Starting phenix.real_space_refine on Sat Mar 23 21:01:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl8_29270/03_2024/8fl8_29270_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl8_29270/03_2024/8fl8_29270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl8_29270/03_2024/8fl8_29270.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl8_29270/03_2024/8fl8_29270.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl8_29270/03_2024/8fl8_29270_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl8_29270/03_2024/8fl8_29270_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 14 5.49 5 Mg 5 5.21 5 S 100 5.16 5 C 24788 2.51 5 N 6540 2.21 5 O 7337 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Y GLU 16": "OE1" <-> "OE2" Residue "Y GLU 102": "OE1" <-> "OE2" Residue "Y PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 15": "OE1" <-> "OE2" Residue "A GLU 53": "OE1" <-> "OE2" Residue "A PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B GLU 86": "OE1" <-> "OE2" Residue "B ASP 98": "OD1" <-> "OD2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 271": "OD1" <-> "OD2" Residue "B ASP 299": "OD1" <-> "OD2" Residue "B PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 456": "OD1" <-> "OD2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "C GLU 318": "OE1" <-> "OE2" Residue "C PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 355": "OE1" <-> "OE2" Residue "C TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 189": "OE1" <-> "OE2" Residue "D PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 294": "OE1" <-> "OE2" Residue "D ASP 359": "OD1" <-> "OD2" Residue "D TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 319": "OD1" <-> "OD2" Residue "E TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 224": "OE1" <-> "OE2" Residue "F GLU 246": "OE1" <-> "OE2" Residue "F TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 294": "OE1" <-> "OE2" Residue "F ASP 352": "OD1" <-> "OD2" Residue "F GLU 395": "OE1" <-> "OE2" Residue "F GLU 422": "OE1" <-> "OE2" Residue "G GLU 35": "OE1" <-> "OE2" Residue "G PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 28": "OE1" <-> "OE2" Residue "I TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 155": "OD1" <-> "OD2" Residue "7 ASP 11": "OD1" <-> "OD2" Residue "6 GLU 43": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 38784 Number of models: 1 Model: "" Number of chains: 32 Chain: "8" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 356 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "J" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 292 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "Y" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1254 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 7, 'TRANS': 158} Chain: "A" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3858 Classifications: {'peptide': 507} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 486} Chain: "B" Number of atoms: 3846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3846 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 20, 'TRANS': 485} Chain: "C" Number of atoms: 3844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3844 Classifications: {'peptide': 505} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 484} Chain: "D" Number of atoms: 3572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3572 Classifications: {'peptide': 473} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 449} Chain: "E" Number of atoms: 3572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3572 Classifications: {'peptide': 473} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 449} Chain: "F" Number of atoms: 3566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3566 Classifications: {'peptide': 472} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 448} Chain: "G" Number of atoms: 2032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2032 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 9, 'TRANS': 251} Chain breaks: 1 Chain: "H" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 990 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "I" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 392 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 56} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "S" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "T" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "K" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "L" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "M" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "N" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "O" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "P" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "Q" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "R" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "X" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1772 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "Z" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1232 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 152} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "7" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1363 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 165} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "6" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 710 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 8, 'TRANS': 80} Chain: "U" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 639 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 77} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 20.02, per 1000 atoms: 0.52 Number of scatterers: 38784 At special positions: 0 Unit cell: (130.38, 151.58, 241.