: W 48 LYS cc_start: 0.4076 (mttt) cc_final: 0.3829 (mptt) REVERT: Y 60 MET cc_start: 0.3974 (mmt) cc_final: 0.3508 (mmm) REVERT: Y 68 LEU cc_start: 0.3686 (tp) cc_final: 0.3370 (mm) outliers start: 16 outliers final: 6 residues processed: 952 average time/residue: 0.5233 time to fit residues: 796.1478 Evaluate side-chains 635 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 629 time to evaluate : 3.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 423 optimal weight: 1.9990 chunk 379 optimal weight: 8.9990 chunk 210 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 256 optimal weight: 0.5980 chunk 202 optimal weight: 0.5980 chunk 392 optimal weight: 0.5980 chunk 151 optimal weight: 5.9990 chunk 238 optimal weight: 0.2980 chunk 292 optimal weight: 2.9990 chunk 454 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 GLN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 HIS C 256 HIS ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 GLN D 25 GLN ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 GLN E 376 GLN ** F 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN F 280 GLN F 310 GLN F 325 GLN d 193 GLN e 37 HIS e 54 ASN g 76 GLN ** g 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 GLN I 134 GLN ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 126 GLN a 36 HIS O 42 GLN S 42 GLN T 28 GLN W 28 GLN Y 28 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 39707 Z= 0.190 Angle : 0.674 20.845 53855 Z= 0.335 Chirality : 0.043 0.248 6440 Planarity : 0.005 0.072 6944 Dihedral : 7.764 144.367 5721 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.85 % Favored : 95.03 % Rotamer: Outliers : 0.15 % Allowed : 5.67 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.12 % Twisted Proline : 0.49 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.11), residues: 5133 helix: -0.68 (0.09), residues: 2787 sheet: -2.25 (0.20), residues: 523 loop : -2.47 (0.13), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP e 57 HIS 0.007 0.001 HIS a 36 PHE 0.032 0.002 PHE E 343 TYR 0.020 0.002 TYR a 164 ARG 0.009 0.000 ARG g 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 802 time to evaluate : 4.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.5261 (tpp) cc_final: 0.4626 (ttm) REVERT: A 68 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6835 (mm-30) REVERT: A 77 MET cc_start: 0.6718 (mtt) cc_final: 0.6336 (ttm) REVERT: A 160 VAL cc_start: 0.7904 (t) cc_final: 0.7617 (t) REVERT: A 172 ARG cc_start: 0.7554 (tmm160) cc_final: 0.7000 (ptt90) REVERT: A 219 MET cc_start: 0.8456 (tpt) cc_final: 0.8215 (tpp) REVERT: A 251 MET cc_start: 0.7446 (ttp) cc_final: 0.7197 (ttm) REVERT: A 473 GLN cc_start: 0.8276 (tt0) cc_final: 0.7640 (tp40) REVERT: B 433 GLU cc_start: 0.7437 (mt-10) cc_final: 0.6478 (mt-10) REVERT: B 466 LYS cc_start: 0.6394 (mttm) cc_final: 0.6081 (tppt) REVERT: C 166 GLU cc_start: 0.8240 (tp30) cc_final: 0.7639 (tp30) REVERT: C 227 GLU cc_start: 0.6212 (mm-30) cc_final: 0.5975 (mm-30) REVERT: C 294 LEU cc_start: 0.8357 (tp) cc_final: 0.8075 (tp) REVERT: C 470 PRO cc_start: 0.6974 (Cg_endo) cc_final: 0.6705 (Cg_exo) REVERT: D 110 ILE cc_start: 0.8146 (mm) cc_final: 0.7821 (mt) REVERT: D 291 ARG cc_start: 0.7616 (mpt-90) cc_final: 0.7292 (mmp-170) REVERT: E 146 LEU cc_start: 0.8043 (mt) cc_final: 0.7810 (mt) REVERT: E 435 PHE cc_start: 0.7250 (m-80) cc_final: 0.6980 (m-80) REVERT: F 269 LEU cc_start: 0.8283 (tp) cc_final: 0.7945 (tp) REVERT: F 462 LEU cc_start: 0.6306 (mt) cc_final: 0.6090 (pp) REVERT: d 234 ASP cc_start: 0.5573 (p0) cc_final: 0.5190 (p0) REVERT: e 105 LYS cc_start: 0.7111 (mtmt) cc_final: 0.6829 (mtmm) REVERT: g 74 ARG cc_start: 0.6274 (mmt180) cc_final: 0.5838 (ttp80) REVERT: g 87 GLU cc_start: 0.6870 (pt0) cc_final: 0.6617 (pt0) REVERT: g 130 CYS cc_start: 0.7303 (m) cc_final: 0.7063 (t) REVERT: g 135 ASN cc_start: 0.6598 (m-40) cc_final: 0.5623 (t0) REVERT: g 227 ILE cc_start: 0.6988 (tp) cc_final: 0.6761 (mt) REVERT: g 236 LYS cc_start: 0.5551 (mmtm) cc_final: 0.5271 (ttmm) REVERT: g 288 PRO cc_start: 0.4735 (Cg_exo) cc_final: 0.4533 (Cg_endo) REVERT: g 323 MET cc_start: 0.7255 (mmp) cc_final: 0.6901 (mmp) REVERT: g 353 ILE cc_start: 0.8863 (mt) cc_final: 0.8605 (tp) REVERT: I 58 GLN cc_start: 0.5779 (tp40) cc_final: 0.4369 (pt0) REVERT: I 90 MET cc_start: 0.3108 (tpt) cc_final: 0.2728 (tpt) REVERT: I 153 LEU cc_start: 0.6979 (tt) cc_final: 0.6583 (mt) REVERT: J 116 MET cc_start: 0.3855 (mmt) cc_final: 0.3062 (mmt) REVERT: J 161 LYS cc_start: 0.6281 (tptt) cc_final: 0.5890 (mttt) REVERT: a 184 LEU cc_start: 0.8090 (tt) cc_final: 0.7380 (tp) REVERT: N 46 GLU cc_start: 0.5085 (tt0) cc_final: 0.4523 (pp20) REVERT: N 57 LEU cc_start: 0.7633 (mt) cc_final: 0.7379 (mt) REVERT: P 61 GLU cc_start: 0.5535 (tp30) cc_final: 0.5076 (mm-30) REVERT: Q 50 ARG cc_start: 0.3883 (mmm-85) cc_final: 0.3491 (ttt180) REVERT: R 75 LEU cc_start: 0.5793 (mt) cc_final: 0.5498 (tp) REVERT: S 60 MET cc_start: 0.4834 (mtm) cc_final: 0.4214 (tpp) REVERT: V 24 PRO cc_start: 0.6957 (Cg_exo) cc_final: 0.6486 (Cg_endo) REVERT: W 37 GLU cc_start: 0.5874 (tt0) cc_final: 0.5146 (tp30) REVERT: X 68 LEU cc_start: 0.5707 (tp) cc_final: 0.5325 (tt) REVERT: Y 68 LEU cc_start: 0.4027 (tp) cc_final: 0.3532 (mm) outliers start: 6 outliers final: 1 residues processed: 805 average time/residue: 0.4994 time to fit residues: 660.6129 Evaluate side-chains 584 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 583 time to evaluate : 4.