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 100 16.00 P 14 15.00 Mg 5 11.99 O 7337 8.00 N 6540 7.00 C 24788 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: 15.97 Conformation dependent library (CDL) restraints added in 6.3 seconds 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9318 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 185 helices and 25 sheets defined 52.6% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.81 Creating SS restraints... Processing helix chain '8' and resid 10 through 28 removed outlier: 4.121A pdb=" N THR 8 14 " --> pdb=" O MET 8 10 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N TYR 8 15 " --> pdb=" O ASN 8 11 " (cutoff:3.500A) Processing helix chain '8' and resid 32 through 46 Processing helix chain 'J' and resid 14 through 33 removed outlier: 4.785A pdb=" N GLY J 26 " --> pdb=" O ALA J 22 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYS J 29 " --> pdb=" O TYR J 25 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA J 31 " --> pdb=" O MET J 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 18 through 30 removed outlier: 4.005A pdb=" N ASN Y 30 " --> pdb=" O ALA Y 26 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 49 Processing helix chain 'Y' and resid 51 through 54 No H-bonds generated for 'chain 'Y' and resid 51 through 54' Processing helix chain 'Y' and resid 56 through 58 No H-bonds generated for 'chain 'Y' and resid 56 through 58' Processing helix chain 'Y' and resid 64 through 74 Processing helix chain 'Y' and resid 85 through 93 Processing helix chain 'Y' and resid 101 through 114 Processing helix chain 'Y' and resid 138 through 148 Processing helix chain 'Y' and resid 160 through 170 Processing helix chain 'A' and resid 5 through 15 Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 153 through 157 Processing helix chain 'A' and resid 177 through 192 removed outlier: 4.123A pdb=" N LYS A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ARG A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N TRP A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 224 Processing helix chain 'A' and resid 242 through 261 Proline residue: A 249 - end of helix removed outlier: 3.703A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 287 Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 298 through 310 removed outlier: 3.893A pdb=" N PHE A 301 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 303 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU A 309 " --> pdb=" O ARG A 306 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG A 310 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 356 through 361 Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 392 through 405 Processing helix chain 'A' and resid 415 through 430 removed outlier: 4.081A pdb=" N ARG A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 442 No H-bonds generated for 'chain 'A' and resid 440 through 442' Processing helix chain 'A' and resid 444 through 451 Processing helix chain 'A' and resid 454 through 456 No H-bonds generated for 'chain 'A' and resid 454 through 456' Processing helix chain 'A' and resid 460 through 476 removed outlier: 5.006A pdb=" N GLY A 464 " --> pdb=" O SER A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 487 Processing helix chain 'A' and resid 493 through 509 removed outlier: 3.597A pdb=" N THR A 509 " --> pdb=" O SER A 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 24 removed outlier: 3.794A pdb=" N GLU B 24 " --> pdb=" O GLY B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 83 No H-bonds generated for 'chain 'B' and resid 81 through 83' Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 153 through 156 No H-bonds generated for 'chain 'B' and resid 153 through 156' Processing helix chain 'B' and resid 177 through 192 removed outlier: 4.001A pdb=" N ALA B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ARG B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N TRP B 191 " --> pdb=" O ASN B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 199 No H-bonds generated for 'chain 'B' and resid 197 through 199' Processing helix chain 'B' and resid 212 through 224 Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 242 through 261 Proline residue: B 249 - end of helix removed outlier: 3.786A pdb=" N PHE B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 286 Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 298 through 310 removed outlier: 4.179A pdb=" N PHE B 301 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR B 302 " --> pdb=" O ASP B 299 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG B 306 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU B 309 " --> pdb=" O ARG B 306 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG B 310 " --> pdb=" O LEU B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 334 No H-bonds generated for 'chain 'B' and resid 332 through 334' Processing helix chain 'B' and resid 339 through 347 Processing helix chain 'B' and resid 356 through 360 Processing helix chain 'B' and resid 383 through 385 No H-bonds generated for 'chain 'B' and resid 383 through 385' Processing helix chain 'B' and resid 391 through 393 No H-bonds generated for 'chain 'B' and resid 391 through 393' Processing helix chain 'B' and resid 395 through 405 Processing helix chain 'B' and resid 414 through 429 Processing helix chain 'B' and resid 440 through 450 Proline residue: B 445 - end of helix Processing helix chain 'B' and resid 460 through 462 No H-bonds generated for 'chain 'B' and resid 460 through 462' Processing helix chain 'B' and resid 464 through 475 Processing helix chain 'B' and resid 479 through 487 Processing helix chain 'B' and resid 493 through 508 Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 153 through 158 Processing helix chain 'C' and resid 177 through 192 removed outlier: 3.903A pdb=" N ALA C 181 " --> pdb=" O LYS C 177 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS C 189 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ARG C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N TRP C 191 " --> pdb=" O ASN C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 224 Processing helix chain 'C' and resid 242 through 261 Proline residue: C 249 - end of helix removed outlier: 3.665A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 286 Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 298 through 309 removed outlier: 4.002A pdb=" N PHE C 301 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N TYR C 302 " --> pdb=" O ASP C 299 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU C 309 " --> pdb=" O ARG C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 339 through 347 Processing helix chain 'C' and resid 356 through 361 Processing helix chain 'C' and resid 383 through 404 removed outlier: 4.051A pdb=" N GLY C 390 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N SER C 391 " --> pdb=" O GLN C 387 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU C 392 " --> pdb=" O VAL C 388 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ALA C 404 " --> pdb=" O ARG C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 430 Processing helix chain 'C' and resid 440 through 451 Proline residue: C 445 - end of helix Processing helix chain 'C' and resid 460 through 476 removed outlier: 3.517A pdb=" N ILE C 463 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLY C 464 " --> pdb=" O SER C 461 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER C 469 " --> pdb=" O PHE C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 487 Processing helix chain 'C' and resid 493 through 509 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 139 through 144 Processing helix chain 'D' and resid 163 through 177 Processing helix chain 'D' and resid 193 through 204 Processing helix chain 'D' and resid 232 through 245 Processing helix chain 'D' and resid 258 through 272 Processing helix chain 'D' and resid 285 through 295 removed outlier: 4.121A pdb=" N ARG D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 315 No H-bonds generated for 'chain 'D' and resid 313 through 315' Processing helix chain 'D' and resid 320 through 328 removed outlier: 4.058A pdb=" N HIS D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 390 removed outlier: 4.285A pdb=" N ASP D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ILE D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 413 Processing helix chain 'D' and resid 434 through 446 Processing helix chain 'D' and resid 454 through 456 No H-bonds generated for 'chain 'D' and resid 454 through 456' Processing helix chain 'D' and resid 463 through 477 Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 139 through 144 Processing helix chain 'E' and resid 163 through 173 Processing helix chain 'E' and resid 191 through 204 Processing helix chain 'E' and resid 226 through 245 removed outlier: 4.876A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 272 removed outlier: 3.560A pdb=" N ALA E 270 " --> pdb=" O SER E 266 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU E 271 " --> pdb=" O GLU E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 280 No H-bonds generated for 'chain 'E' and resid 278 through 280' Processing helix chain 'E' and resid 285 through 295 removed outlier: 3.811A pdb=" N ARG E 295 " --> pdb=" O LEU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 315 No H-bonds generated for 'chain 'E' and resid 313 through 315' Processing helix chain 'E' and resid 320 through 326 Processing helix chain 'E' and resid 337 through 341 Processing helix chain 'E' and resid 360 through 363 No H-bonds generated for 'chain 'E' and resid 360 through 363' Processing helix chain 'E' and resid 365 through 390 removed outlier: 3.639A pdb=" N TYR E 381 " --> pdb=" O THR E 377 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ILE E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 395 No H-bonds generated for 'chain 'E' and resid 393 through 395' Processing helix chain 'E' and resid 398 through 413 Processing helix chain 'E' and resid 434 through 446 Processing helix chain 'E' and resid 454 through 457 Processing helix chain 'E' and resid 463 through 475 Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 124 through 126 No H-bonds generated for 'chain 'F' and resid 124 through 126' Processing helix chain 'F' and resid 140 through 143 No H-bonds generated for 'chain 'F' and resid 140 through 143' Processing helix chain 'F' and resid 163 through 174 Processing helix chain 'F' and resid 191 through 204 Processing helix chain 'F' and resid 226 through 229 No H-bonds generated for 'chain 'F' and resid 226 through 229' Processing helix chain 'F' and resid 232 through 245 Processing helix chain 'F' and resid 258 through 272 removed outlier: 4.731A pdb=" N ALA F 270 " --> pdb=" O GLU F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 280 No H-bonds generated for 'chain 'F' and resid 278 through 280' Processing helix chain 'F' and resid 285 through 294 Processing helix chain 'F' and resid 313 through 315 No H-bonds generated for 'chain 'F' and resid 313 through 315' Processing helix chain 'F' and resid 320 through 328 removed outlier: 4.017A pdb=" N ALA F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N HIS F 328 " --> pdb=" O THR F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 341 Processing helix chain 'F' and resid 365 through 383 Processing helix chain 'F' and resid 385 through 389 Processing helix chain 'F' and resid 398 through 413 Processing helix chain 'F' and resid 419 through 421 No H-bonds generated for 'chain 'F' and resid 419 through 421' Processing helix chain 'F' and resid 434 through 446 Processing helix chain 'F' and resid 454 through 457 Processing helix chain 'F' and resid 463 through 477 Processing helix chain 'G' and resid 6 through 54 removed outlier: 4.757A pdb=" N SER G 40 " --> pdb=" O LYS G 36 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU G 48 " --> pdb=" O MET G 44 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN G 54 " --> pdb=" O LEU G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 101 Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'G' and resid 141 through 154 Processing helix chain 'G' and resid 156 through 158 No H-bonds generated for 'chain 'G' and resid 156 through 158' Processing helix chain 'G' and resid 185 through 190 removed outlier: 4.030A pdb=" N GLU G 189 " --> pdb=" O ALA G 185 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLN G 190 " --> pdb=" O LYS G 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 185 through 190' Processing helix chain 'G' and resid 194 through 196 No H-bonds generated for 'chain 'G' and resid 194 through 196' Processing helix chain 'G' and resid 205 through 273 Processing helix chain 'H' and resid 99 through 114 removed outlier: 4.138A pdb=" N ASN H 111 " --> pdb=" O GLU H 107 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL H 112 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N SER H 114 " --> pdb=" O LYS H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 137 Processing helix chain 'I' and resid 10 through 23 Processing helix chain 'I' and resid 32 through 38 Processing helix chain 'S' and resid 2 through 39 removed outlier: 4.298A pdb=" N ILE S 17 " --> pdb=" O GLY S 13 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N GLY S 18 " --> pdb=" O ILE S 14 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU S 19 " --> pdb=" O SER S 15 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LEU S 20 " --> pdb=" O THR S 16 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY S 21 " --> pdb=" O ILE S 17 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 73 removed outlier: 4.145A pdb=" N ASP S 45 " --> pdb=" O SER S 42 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE S 48 " --> pdb=" O ASP S 45 " (cutoff:3.500A) Proline residue: S 49 - end of helix Processing helix chain 'T' and resid 2 through 39 removed outlier: 3.888A pdb=" N ILE T 17 " --> pdb=" O GLY T 13 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLY T 18 " --> pdb=" O ILE T 14 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LEU T 19 " --> pdb=" O SER T 15 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LEU T 20 " --> pdb=" O THR T 16 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLY T 21 " --> pdb=" O ILE T 17 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA T 22 " --> pdb=" O GLY T 18 " (cutoff:3.500A) Processing helix chain 'T' and resid 41 through 73 removed outlier: 3.980A pdb=" N ASP T 45 " --> pdb=" O SER T 42 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE T 48 " --> pdb=" O ASP T 45 " (cutoff:3.500A) Proline residue: T 49 - end of helix Processing helix chain 'K' and resid 3 through 39 removed outlier: 4.021A pdb=" N ILE K 17 " --> pdb=" O GLY K 13 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N GLY K 18 " --> pdb=" O ILE K 14 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LEU K 19 " --> pdb=" O SER K 15 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU K 20 " --> pdb=" O THR K 16 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY K 21 " --> pdb=" O ILE K 17 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA K 22 " --> pdb=" O GLY K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 74 removed outlier: 3.871A pdb=" N LYS K 44 " --> pdb=" O PRO K 41 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASP K 45 " --> pdb=" O SER K 42 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE K 48 " --> pdb=" O ASP K 45 " (cutoff:3.500A) Proline residue: K 49 - end of helix removed outlier: 3.594A pdb=" N PHE K 64 " --> pdb=" O THR K 61 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE K 74 " --> pdb=" O LEU K 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 39 removed outlier: 3.660A pdb=" N THR L 16 " --> pdb=" O ALA L 12 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE L 17 " --> pdb=" O GLY L 13 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLY L 18 " --> pdb=" O ILE L 14 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LEU L 19 " --> pdb=" O SER L 15 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU L 20 " --> pdb=" O THR L 16 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY L 21 " --> pdb=" O ILE L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 73 removed outlier: 4.217A pdb=" N LYS L 44 " --> pdb=" O PRO L 41 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ASP L 45 " --> pdb=" O SER L 42 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N PHE L 48 " --> pdb=" O ASP L 45 " (cutoff:3.500A) Proline residue: L 49 - end of helix Processing helix chain 'M' and resid 2 through 39 removed outlier: 4.653A pdb=" N ILE M 17 " --> pdb=" O GLY M 13 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N GLY M 18 " --> pdb=" O ILE M 14 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LEU M 19 " --> pdb=" O SER M 15 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU M 20 " --> pdb=" O THR M 16 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 73 removed outlier: 3.560A pdb=" N LYS M 44 " --> pdb=" O PRO M 41 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASP M 45 " --> pdb=" O SER M 42 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE M 48 " --> pdb=" O ASP M 45 " (cutoff:3.500A) Proline residue: M 49 - end of helix Processing helix chain 'N' and resid 2 through 39 removed outlier: 4.554A pdb=" N ILE N 17 " --> pdb=" O GLY N 13 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N GLY N 18 " --> pdb=" O ILE N 14 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N LEU N 19 " --> pdb=" O SER N 15 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LEU N 20 " --> pdb=" O THR N 16 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY N 21 " --> pdb=" O ILE N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 71 removed outlier: 3.566A pdb=" N ASP N 45 " --> pdb=" O SER N 42 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE N 48 " --> pdb=" O ASP N 45 " (cutoff:3.500A) Proline residue: N 49 - end of helix removed outlier: 3.554A pdb=" N LEU N 71 " --> pdb=" O VAL N 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 39 removed outlier: 3.951A pdb=" N ILE O 17 " --> pdb=" O GLY O 13 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N GLY O 18 " --> pdb=" O ILE O 14 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU O 19 " --> pdb=" O SER O 15 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N LEU O 20 " --> pdb=" O THR O 16 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLY O 21 " --> pdb=" O ILE O 17 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA O 22 " --> pdb=" O GLY O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 41 through 71 removed outlier: 3.975A pdb=" N ASP O 45 " --> pdb=" O SER O 42 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE O 48 " --> pdb=" O ASP O 45 " (cutoff:3.500A) Proline residue: O 49 - end of helix removed outlier: 3.600A pdb=" N GLU O 59 " --> pdb=" O ALA O 56 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 39 removed outlier: 4.391A pdb=" N ILE P 17 " --> pdb=" O GLY P 13 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLY P 18 " --> pdb=" O ILE P 14 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LEU P 19 " --> pdb=" O SER P 15 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LEU P 20 " --> pdb=" O THR P 16 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY P 21 " --> pdb=" O ILE P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 74 removed outlier: 3.890A pdb=" N ASP P 45 " --> pdb=" O SER P 42 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE P 48 " --> pdb=" O ASP P 45 " (cutoff:3.500A) Proline residue: P 49 - end of helix removed outlier: 3.542A pdb=" N GLU P 59 " --> pdb=" O ALA P 56 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE P 74 " --> pdb=" O LEU P 71 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 39 removed outlier: 5.079A pdb=" N GLY Q 18 " --> pdb=" O ILE Q 14 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LEU Q 19 " --> pdb=" O SER Q 15 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LEU Q 20 " --> pdb=" O THR Q 16 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N GLY Q 21 " --> pdb=" O ILE Q 17 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA Q 22 " --> pdb=" O GLY Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 72 removed outlier: 3.906A pdb=" N LYS Q 44 " --> pdb=" O PRO Q 41 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ASP Q 45 " --> pdb=" O SER Q 42 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE Q 48 " --> pdb=" O ASP Q 45 " (cutoff:3.500A) Proline residue: Q 49 - end of helix removed outlier: 3.695A pdb=" N LEU Q 71 " --> pdb=" O VAL Q 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 18 removed outlier: 3.785A pdb=" N ILE R 17 " --> pdb=" O GLY R 13 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLY R 18 " --> pdb=" O ILE R 14 " (cutoff:3.500A) Processing helix chain 'R' and resid 20 through 39 Processing helix chain 'R' and resid 42 through 73 removed outlier: 4.122A pdb=" N ASP R 45 " --> pdb=" O SER R 42 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE R 48 " --> pdb=" O ASP R 45 " (cutoff:3.500A) Proline residue: R 49 - end of helix Processing helix chain 'X' and resid 28 through 44 removed outlier: 3.657A pdb=" N SER X 42 " --> pdb=" O LEU X 38 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU X 43 " --> pdb=" O VAL X 39 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TYR X 44 " --> pdb=" O ILE X 40 " (cutoff:3.500A) Processing helix chain 'X' and resid 57 through 77 removed outlier: 3.527A pdb=" N GLN X 62 " --> pdb=" O TRP X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 86 through 101 Processing helix chain 'X' and resid 110 through 113 Processing helix chain 'X' and resid 116 through 145 removed outlier: 7.637A pdb=" N TRP X 139 " --> pdb=" O TYR X 135 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL X 140 " --> pdb=" O LYS X 136 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE X 141 " --> pdb=" O HIS X 137 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE X 142 " --> pdb=" O GLY X 138 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER X 143 " --> pdb=" O TRP X 139 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU X 144 " --> pdb=" O VAL X 140 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N PHE X 145 " --> pdb=" O PHE X 141 " (cutoff:3.500A) Processing helix chain 'X' and resid 152 through 201 Proline residue: X 156 - end of helix removed outlier: 3.821A pdb=" N ALA X 170 " --> pdb=" O TYR X 166 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY X 174 " --> pdb=" O ALA X 170 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU X 177 " --> pdb=" O LEU X 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU X 191 " --> pdb=" O LEU X 187 " (cutoff:3.500A) Processing helix chain 'X' and resid 210 through 246 removed outlier: 3.616A pdb=" N ILE X 228 " --> pdb=" O PHE X 224 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP X 244 " --> pdb=" O SER X 240 " (cutoff:3.500A) Processing helix chain 'Z' and resid 54 through 71 Processing helix chain 'Z' and resid 76 through 112 removed outlier: 3.668A pdb=" N ARG Z 84 " --> pdb=" O PHE Z 80 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS Z 86 " --> pdb=" O ASP Z 82 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU Z 92 " --> pdb=" O VAL Z 88 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS Z 99 " --> pdb=" O SER Z 95 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA Z 102 " --> pdb=" O LYS Z 98 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL Z 103 " --> pdb=" O HIS Z 99 " (cutoff:3.500A) Processing helix chain 'Z' and resid 116 through 131 removed outlier: 3.543A pdb=" N LYS Z 121 " --> pdb=" O ALA Z 117 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL Z 122 " --> pdb=" O GLU Z 118 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU Z 129 " --> pdb=" O ASP Z 125 " (cutoff:3.500A) Processing helix chain 'Z' and resid 136 through 183 removed outlier: 3.738A pdb=" N TYR Z 160 " --> pdb=" O SER Z 156 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU Z 161 " --> pdb=" O TRP Z 157 " (cutoff:3.500A) Processing helix chain 'Z' and resid 187 through 206 removed outlier: 3.712A pdb=" N LYS Z 192 " --> pdb=" O PHE Z 189 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL Z 193 " --> pdb=" O GLN Z 190 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE Z 198 " --> pdb=" O GLN Z 195 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU Z 200 " --> pdb=" O SER Z 197 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU Z 204 " --> pdb=" O ILE Z 201 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU Z 205 " --> pdb=" O GLU Z 202 " (cutoff:3.500A) Processing helix chain '7' and resid 4 through 9 removed outlier: 3.580A pdb=" N ASN 7 8 " --> pdb=" O LYS 7 4 " (cutoff:3.500A) Processing helix chain '7' and resid 11 through 17 removed outlier: 3.745A pdb=" N ILE 7 16 " --> pdb=" O TRP 7 12 " (cutoff:3.500A) Processing helix chain '7' and resid 27 through 46 removed outlier: 3.723A pdb=" N GLU 7 38 " --> pdb=" O LYS 7 34 " (cutoff:3.500A) Processing helix chain '7' and resid 68 through 77 Processing helix chain '7' and resid 92 through 125 removed outlier: 3.743A pdb=" N LYS 7 115 " --> pdb=" O SER 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 135 through 141 Processing helix chain '7' and resid 143 through 155 removed outlier: 4.009A pdb=" N VAL 7 149 " --> pdb=" O ILE 7 145 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU 7 150 " --> pdb=" O ASP 7 146 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU 7 151 " --> pdb=" O ALA 7 147 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N MET 7 152 " --> pdb=" O LYS 7 148 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL 7 153 " --> pdb=" O VAL 7 149 " (cutoff:3.500A) Processing helix chain '6' and resid 5 through 15 removed outlier: 3.679A pdb=" N GLU 6 10 " --> pdb=" O LEU 6 6 " (cutoff:3.500A) Processing helix chain '6' and resid 36 through 39 No H-bonds generated for 'chain '6' and resid 36 through 39' Processing helix chain '6' and resid 46 through 50 Processing helix chain '6' and resid 75 through 91 removed outlier: 3.793A pdb=" N TRP 6 79 " --> pdb=" O ILE 6 75 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU 6 80 " --> pdb=" O GLU 6 76 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 26 Processing helix chain 'U' and resid 28 through 31 No H-bonds generated for 'chain 'U' and resid 28 through 31' Processing helix chain 'U' and resid 49 through 54 Processing helix chain 'U' and resid 64 through 75 Processing sheet with id= A, first strand: chain 'A' and resid 89 through 91 removed outlier: 6.703A pdb=" N ARG A 42 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N VAL A 36 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL A 76 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ALA A 65 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE A 78 " --> pdb=" O GLY A 63 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLY A 63 " --> pdb=" O PHE A 78 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 98 through 101 Processing sheet with id= C, first strand: chain 'A' and resid 351 through 354 removed outlier: 6.756A pdb=" N LEU A 168 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LEU A 354 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE A 170 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 322 through 327 removed outlier: 3.851A pdb=" N VAL A 208 " --> pdb=" O ASP A 271 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 32 through 36 removed outlier: 7.071A pdb=" N ARG B 42 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL B 36 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL B 76 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ALA B 65 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N PHE B 78 " --> pdb=" O GLY B 63 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLY B 63 " --> pdb=" O PHE B 78 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 98 through 101 Processing sheet with id= G, first strand: chain 'B' and resid 169 through 171 Processing sheet with id= H, first strand: chain 'B' and resid 231 through 237 removed outlier: 6.795A pdb=" N CYS B 203 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N VAL B 234 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ALA B 236 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ALA B 207 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N SER B 322 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ILE B 268 " --> pdb=" O SER B 322 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N THR B 324 " --> pdb=" O ILE B 268 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 30 through 32 removed outlier: 3.647A pdb=" N LEU C 66 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLY C 74 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LEU C 68 " --> pdb=" O GLN C 72 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLN C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N PHE C 44 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N VAL C 33 " --> pdb=" O PHE C 44 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 98 through 101 Processing sheet with id= K, first strand: chain 'C' and resid 351 through 354 removed outlier: 6.691A pdb=" N LEU C 168 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU C 354 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE C 170 " --> pdb=" O LEU C 354 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY C 171 " --> pdb=" O ILE C 329 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 231 through 236 removed outlier: 8.920A pdb=" N ILE C 232 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N CYS C 203 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N VAL C 234 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR C 205 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ALA C 236 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ALA C 207 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N HIS C 265 " --> pdb=" O TYR C 202 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N VAL C 204 " --> pdb=" O HIS C 265 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU C 267 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N VAL C 206 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL C 269 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL C 208 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N SER C 322 " --> pdb=" O ALA C 266 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE C 268 " --> pdb=" O SER C 322 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N THR C 324 " --> pdb=" O ILE C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 10 through 12 removed outlier: 7.113A pdb=" N LYS D 75 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LYS D 40 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU D 46 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N HIS D 24 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL D 13 " --> pdb=" O HIS D 24 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 84 through 87 removed outlier: 3.950A pdb=" N LEU D 113 " --> pdb=" O VAL D 87 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 152 through 155 removed outlier: 8.326A pdb=" N ILE D 153 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N SER D 306 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEU D 155 " --> pdb=" O SER D 306 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLN D 308 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL D 183 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA D 216 " --> pdb=" O SER D 182 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 37 through 39 removed outlier: 6.448A pdb=" N ASP E 22 " --> pdb=" O THR E 14 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL E 16 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 84 through 87 removed outlier: 3.951A pdb=" N LEU E 113 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 182 through 184 Processing sheet with id= S, first strand: chain 'F' and resid 45 through 49 removed outlier: 4.392A pdb=" N LYS F 40 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LYS F 75 " --> pdb=" O LYS F 40 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASP F 22 " --> pdb=" O THR F 14 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL F 16 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE F 20 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 84 through 86 Processing sheet with id= U, first strand: chain 'F' and resid 331 through 334 removed outlier: 8.230A pdb=" N ILE F 153 " --> pdb=" O VAL F 304 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER F 306 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N LEU F 155 " --> pdb=" O SER F 306 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N GLN F 308 " --> pdb=" O LEU F 155 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N GLY F 157 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL F 310 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL F 251 " --> pdb=" O THR F 305 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N VAL F 307 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU F 253 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ALA F 309 " --> pdb=" O LEU F 253 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE F 255 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 9.154A pdb=" N TYR F 311 " --> pdb=" O ILE F 255 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE F 181 " --> pdb=" O LEU F 252 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N PHE F 254 " --> pdb=" O PHE F 181 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL F 183 " --> pdb=" O PHE F 254 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ASP F 256 " --> pdb=" O VAL F 183 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N THR F 185 " --> pdb=" O ASP F 256 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 73 through 76 Processing sheet with id= W, first strand: chain 'G' and resid 166 through 168 removed outlier: 3.657A pdb=" N TYR G 166 " --> pdb=" O SER G 178 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU G 176 " --> pdb=" O ASP G 168 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.206A pdb=" N LEU H 10 " --> pdb=" O VAL H 27 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER H 25 " --> pdb=" O LEU H 12 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'H' and resid 73 through 78 removed outlier: 3.513A pdb=" N PHE H 74 " --> pdb=" O THR H 86 " (cutoff:3.500A) 1915 hydrogen bonds defined for protein. 4815 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: 13.84 Time building geometry restraints manager: 17.25 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: 12641 1.34 - 1.46: 7063 1.46 - 1.58: 19501 1.58 - 1.70: 20 1.70 - 1.82: 184 Bond restraints: 39409 Sorted by residual: bond pdb=" CB PRO G 181 " pdb=" CG PRO G 181 " ideal model delta sigma weight residual 1.492 1.604 -0.112 5.00e-02 4.00e+02 5.01e+00 bond pdb=" C LEU C 139 " pdb=" N PRO C 140 " ideal model delta sigma weight residual 1.337 1.358 -0.021 9.80e-03 1.04e+04 4.66e+00 bond pdb=" C TYR D 345 " pdb=" N PRO D 346 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.38e-02 5.25e+03 3.24e+00 bond pdb=" C LEU A 139 " pdb=" N PRO A 140 " ideal model delta sigma weight residual 1.337 1.355 -0.019 1.06e-02 8.90e+03 3.21e+00 bond pdb=" CA PHE B 405 " pdb=" CB PHE B 405 " ideal model delta sigma weight residual 1.528 1.550 -0.022 1.47e-02 4.63e+03 2.30e+00 ... (remaining 39404 not shown) Histogram of bond angle deviations from ideal: 97.62 - 106.10: 895 106.10 - 114.57: 23770 114.57 - 123.04: 27061 123.04 - 131.52: 1638 131.52 - 139.99: 34 Bond angle restraints: 53398 Sorted by residual: angle pdb=" C LEU C 412 " pdb=" N ASP C 413 " pdb=" CA ASP C 413 " ideal model delta sigma weight residual 121.54 132.17 -10.63 1.91e+00 2.74e-01 3.10e+01 angle pdb=" C SER B 476 " pdb=" N ASN B 477 " pdb=" CA ASN B 477 " ideal model delta sigma weight residual 121.54 129.91 -8.37 1.91e+00 2.74e-01 1.92e+01 angle pdb=" C ASN G 204 " pdb=" N VAL G 205 " pdb=" CA VAL G 205 " ideal model delta sigma weight residual 120.24 122.97 -2.73 6.30e-01 2.52e+00 1.87e+01 angle pdb=" N HIS B 454 " pdb=" CA HIS B 454 " pdb=" C HIS B 454 " ideal model delta sigma weight residual 114.62 109.72 4.90 1.14e+00 7.69e-01 1.84e+01 angle pdb=" CA PRO G 181 " pdb=" N PRO G 181 " pdb=" CD PRO G 181 " ideal model delta sigma weight residual 112.00 106.14 5.86 1.40e+00 5.10e-01 1.75e+01 ... (remaining 