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 252 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 378 optimal weight: 0.7980 chunk 309 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 455 optimal weight: 4.9990 chunk 492 optimal weight: 3.9990 chunk 405 optimal weight: 0.6980 chunk 451 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 365 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 ASN ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 GLN D 25 GLN D 66 GLN ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 GLN D 479 ASN E 25 GLN F 25 GLN ** F 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN g 340 ASN ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 120 GLN ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 161 ASN ** J 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 36 HIS a 193 ASN ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 39707 Z= 0.224 Angle : 0.668 18.933 53855 Z= 0.330 Chirality : 0.043 0.189 6440 Planarity : 0.005 0.063 6944 Dihedral : 7.529 140.041 5721 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.63 % Favored : 94.29 % Rotamer: Outliers : 0.05 % Allowed : 5.01 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.12 % Twisted Proline : 0.49 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.11), residues: 5133 helix: -0.31 (0.09), residues: 2797 sheet: -2.00 (0.21), residues: 499 loop : -2.27 (0.13), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP e 57 HIS 0.005 0.001 HIS a 36 PHE 0.028 0.002 PHE W 59 TYR 0.033 0.002 TYR W 66 ARG 0.006 0.000 ARG J 178 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 739 time to evaluate : 4.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6859 (mm-30) REVERT: A 82 MET cc_start: 0.7764 (mmp) cc_final: 0.7369 (mmm) REVERT: A 130 ILE cc_start: 0.7985 (pt) cc_final: 0.7767 (pt) REVERT: A 219 MET cc_start: 0.8446 (tpt) cc_final: 0.8220 (tpp) REVERT: A 251 MET cc_start: 0.7390 (ttp) cc_final: 0.7085 (ttm) REVERT: A 344 PHE cc_start: 0.6941 (m-80) cc_final: 0.6460 (m-80) REVERT: A 473 GLN cc_start: 0.8280 (tt0) cc_final: 0.7663 (tp40) REVERT: B 429 LEU cc_start: 0.7737 (mt) cc_final: 0.7368 (mt) REVERT: B 434 GLN cc_start: 0.8390 (mt0) cc_final: 0.8178 (mt0) REVERT: C 81 LEU cc_start: 0.7296 (mt) cc_final: 0.7042 (mp) REVERT: C 285 GLU cc_start: 0.6861 (mp0) cc_final: 0.6213 (mp0) REVERT: C 470 PRO cc_start: 0.6961 (Cg_endo) cc_final: 0.6745 (Cg_exo) REVERT: D 110 ILE cc_start: 0.8226 (mm) cc_final: 0.7931 (mt) REVERT: D 247 MET cc_start: 0.7397 (ttp) cc_final: 0.7169 (tpt) REVERT: D 248 ARG cc_start: 0.6034 (mpt90) cc_final: 0.5475 (mmt90) REVERT: E 85 LEU cc_start: 0.8973 (mm) cc_final: 0.8766 (mm) REVERT: E 197 SER cc_start: 0.6902 (m) cc_final: 0.6634 (m) REVERT: E 204 GLU cc_start: 0.3356 (mm-30) cc_final: 0.2869 (mm-30) REVERT: E 306 MET cc_start: 0.7959 (tpp) cc_final: 0.7669 (tpp) REVERT: E 435 PHE cc_start: 0.7294 (m-80) cc_final: 0.7031 (m-80) REVERT: F 269 LEU cc_start: 0.8192 (tp) cc_final: 0.7954 (tp) REVERT: F 462 LEU cc_start: 0.6399 (mt) cc_final: 0.6078 (pp) REVERT: d 234 ASP cc_start: 0.5878 (p0) cc_final: 0.5398 (p0) REVERT: e 105 LYS cc_start: 0.7443 (mtmt) cc_final: 0.6969 (mtmm) REVERT: g 74 ARG cc_start: 0.6399 (mmt180) cc_final: 0.5806 (ttp80) REVERT: g 87 GLU cc_start: 0.6553 (pt0) cc_final: 0.6260 (pt0) REVERT: g 135 ASN cc_start: 0.6695 (m-40) cc_final: 0.5562 (t0) REVERT: g 227 ILE cc_start: 0.7068 (tp) cc_final: 0.6798 (mt) REVERT: g 236 LYS cc_start: 0.5751 (mmtm) cc_final: 0.5347 (ttmm) REVERT: g 270 MET cc_start: 0.3474 (tpt) cc_final: 0.3157 (mmm) REVERT: g 288 PRO cc_start: 0.4460 (Cg_exo) cc_final: 0.4033 (Cg_endo) REVERT: g 300 LEU cc_start: 0.7310 (tt) cc_final: 0.6802 (mp) REVERT: g 320 MET cc_start: 0.7236 (tmm) cc_final: 0.6985 (tmm) REVERT: g 323 MET cc_start: 0.7271 (mmp) cc_final: 0.6930 (mmp) REVERT: I 54 ASP cc_start: 0.3156 (t70) cc_final: 0.2557 (t70) REVERT: I 58 GLN cc_start: 0.5666 (tp40) cc_final: 0.4306 (pt0) REVERT: I 105 ARG cc_start: 0.5160 (mmm160) cc_final: 0.4958 (mmm160) REVERT: I 134 GLN cc_start: 0.6233 (mm110) cc_final: 0.5582 (tp40) REVERT: I 175 MET cc_start: 0.5995 (mtm) cc_final: 0.5792 (mtm) REVERT: J 116 MET cc_start: 0.3981 (mmt) cc_final: 0.3227 (mmt) REVERT: J 181 ILE cc_start: 0.6313 (mm) cc_final: 0.5649 (mm) REVERT: J 182 GLU cc_start: 0.8647 (mp0) cc_final: 0.8148 (mp0) REVERT: N 46 GLU cc_start: 0.5255 (tt0) cc_final: 0.4588 (pp20) REVERT: N 57 LEU cc_start: 0.7741 (mt) cc_final: 0.7179 (mt) REVERT: N 60 MET cc_start: 0.4454 (mmt) cc_final: 0.3350 (mtp) REVERT: Q 50 ARG cc_start: 0.3674 (mmm-85) cc_final: 0.3357 (ttt180) REVERT: Q 60 MET cc_start: 0.1745 (mtp) cc_final: 0.0824 (tpp) REVERT: T 60 MET cc_start: 0.2836 (tpp) cc_final: 0.2452 (tpp) REVERT: V 24 PRO cc_start: 0.6579 (Cg_exo) cc_final: 0.6006 (Cg_endo) REVERT: W 37 GLU cc_start: 0.5843 (tt0) cc_final: 0.5072 (tp30) REVERT: W 46 GLU cc_start: 0.4738 (tm-30) cc_final: 0.4464 (tt0) REVERT: Y 68 LEU cc_start: 0.4014 (tp) cc_final: 0.3581 (mm) REVERT: Z 60 MET cc_start: 0.5619 (ttm) cc_final: 0.5282 (ttt) outliers start: 2 outliers final: 0 residues processed: 739 average time/residue: 0.4994 time to fit residues: 607.5370 Evaluate side-chains 555 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 555 time to evaluate : 5.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 450 optimal weight: 0.7980 chunk 342 optimal weight: 3.9990 chunk 236 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 217 optimal weight: 5.9990 chunk 306 optimal weight: 4.9990 chunk 457 optimal weight: 0.6980 chunk 484 optimal weight: 0.8980 chunk 238 optimal weight: 0.6980 chunk 433 optimal weight: 0.0370 chunk 130 optimal weight: 2.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 GLN ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 376 GLN ** F 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 ASN F 479 ASN g 286 GLN g 346 GLN ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 36 HIS a 86 GLN N 28 GLN U 28 GLN ** V 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 28 GLN ** Y 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 39707 Z= 0.191 Angle : 0.651 19.250 53855 Z= 0.319 Chirality : 0.042 0.193 6440 Planarity : 0.005 0.067 6944 Dihedral : 7.236 135.114 5721 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.83 % Favored : 95.09 % Rotamer: Outliers : 0.05 % Allowed : 4.11 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.12 % Twisted Proline : 0.49 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.11), residues: 5133 helix: 0.03 (0.10), residues: 2790 sheet: -1.91 (0.22), residues: 501 loop : -2.10 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP e 57 HIS 0.003 0.001 HIS a 36 PHE 0.031 0.002 PHE I 121 TYR 0.030 0.002 TYR W 66 ARG 0.011 0.000 ARG E 429 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 751 time to evaluate : 4.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 PHE cc_start: 0.6838 (m-80) cc_final: 0.6202 (m-80) REVERT: A 473 GLN cc_start: 0.8231 (tt0) cc_final: 0.7668 (tp40) REVERT: B 434 GLN cc_start: 0.8311 (mt0) cc_final: 0.8056 (mt0) REVERT: C 75 VAL cc_start: 0.8969 (t) cc_final: 0.8722 (t) REVERT: C 81 LEU cc_start: 0.7238 (mt) cc_final: 0.6996 (mp) REVERT: C 251 MET cc_start: 0.7669 (ttp) cc_final: 0.7409 (ptm) REVERT: C 470 PRO cc_start: 0.6955 (Cg_endo) cc_final: 0.6634 (Cg_exo) REVERT: D 110 ILE cc_start: 0.8182 (mm) cc_final: 0.7870 (mt) REVERT: D 239 MET cc_start: 0.7577 (mtp) cc_final: 0.7325 (mtp) REVERT: D 277 ARG cc_start: 0.6767 (mmp80) cc_final: 0.6529 (mmt-90) REVERT: D 314 THR cc_start: 0.7819 (t) cc_final: 0.7600 (t) REVERT: E 306 MET cc_start: 0.8017 (tpp) cc_final: 0.7340 (tpp) REVERT: E 385 TYR cc_start: 0.6728 (t80) cc_final: 0.6461 (t80) REVERT: E 435 PHE cc_start: 0.7296 (m-80) cc_final: 0.7061 (m-80) REVERT: F 462 LEU cc_start: 0.6442 (mt) cc_final: 0.6183 (pp) REVERT: F 481 ASP cc_start: 0.7977 (p0) cc_final: 0.7331 (p0) REVERT: d 234 ASP cc_start: 0.5715 (p0) cc_final: 0.5355 (p0) REVERT: e 105 LYS cc_start: 0.7294 (mtmt) cc_final: 0.6880 (mtmm) REVERT: g 74 ARG cc_start: 0.6364 (mmt180) cc_final: 0.5816 (ttp80) REVERT: g 121 MET cc_start: 0.6914 (ptp) cc_final: 0.6214 (ptm) REVERT: g 135 ASN cc_start: 0.6657 (m-40) cc_final: 0.5588 (t0) REVERT: g 220 LEU cc_start: 0.7351 (mt) cc_final: 0.6148 (pt) REVERT: g 227 ILE cc_start: 0.6875 (tp) cc_final: 0.6632 (mt) REVERT: g 236 LYS cc_start: 0.5632 (mmtm) cc_final: 0.5296 (ttmm) REVERT: g 256 ARG cc_start: 0.6491 (ttm170) cc_final: 0.6278 (ttp-170) REVERT: g 288 PRO cc_start: 0.4297 (Cg_exo) cc_final: 0.4005 (Cg_endo) REVERT: g 323 MET cc_start: 0.7284 (mmp) cc_final: 0.6915 (mmp) REVERT: I 105 ARG cc_start: 0.5470 (mmm160) cc_final: 0.5246 (mmm160) REVERT: I 134 GLN cc_start: 0.6320 (mm110) cc_final: 0.5759 (tp40) REVERT: I 153 LEU cc_start: 0.6866 (tt) cc_final: 0.6492 (mt) REVERT: J 116 MET cc_start: 0.3945 (mmt) cc_final: 0.3246 (mmt) REVERT: J 182 GLU cc_start: 0.8418 (mp0) cc_final: 0.8058 (mp0) REVERT: a 25 HIS cc_start: 0.2458 (p-80) cc_final: 0.1970 (m-70) REVERT: N 46 GLU cc_start: 0.5153 (tt0) cc_final: 0.4579 (pp20) REVERT: N 57 LEU cc_start: 0.7582 (mt) cc_final: 0.7113 (mt) REVERT: P 60 MET cc_start: 0.4017 (mtt) cc_final: 0.2340 (ttm) REVERT: Q 50 ARG cc_start: 0.3817 (mmm-85) cc_final: 0.3409 (ttt180) REVERT: Q 60 MET cc_start: 0.1698 (mtp) cc_final: 0.0738 (tpp) REVERT: T 60 MET cc_start: 0.3283 (tpp) cc_final: 0.3027 (tpp) REVERT: W 37 GLU cc_start: 0.5999 (tt0) cc_final: 0.5239 (tp30) REVERT: X 28 GLN cc_start: 0.5137 (mp-120) cc_final: 0.4170 (mt0) REVERT: Y 68 LEU cc_start: 0.4014 (tp) cc_final: 0.3679 (mm) outliers start: 2 outliers final: 0 residues processed: 751 average time/residue: 0.4986 time to fit residues: 619.2087 Evaluate side-chains 565 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 565 time to evaluate : 4.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 403 optimal weight: 3.9990 chunk 274 optimal weight: 7.9990 chunk 7 optimal weight: 0.0470 chunk 360 optimal weight: 2.9990 chunk 199 optimal weight: 7.9990 chunk 413 optimal weight: 3.9990 chunk 334 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 247 optimal weight: 0.7980 chunk 434 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 overall best weight: 1.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 256 HIS A 372 GLN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 376 GLN ** F 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 GLN ** d 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 GLN a 135 ASN ** Z 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 39707 Z= 0.296 Angle : 0.714 18.236 53855 Z= 0.356 Chirality : 0.045 0.248 6440 Planarity : 0.005 0.065 6944 Dihedral : 7.409 133.777 5721 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.49 % Favored : 93.43 % Rotamer: Outliers : 0.02 % Allowed : 4.20 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.12 % Twisted Proline : 0.49 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.11), residues: 5133 helix: -0.09 (0.10), residues: 2816 sheet: -1.94 (0.21), residues: 525 loop : -2.03 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP e 57 HIS 0.008 0.001 HIS a 36 PHE 0.031 0.002 PHE W 59 TYR 0.031 0.002 TYR O 66 ARG 0.008 0.001 ARG F 246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 707 time to evaluate : 4.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.8028 (tpp) cc_final: 0.7801 (tpp) REVERT: A 252 TYR cc_start: 0.6628 (m-10) cc_final: 0.6270 (m-80) REVERT: A 344 PHE cc_start: 0.7117 (m-80) cc_final: 0.6550 (m-80) REVERT: A 473 GLN cc_start: 0.8301 (tt0) cc_final: 0.7749 (tp40) REVERT: B 251 MET cc_start: 0.6932 (ppp) cc_final: 0.6654 (ppp) REVERT: B 436 MET cc_start: 0.8015 (ptp) cc_final: 0.7731 (ptp) REVERT: C 81 LEU cc_start: 0.7321 (mt) cc_final: 0.7103 (mp) REVERT: C 470 PRO cc_start: 0.6882 (Cg_endo) cc_final: 0.6523 (Cg_exo) REVERT: D 110 ILE cc_start: 0.8264 (mm) cc_final: 0.7927 (mt) REVERT: E 306 MET cc_start: 0.7981 (tpp) cc_final: 0.7470 (tpp) REVERT: E 435 PHE cc_start: 0.7292 (m-80) cc_final: 0.7042 (m-80) REVERT: F 411 ASP cc_start: 0.7363 (t70) cc_final: 0.7047 (t70) REVERT: F 462 LEU cc_start: 0.6452 (mt) cc_final: 0.6146 (pp) REVERT: F 481 ASP cc_start: 0.7928 (p0) cc_final: 0.7308 (p0) REVERT: d 234 ASP cc_start: 0.5589 (p0) cc_final: 0.5224 (p0) REVERT: e 45 ASP cc_start: 0.7137 (p0) cc_final: 0.6752 (p0) REVERT: e 105 LYS cc_start: 0.7406 (mtmt) cc_final: 0.6995 (mtmm) REVERT: g 74 ARG cc_start: 0.6302 (mmt180) cc_final: 0.5876 (ttp80) REVERT: g 135 ASN cc_start: 0.6740 (m-40) cc_final: 0.5644 (t0) REVERT: g 236 LYS cc_start: 0.5546 (mmtm) cc_final: 0.5168 (ttmm) REVERT: g 288 PRO cc_start: 0.4153 (Cg_exo) cc_final: 0.3868 (Cg_endo) REVERT: g 323 MET cc_start: 0.7356 (mmp) cc_final: 0.6984 (mmp) REVERT: I 134 GLN cc_start: 0.6181 (mm110) cc_final: 0.5905 (tp40) REVERT: I 153 LEU cc_start: 0.7071 (tt) cc_final: 0.6736 (mt) REVERT: J 116 MET cc_start: 0.4000 (mmt) cc_final: 0.3305 (mmt) REVERT: N 57 LEU cc_start: 0.7379 (mt) cc_final: 0.7079 (mt) REVERT: P 28 GLN cc_start: 0.5503 (mm110) cc_final: 0.4776 (mm-40) REVERT: P 50 ARG cc_start: 0.2674 (mtt-85) cc_final: 0.0656 (mtp-110) REVERT: P 60 MET cc_start: 0.3854 (mtt) cc_final: 0.3049 (mtt) REVERT: Q 50 ARG cc_start: 0.4137 (mmm-85) cc_final: 0.3778 (ttt180) REVERT: Q 60 MET cc_start: 0.1705 (mtp) cc_final: -0.0070 (tpp) REVERT: S 60 MET cc_start: 0.5004 (mmt) cc_final: 0.4726 (mmt) REVERT: T 60 MET cc_start: 0.3307 (tpp) cc_final: 0.2837 (mmm) REVERT: V 28 GLN cc_start: 0.4842 (mt0) cc_final: 0.4520 (mm-40) REVERT: W 37 GLU cc_start: 0.5891 (tt0) cc_final: 0.5115 (tp30) REVERT: X 28 GLN cc_start: 0.3711 (mp-120) cc_final: 0.3144 (mt0) REVERT: X 60 MET cc_start: 0.5299 (ttm) cc_final: 0.4526 (tpp) REVERT: Y 68 LEU cc_start: 0.4009 (tp) cc_final: 0.3631 (mt) outliers start: 1 outliers final: 0 residues processed: 707 average time/residue: 0.4811 time to fit residues: 565.1654 Evaluate side-chains 538 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 538 time to evaluate : 4.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 162 optimal weight: 0.9990 chunk 436 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 284 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 484 optimal weight: 0.8980 chunk 402 optimal weight: 0.9990 chunk 224 optimal weight: 0.0050 chunk 40 optimal weight: 0.9990 chunk 160 optimal weight: 0.8980 chunk 254 optimal weight: 0.0170 overall best weight: 0.5634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 186 ASN ** A 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 GLN D 226 ASN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 376 GLN ** F 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 76 GLN ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 GLN ** P 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 39707 Z= 0.188 Angle : 0.653 19.151 53855 Z= 0.319 Chirality : 0.043 0.218 6440 Planarity : 0.004 0.061 6944 Dihedral : 7.018 131.156 5721 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.87 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.12 % Twisted Proline : 0.49 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.12), residues: 5133 helix: 0.19 (0.10), residues: 2800 sheet: -1.83 (0.21), residues: 520 loop : -1.91 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP e 57 HIS 0.005 0.001 HIS D 384 PHE 0.029 0.002 PHE a 222 TYR 0.042 0.002 TYR W 66 ARG 0.011 0.000 ARG F 246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 753 time to evaluate : 4.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.7971 (tpp) cc_final: 0.7759 (tpp) REVERT: A 344 PHE cc_start: 0.7029 (m-80) cc_final: 0.6534 (m-80) REVERT: A 473 GLN cc_start: 0.8228 (tt0) cc_final: 0.7692 (tp40) REVERT: B 5 ARG cc_start: 0.7717 (tmm-80) cc_final: 0.6976 (tpt170) REVERT: B 194 CYS cc_start: 0.7424 (m) cc_final: 0.7109 (m) REVERT: B 436 MET cc_start: 0.7919 (ptp) cc_final: 0.7514 (ptp) REVERT: C 81 LEU cc_start: 0.7256 (mt) cc_final: 0.7034 (mp) REVERT: C 470 PRO cc_start: 0.6829 (Cg_endo) cc_final: 0.6542 (Cg_exo) REVERT: D 110 ILE cc_start: 0.8207 (mm) cc_final: 0.7933 (mt) REVERT: D 185 LEU cc_start: 0.8993 (mt) cc_final: 0.8757 (mm) REVERT: E 306 MET cc_start: 0.8020 (tpp) cc_final: 0.7544 (tpp) REVERT: E 385 TYR cc_start: 0.6738 (t80) cc_final: 0.6524 (t80) REVERT: F 411 ASP cc_start: 0.7351 (t70) cc_final: 0.7027 (t70) REVERT: F 462 LEU cc_start: 0.6478 (mt) cc_final: 0.6202 (pp) REVERT: d 234 ASP cc_start: 0.5622 (p0) cc_final: 0.5346 (p0) REVERT: e 45 ASP cc_start: 0.6970 (p0) cc_final: 0.6598 (p0) REVERT: e 105 LYS cc_start: 0.7422 (mtmt) cc_final: 0.7019 (mtmm) REVERT: g 74 ARG cc_start: 0.6368 (mmt180) cc_final: 0.5807 (ttp80) REVERT: g 135 ASN cc_start: 0.6584 (m-40) cc_final: 0.5511 (t0) REVERT: g 160 ILE cc_start: 0.6598 (pt) cc_final: 0.6231 (mt) REVERT: g 236 LYS cc_start: 0.5607 (mmtm) cc_final: 0.5297 (ttmm) REVERT: g 323 MET cc_start: 0.7304 (mmp) cc_final: 0.6958 (mmp) REVERT: I 96 ARG cc_start: 0.2797 (tpt-90) cc_final: 0.1513 (mtm-85) REVERT: I 134 GLN cc_start: 0.6196 (mm110) cc_final: 0.5912 (tp40) REVERT: J 116 MET cc_start: 0.3924 (mmt) cc_final: 0.3274 (mmt) REVERT: N 57 LEU cc_start: 0.7329 (mt) cc_final: 0.7095 (mt) REVERT: P 50 ARG cc_start: 0.2607 (mtt-85) cc_final: 0.0713 (mtp-110) REVERT: P 60 MET cc_start: 0.4145 (mtt) cc_final: 0.3847 (mtp) REVERT: Q 50 ARG cc_start: 0.3813 (mmm-85) cc_final: 0.3590 (ttt180) REVERT: Q 60 MET cc_start: 0.1701 (mtp) cc_final: 0.0652 (tpp) REVERT: T 60 MET cc_start: 0.3397 (tpp) cc_final: 0.2975 (mmm) REVERT: U 61 GLU cc_start: 0.5358 (tp30) cc_final: 0.4639 (mm-30) REVERT: W 37 GLU cc_start: 0.5835 (tt0) cc_final: 0.5055 (tp30) REVERT: X 28 GLN cc_start: 0.3734 (mp-120) cc_final: 0.3254 (mt0) REVERT: X 60 MET cc_start: 0.5354 (ttm) cc_final: 0.4848 (tpp) REVERT: Y 68 LEU cc_start: 0.3903 (tp) cc_final: 0.3506 (mm) outliers start: 0 outliers final: 0 residues processed: 753 average time/residue: 0.5031 time to fit residues: 625.9907 Evaluate side-chains 567 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 567 time to evaluate : 4.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 467 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 276 optimal weight: 0.5980 chunk 353 optimal weight: 5.9990 chunk 274 optimal weight: 4.9990 chunk 408 optimal weight: 1.9990 chunk 270 optimal weight: 2.9990 chunk 482 optimal weight: 5.9990 chunk 302 optimal weight: 0.0670 chunk 294 optimal weight: 0.8980 chunk 222 optimal weight: 1.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 267 GLN A 423 GLN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 GLN D 193 HIS ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 376 GLN ** F 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 GLN ** V 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 39707 Z= 0.213 Angle : 0.666 18.921 53855 Z= 0.328 Chirality : 0.043 0.201 6440 Planarity : 0.005 0.098 6944 Dihedral : 6.907 129.997 5721 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.61 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.12 % Twisted Proline : 0.49 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.12), residues: 5133 helix: 0.24 (0.10), residues: 2803 sheet: -1.73 (0.21), residues: 531 loop : -1.82 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP e 57 HIS 0.003 0.001 HIS F 384 PHE 0.035 0.002 PHE a 222 TYR 0.034 0.002 TYR W 66 ARG 0.009 0.000 ARG E 429 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 712 time to evaluate : 4.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.7956 (tpp) cc_final: 0.7747 (tpp) REVERT: A 344 PHE cc_start: 0.7007 (m-80) cc_final: 0.6527 (m-80) REVERT: B 5 ARG cc_start: 0.7698 (tmm-80) cc_final: 0.6927 (tpt170) REVERT: B 251 MET cc_start: 0.6641 (ppp) cc_final: 0.6441 (ppp) REVERT: B 399 PHE cc_start: 0.7202 (m-10) cc_final: 0.6715 (m-10) REVERT: B 436 MET cc_start: 0.7882 (ptp) cc_final: 0.7487 (ptp) REVERT: C 81 LEU cc_start: 0.7287 (mt) cc_final: 0.7050 (mp) REVERT: C 251 MET cc_start: 0.7770 (ttp) cc_final: 0.7449 (ptm) REVERT: C 470 PRO cc_start: 0.6817 (Cg_endo) cc_final: 0.6483 (Cg_exo) REVERT: D 110 ILE cc_start: 0.8114 (mm) cc_final: 0.7743 (mt) REVERT: D 185 LEU cc_start: 0.9007 (mt) cc_final: 0.8694 (mm) REVERT: E 306 MET cc_start: 0.8116 (tpp) cc_final: 0.7596 (tpp) REVERT: F 167 LYS cc_start: 0.8505 (mmtt) cc_final: 0.8302 (mmtt) REVERT: F 411 ASP cc_start: 0.7445 (t70) cc_final: 0.7109 (t70) REVERT: F 462 LEU cc_start: 0.6474 (mt) cc_final: 0.6205 (pp) REVERT: F 481 ASP cc_start: 0.7982 (p0) cc_final: 0.7216 (p0) REVERT: e 45 ASP cc_start: 0.6823 (p0) cc_final: 0.6593 (p0) REVERT: e 105 LYS cc_start: 0.7384 (mtmt) cc_final: 0.6955 (mtmm) REVERT: g 74 ARG cc_start: 0.6239 (mmt180) cc_final: 0.5876 (ttp80) REVERT: g 135 ASN cc_start: 0.6657 (m-40) cc_final: 0.5626 (t0) REVERT: g 236 LYS cc_start: 0.5463 (mmtm) cc_final: 0.5217 (ttmm) REVERT: g 320 MET cc_start: 0.7337 (tmm) cc_final: 0.7091 (tmm) REVERT: g 323 MET cc_start: 0.7368 (mmp) cc_final: 0.6997 (mmp) REVERT: I 96 ARG cc_start: 0.2706 (tpt-90) cc_final: 0.1204 (mtm180) REVERT: I 153 LEU cc_start: 0.7014 (tt) cc_final: 0.6671 (mt) REVERT: J 116 MET cc_start: 0.3982 (mmt) cc_final: 0.3334 (mmt) REVERT: a 184 LEU cc_start: 0.7869 (tp) cc_final: 0.7512 (tp) REVERT: N 57 LEU cc_start: 0.7355 (mt) cc_final: 0.7136 (mt) REVERT: P 50 ARG cc_start: 0.2569 (mtt-85) cc_final: 0.0613 (mtp-110) REVERT: P 60 MET cc_start: 0.4702 (mtt) cc_final: 0.3830 (mtt) REVERT: R 60 MET cc_start: 0.4901 (ptp) cc_final: 0.4449 (ptp) REVERT: T 60 MET cc_start: 0.3254 (tpp) cc_final: 0.2948 (mmm) REVERT: U 61 GLU cc_start: 0.5236 (tp30) cc_final: 0.4574 (mm-30) REVERT: W 37 GLU cc_start: 0.6000 (tt0) cc_final: 0.5181 (tp30) REVERT: X 28 GLN cc_start: 0.3674 (mp-120) cc_final: 0.3281 (mt0) REVERT: X 60 MET cc_start: 0.5473 (ttm) cc_final: 0.4786 (tpp) REVERT: Y 60 MET cc_start: 0.3354 (mmt) cc_final: 0.3074 (mmm) REVERT: Y 68 LEU cc_start: 0.4038 (tp) cc_final: 0.3551 (mt) REVERT: Z 37 GLU cc_start: 0.2791 (tp30) cc_final: 0.2247 (tm-30) outliers start: 0 outliers final: 0 residues processed: 712 average time/residue: 0.4690 time to fit residues: 556.0727 Evaluate side-chains 547 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 547 time to evaluate : 4.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 298 optimal weight: 6.9990 chunk 192 optimal weight: 0.9990 chunk 288 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 94 optimal weight: 0.3980 chunk 93 optimal weight: 1.9990 chunk 306 optimal weight: 3.9990 chunk 328 optimal weight: 0.0040 chunk 238 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 379 optimal weight: 0.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 423 GLN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 372 GLN ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 GLN D 299 GLN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 HIS E 187 ASN E 376 GLN ** F 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 39707 Z= 0.182 Angle : 0.656 19.063 53855 Z= 0.322 Chirality : 0.043 0.178 6440 Planarity : 0.004 0.105 6944 Dihedral : 6.768 127.445 5721 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.12 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.12 % Twisted Proline : 0.49 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.12), residues: 5133 helix: 0.35 (0.10), residues: 2803 sheet: -1.60 (0.21), residues: 534 loop : -1.76 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP e 57 HIS 0.006 0.001 HIS D 384 PHE 0.043 0.002 PHE a 222 TYR 0.033 0.002 TYR D 385 ARG 0.008 0.000 ARG E 429 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 729 time to evaluate : 4.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 PHE cc_start: 0.6937 (m-80) cc_final: 0.6359 (m-80) REVERT: B 5 ARG cc_start: 0.7746 (tmm-80) cc_final: 0.7052 (tpt170) REVERT: B 309 LEU cc_start: 0.8377 (mm) cc_final: 0.7947 (mt) REVERT: B 436 MET cc_start: 0.7820 (ptp) cc_final: 0.7446 (ptp) REVERT: C 251 MET cc_start: 0.7635 (ttp) cc_final: 0.7350 (ptm) REVERT: C 470 PRO cc_start: 0.6906 (Cg_endo) cc_final: 0.6564 (Cg_exo) REVERT: D 110 ILE cc_start: 0.8069 (mm) cc_final: 0.7770 (mt) REVERT: D 239 MET cc_start: 0.7560 (mtp) cc_final: 0.7308 (mtp) REVERT: E 306 MET cc_start: 0.8120 (tpp) cc_final: 0.7574 (tpp) REVERT: F 411 ASP cc_start: 0.7282 (t70) cc_final: 0.6975 (t70) REVERT: F 462 LEU cc_start: 0.6524 (mt) cc_final: 0.6187 (pp) REVERT: F 481 ASP cc_start: 0.7982 (p0) cc_final: 0.7235 (p0) REVERT: e 45 ASP cc_start: 0.6738 (p0) cc_final: 0.6464 (p0) REVERT: e 62 LEU cc_start: 0.6302 (mt) cc_final: 0.5795 (mp) REVERT: g 74 ARG cc_start: 0.6248 (mmt180) cc_final: 0.5883 (ttp80) REVERT: g 135 ASN cc_start: 0.6510 (m-40) cc_final: 0.5485 (t0) REVERT: g 160 ILE cc_start: 0.6126 (mp) cc_final: 0.5113 (tt) REVERT: g 162 LYS cc_start: 0.6194 (tptt) cc_final: 0.4887 (tppt) REVERT: g 236 LYS cc_start: 0.5403 (mmtm) cc_final: 0.5157 (mtpp) REVERT: g 320 MET cc_start: 0.7383 (tmm) cc_final: 0.7125 (tmm) REVERT: g 323 MET cc_start: 0.7359 (mmp) cc_final: 0.6996 (mmp) REVERT: I 96 ARG cc_start: 0.2493 (tpt-90) cc_final: 0.0943 (mtm180) REVERT: I 153 LEU cc_start: 0.7024 (tt) cc_final: 0.6624 (mt) REVERT: J 116 MET cc_start: 0.3992 (mmt) cc_final: 0.3375 (mmt) REVERT: a 175 ASN cc_start: 0.5896 (t0) cc_final: 0.5415 (m-40) REVERT: a 184 LEU cc_start: 0.7805 (tp) cc_final: 0.7539 (tp) REVERT: N 57 LEU cc_start: 0.7455 (mt) cc_final: 0.7053 (mt) REVERT: P 28 GLN cc_start: 0.5975 (tt0) cc_final: 0.5469 (tt0) REVERT: P 50 ARG cc_start: 0.2461 (mtt-85) cc_final: 0.0481 (mtp-110) REVERT: P 60 MET cc_start: 0.4540 (mtt) cc_final: 0.4058 (mtt) REVERT: R 60 MET cc_start: 0.4871 (ptp) cc_final: 0.4519 (ptp) REVERT: R 61 GLU cc_start: 0.3616 (mm-30) cc_final: 0.2426 (mt-10) REVERT: T 46 GLU cc_start: 0.5850 (pm20) cc_final: 0.5470 (pm20) REVERT: T 60 MET cc_start: 0.3576 (tpp) cc_final: 0.3263 (mmm) REVERT: V 64 THR cc_start: 0.4601 (t) cc_final: 0.4278 (p) REVERT: W 37 GLU cc_start: 0.5973 (tt0) cc_final: 0.5135 (tp30) REVERT: X 28 GLN cc_start: 0.3570 (mp-120) cc_final: 0.3352 (mt0) REVERT: X 60 MET cc_start: 0.5578 (ttm) cc_final: 0.4813 (tpp) REVERT: Y 68 LEU cc_start: 0.4042 (tp) cc_final: 0.3617 (mt) outliers start: 0 outliers final: 0 residues processed: 729 average time/residue: 0.4706 time to fit residues: 575.1173 Evaluate side-chains 579 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 579 time to evaluate : 4.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 439 optimal weight: 0.6980 chunk 462 optimal weight: 2.9990 chunk 422 optimal weight: 0.9990 chunk 449 optimal weight: 0.9990 chunk 270 optimal weight: 0.5980 chunk 196 optimal weight: 1.9990 chunk 353 optimal weight: 1.9990 chunk 138 optimal weight: 0.5980 chunk 406 optimal weight: 4.9990 chunk 425 optimal weight: 9.9990 chunk 448 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 423 GLN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 GLN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 325 GLN E 376 GLN ** F 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 GLN ** d 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 28 GLN ** V 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 39707 Z= 0.205 Angle : 0.665 18.524 53855 Z= 0.326 Chirality : 0.043 0.186 6440 Planarity : 0.005 0.106 6944 Dihedral : 6.686 126.651 5721 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.51 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.12 % Twisted Proline : 0.49 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.12), residues: 5133 helix: 0.43 (0.10), residues: 2792 sheet: -1.49 (0.21), residues: 523 loop : -1.73 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP e 57 HIS 0.004 0.001 HIS E 133 PHE 0.030 0.002 PHE a 222 TYR 0.030 0.002 TYR W 66 ARG 0.020 0.000 ARG F 246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 723 time to evaluate : 4.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.7890 (mmp) cc_final: 0.7466 (mmm) REVERT: A 344 PHE cc_start: 0.6959 (m-80) cc_final: 0.6549 (m-80) REVERT: B 5 ARG cc_start: 0.7717 (tmm-80) cc_final: 0.7006 (tpt170) REVERT: B 251 MET cc_start: 0.6904 (ppp) cc_final: 0.6634 (ppp) REVERT: B 436 MET cc_start: 0.7928 (ptp) cc_final: 0.7306 (ptp) REVERT: C 251 MET cc_start: 0.7574 (ttp) cc_final: 0.7327 (ptm) REVERT: C 292 PHE cc_start: 0.8233 (t80) cc_final: 0.7272 (t80) REVERT: C 470 PRO cc_start: 0.6925 (Cg_endo) cc_final: 0.6553 (Cg_exo) REVERT: D 110 ILE cc_start: 0.8122 (mm) cc_final: 0.7777 (mt) REVERT: D 185 LEU cc_start: 0.8919 (mt) cc_final: 0.8607 (mm) REVERT: E 204 GLU cc_start: 0.3935 (mm-30) cc_final: 0.3500 (mm-30) REVERT: E 277 ARG cc_start: 0.7888 (mmt180) cc_final: 0.7645 (mmm-85) REVERT: E 306 MET cc_start: 0.8179 (tpp) cc_final: 0.7632 (tpp) REVERT: F 411 ASP cc_start: 0.7399 (t70) cc_final: 0.7085 (t70) REVERT: F 462 LEU cc_start: 0.6448 (mt) cc_final: 0.6214 (pp) REVERT: F 481 ASP cc_start: 0.7946 (p0) cc_final: 0.7215 (p0) REVERT: e 45 ASP cc_start: 0.6638 (p0) cc_final: 0.6338 (p0) REVERT: e 80 ASP cc_start: 0.4769 (t70) cc_final: 0.4482 (t0) REVERT: g 45 ARG cc_start: 0.6548 (tpp80) cc_final: 0.6265 (tpt170) REVERT: g 74 ARG cc_start: 0.6245 (mmt180) cc_final: 0.5874 (ttp80) REVERT: g 135 ASN cc_start: 0.6622 (m-40) cc_final: 0.5593 (t0) REVERT: g 162 LYS cc_start: 0.6366 (tptt) cc_final: 0.4968 (tppt) REVERT: g 220 LEU cc_start: 0.6702 (mt) cc_final: 0.5798 (pt) REVERT: g 236 LYS cc_start: 0.5694 (mmtm) cc_final: 0.5352 (mtpp) REVERT: g 286 GLN cc_start: 0.7009 (mp10) cc_final: 0.6790 (mp10) REVERT: g 320 MET cc_start: 0.7419 (tmm) cc_final: 0.7127 (tmm) REVERT: I 58 GLN cc_start: 0.6284 (tp40) cc_final: 0.5153 (pt0) REVERT: I 153 LEU cc_start: 0.7100 (tt) cc_final: 0.6686 (mt) REVERT: J 116 MET cc_start: 0.3861 (mmt) cc_final: 0.3218 (mmt) REVERT: a 184 LEU cc_start: 0.7816 (tp) cc_final: 0.7585 (tp) REVERT: N 57 LEU cc_start: 0.7433 (mt) cc_final: 0.7001 (mt) REVERT: P 28 GLN cc_start: 0.5862 (tt0) cc_final: 0.5354 (tt0) REVERT: P 50 ARG cc_start: 0.2541 (mtt-85) cc_final: 0.0491 (mtp-110) REVERT: P 60 MET cc_start: 0.4498 (mtt) cc_final: 0.3904 (mtt) REVERT: R 60 MET cc_start: 0.4908 (ptp) cc_final: 0.4484 (ptp) REVERT: R 61 GLU cc_start: 0.3620 (mm-30) cc_final: 0.2331 (mt-10) REVERT: T 46 GLU cc_start: 0.6024 (pm20) cc_final: 0.5608 (pm20) REVERT: T 60 MET cc_start: 0.2993 (tpp) cc_final: 0.2739 (mmm) REVERT: U 61 GLU cc_start: 0.5174 (tp30) cc_final: 0.4910 (tp30) REVERT: V 64 THR cc_start: 0.4770 (t) cc_final: 0.4565 (p) REVERT: W 37 GLU cc_start: 0.5885 (tt0) cc_final: 0.5101 (tp30) REVERT: Y 68 LEU cc_start: 0.4084 (tp) cc_final: 0.3635 (mt) outliers start: 0 outliers final: 0 residues processed: 723 average time/residue: 0.4719 time to fit residues: 570.9013 Evaluate side-chains 578 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 578 time to evaluate : 4.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 295 optimal weight: 0.0980 chunk 475 optimal weight: 5.9990 chunk 290 optimal weight: 3.9990 chunk 225 optimal weight: 0.5980 chunk 330 optimal weight: 0.9990 chunk 499 optimal weight: 1.9990 chunk 459 optimal weight: 0.8980 chunk 397 optimal weight: 0.7980 chunk 41 optimal weight: 9.9990 chunk 307 optimal weight: 3.9990 chunk 243 optimal weight: 4.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 423 GLN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 GLN ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 GLN ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 GLN ** E 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 39707 Z= 0.195 Angle : 0.670 18.798 53855 Z= 0.327 Chirality : 0.043 0.185 6440 Planarity : 0.004 0.101 6944 Dihedral : 6.623 126.095 5721 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.22 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.12 % Twisted Proline : 0.49 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.12), residues: 5133 helix: 0.46 (0.10), residues: 2793 sheet: -1.38 (0.21), residues: 524 loop : -1.74 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP e 57 HIS 0.005 0.001 HIS E 133 PHE 0.025 0.002 PHE E 276 TYR 0.043 0.002 TYR D 385 ARG 0.007 0.000 ARG E 429 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10266 Ramachandran restraints generated. 5133 Oldfield, 0 Emsley, 5133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 718 time to evaluate : 4.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.8108 (pt) cc_final: 0.7855 (pt) REVERT: A 344 PHE cc_start: 0.6960 (m-80) cc_final: 0.6587 (m-80) REVERT: A 346 SER cc_start: 0.8435 (p) cc_final: 0.8206 (p) REVERT: B 5 ARG cc_start: 0.7669 (tmm-80) cc_final: 0.6969 (tpt170) REVERT: B 251 MET cc_start: 0.6803 (ppp) cc_final: 0.6569 (ppp) REVERT: B 309 LEU cc_start: 0.8430 (mm) cc_final: 0.8128 (mt) REVERT: B 436 MET cc_start: 0.7786 (ptp) cc_final: 0.7190 (ptp) REVERT: C 470 PRO cc_start: 0.6934 (Cg_endo) cc_final: 0.6629 (Cg_exo) REVERT: D 110 ILE cc_start: 0.8173 (mm) cc_final: 0.7821 (mt) REVERT: E 204 GLU cc_start: 0.3823 (mm-30) cc_final: 0.3440 (mm-30) REVERT: E 306 MET cc_start: 0.8215 (tpp) cc_final: 0.7681 (tpp) REVERT: E 400 GLU cc_start: 0.6587 (tm-30) cc_final: 0.6323 (tm-30) REVERT: F 411 ASP cc_start: 0.7315 (t70) cc_final: 0.7010 (t70) REVERT: F 462 LEU cc_start: 0.6502 (mt) cc_final: 0.6251 (pp) REVERT: F 481 ASP cc_start: 0.7934 (p0) cc_final: 0.7229 (p0) REVERT: e 45 ASP cc_start: 0.6622 (p0) cc_final: 0.6274 (p0) REVERT: e 80 ASP cc_start: 0.5118 (t70) cc_final: 0.4826 (t0) REVERT: g 74 ARG cc_start: 0.6260 (mmt180) cc_final: 0.5891 (ttp80) REVERT: g 135 ASN cc_start: 0.6625 (m-40) cc_final: 0.5611 (t0) REVERT: g 162 LYS cc_start: 0.6382 (tptt) cc_final: 0.5039 (tppt) REVERT: g 220 LEU cc_start: 0.6549 (mt) cc_final: 0.5681 (pt) REVERT: g 236 LYS cc_start: 0.5768 (mmtm) cc_final: 0.5448 (mtmm) REVERT: I 58 GLN cc_start: 0.6444 (tp40) cc_final: 0.5322 (pt0) REVERT: I 90 MET cc_start: 0.2047 (tpt) cc_final: 0.1718 (tpt) REVERT: I 153 LEU cc_start: 0.7095 (tt) cc_final: 0.6671 (mt) REVERT: J 116 MET cc_start: 0.3837 (mmt) cc_final: 0.3148 (mmt) REVERT: a 87 ILE cc_start: 0.4548 (mm) cc_final: 0.4334 (mm) REVERT: N 57 LEU cc_start: 0.7385 (mt) cc_final: 0.6915 (mt) REVERT: P 28 GLN cc_start: 0.5811 (tt0) cc_final: 0.5320 (tt0) REVERT: P 50 ARG cc_start: 0.2559 (mtt-85) cc_final: 0.0498 (mtp-110) REVERT: P 60 MET cc_start: 0.4399 (mtt) cc_final: 0.3712 (mtt) REVERT: R 60 MET cc_start: 0.5034 (ptp) cc_final: 0.4461 (ptp) REVERT: R 61 GLU cc_start: 0.3407 (mm-30) cc_final: 0.2323 (mt-10) REVERT: T 46 GLU cc_start: 0.6123 (pm20) cc_final: 0.5728 (pm20) REVERT: T 60 MET cc_start: 0.3146 (tpp) cc_final: 0.2844 (mmm) REVERT: U 61 GLU cc_start: 0.5194 (tp30) cc_final: 0.4887 (tp30) REVERT: V 64 THR cc_start: 0.4913 (t) cc_final: 0.4649 (p) REVERT: W 37 GLU cc_start: 0.5824 (tt0) cc_final: 0.5062 (tp30) REVERT: Y 68 LEU cc_start: 0.4126 (tp) cc_final: 0.3691 (mt) outliers start: 0 outliers final: 0 residues processed: 718 average time/residue: 0.4701 time to fit residues: 564.7927 Evaluate side-chains 580 residues out of total 4091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 580 time to evaluate : 4.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 315 optimal weight: 0.9980 chunk 423 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 366 optimal weight: 0.9990 chunk 58 optimal weight: 0.0470 chunk 110 optimal weight: 0.0470 chunk 398 optimal weight: 0.5980 chunk 166 optimal weight: 4.9990 chunk 408 optimal weight: 0.9980 chunk 50 optimal weight: 0.0070 chunk 73 optimal weight: 0.9980 overall best weight: 0.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 423 GLN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 GLN ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 346 GLN ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.118701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.103063 restraints weight = 132594.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.102703 restraints weight = 127035.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.103454 restraints weight = 96003.364| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 39707 Z= 0.173 Angle : 0.657 19.019 53855 Z= 0.319 Chirality : 0.042 0.183 6440 Planarity : 0.004 0.095 6944 Dihedral : 6.444 123.440 5721 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.85 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.12 % Twisted Proline : 0.49 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.12), residues: 5133 helix: 0.57 (0.10), residues: 2778 sheet: -1.29 (0.22), residues: 521 loop : -1.67 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP e 57 HIS 0.005 0.001 HIS E 133 PHE 0.036 0.001 PHE a 222 TYR 0.029 0.001 TYR I 124 ARG 0.023 0.000 ARG E 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10138.98 seconds wall clock time: 181 minutes 57.05 seconds (10917.05 seconds total)