53393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.75: 22672 25.75 - 51.51: 1053 51.51 - 77.26: 122 77.26 - 103.01: 18 103.01 - 128.77: 1 Dihedral angle restraints: 23866 sinusoidal: 9350 harmonic: 14516 Sorted by residual: dihedral pdb=" C5' ADP F 501 " pdb=" O5' ADP F 501 " pdb=" PA ADP F 501 " pdb=" O2A ADP F 501 " ideal model delta sinusoidal sigma weight residual -60.00 68.77 -128.77 1 2.00e+01 2.50e-03 3.90e+01 dihedral pdb=" CA GLY D 426 " pdb=" C GLY D 426 " pdb=" N ILE D 427 " pdb=" CA ILE D 427 " ideal model delta harmonic sigma weight residual -180.00 -152.98 -27.02 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA GLY D 179 " pdb=" C GLY D 179 " pdb=" N GLY D 180 " pdb=" CA GLY D 180 " ideal model delta harmonic sigma weight residual 180.00 -154.02 -25.98 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 23863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 5548 0.068 - 0.136: 738 0.136 - 0.204: 29 0.204 - 0.272: 4 0.272 - 0.340: 3 Chirality restraints: 6322 Sorted by residual: chirality pdb=" CB ILE D 296 " pdb=" CA ILE D 296 " pdb=" CG1 ILE D 296 " pdb=" CG2 ILE D 296 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CB ILE 7 21 " pdb=" CA ILE 7 21 " pdb=" CG1 ILE 7 21 " pdb=" CG2 ILE 7 21 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CB ILE E 296 " pdb=" CA ILE E 296 " pdb=" CG1 ILE E 296 " pdb=" CG2 ILE E 296 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 6319 not shown) Planarity restraints: 6814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS G 180 " -0.046 5.00e-02 4.00e+02 6.68e-02 7.13e+00 pdb=" N PRO G 181 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO G 181 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO G 181 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 405 " -0.013 2.00e-02 2.50e+03 2.53e-02 6.42e+00 pdb=" C PHE B 405 " 0.044 2.00e-02 2.50e+03 pdb=" O PHE B 405 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA B 406 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 476 " 0.010 2.00e-02 2.50e+03 2.14e-02 4.57e+00 pdb=" C SER B 476 " -0.037 2.00e-02 2.50e+03 pdb=" O SER B 476 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN B 477 " 0.012 2.00e-02 2.50e+03 ... (remaining 6811 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 449 2.55 - 3.14: 33901 3.14 - 3.72: 67820 3.72 - 4.31: 90155 4.31 - 4.90: 143023 Nonbonded interactions: 335348 Sorted by model distance: nonbonded pdb=" O1G ATP B 601 " pdb="MG MG B 602 " model vdw 1.962 2.170 nonbonded pdb=" O2B ATP E 501 " pdb="MG MG E 502 " model vdw 1.988 2.170 nonbonded pdb=" O2B ADP F 501 " pdb="MG MG F 502 " model vdw 1.995 2.170 nonbonded pdb=" O2B ATP B 601 " pdb="MG MG B 602 " model vdw 2.016 2.170 nonbonded pdb=" O2B ATP C 601 " pdb="MG MG C 602 " model vdw 2.025 2.170 ... (remaining 335343 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 6 through 509 or resid 601 through 602)) selection = (chain 'B' and (resid 6 through 509 or resid 601 through 602)) selection = (chain 'C' and (resid 6 through 509 or resid 601 through 602)) } ncs_group { reference = (chain 'D' and resid 7 through 478) selection = (chain 'E' and resid 7 through 478) selection = (chain 'F' and resid 7 through 478) } ncs_group { reference = (chain 'K' and resid 1 through 74) selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = (chain 'P' and resid 1 through 74) selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 0.800 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: 0.050 Extract box with map and model: 5.360 Check model and map are aligned: 0.560 Set scattering table: 0.400 Process input model: 99.540 Find NCS groups from input model: 2.550 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 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 : 0.003 0.112 39409 Z= 0.195 Angle : 0.724 11.674 53398 Z= 0.391 Chirality : 0.044 0.340 6322 Planarity : 0.004 0.067 6814 Dihedral : 14.243 128.768 14548 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.65 % Favored : 94.15 % Rotamer: Outliers : 0.05 % Allowed : 0.51 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.12), residues: 5042 helix: 0.71 (0.10), residues: 2662 sheet: -0.92 (0.24), residues: 487 loop : -1.60 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 191 HIS 0.005 0.001 HIS Y 115 PHE 0.030 0.001 PHE Y 108 TYR 0.036 0.001 TYR Z 72 ARG 0.019 0.001 ARG E 244 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 641 time to evaluate : 4.504 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 11 ARG cc_start: 0.8194 (mmp80) cc_final: 0.7867 (mmp-170) REVERT: Y 97 ARG cc_start: 0.8018 (tpm170) cc_final: 0.7530 (tpm170) REVERT: Y 101 PHE cc_start: 0.8591 (m-10) cc_final: 0.8193 (m-10) REVERT: Y 112 ASN cc_start: 0.8255 (m-40) cc_final: 0.8045 (m-40) REVERT: A 67 ASN cc_start: 0.8466 (t0) cc_final: 0.8095 (t0) REVERT: A 183 ASP cc_start: 0.9185 (m-30) cc_final: 0.8900 (m-30) REVERT: A 271 ASP cc_start: 0.7682 (t70) cc_final: 0.6429 (t0) REVERT: A 272 ASP cc_start: 0.8469 (m-30) cc_final: 0.7714 (m-30) REVERT: A 351 GLN cc_start: 0.9547 (pm20) cc_final: 0.9308 (pm20) REVERT: B 228 MET cc_start: 0.8688 (ppp) cc_final: 0.8234 (tpp) REVERT: B 275 LYS cc_start: 0.9592 (mtmt) cc_final: 0.9132 (mtmm) REVERT: B 378 SER cc_start: 0.8911 (t) cc_final: 0.8518 (p) REVERT: B 399 TYR cc_start: 0.8929 (m-80) cc_final: 0.8726 (m-80) REVERT: C 276 GLN cc_start: 0.8993 (tm-30) cc_final: 0.8760 (tm-30) REVERT: C 307 LEU cc_start: 0.9832 (tp) cc_final: 0.9434 (tp) REVERT: D 173 ASN cc_start: 0.9338 (m-40) cc_final: 0.9106 (m-40) REVERT: D 197 LEU cc_start: 0.9829 (tt) cc_final: 0.9544 (tt) REVERT: D 201 MET cc_start: 0.9584 (mmp) cc_final: 0.9171 (mmm) REVERT: D 222 MET cc_start: 0.8929 (mtp) cc_final: 0.8369 (mpp) REVERT: D 237 LEU cc_start: 0.9831 (tp) cc_final: 0.9609 (tp) REVERT: D 257 ASN cc_start: 0.9223 (t0) cc_final: 0.8841 (t0) REVERT: D 271 LEU cc_start: 0.9782 (mt) cc_final: 0.9526 (mt) REVERT: D 393 MET cc_start: 0.9130 (tpt) cc_final: 0.8748 (tpp) REVERT: D 459 MET cc_start: 0.9149 (mmp) cc_final: 0.8737 (mmm) REVERT: E 201 MET cc_start: 0.9245 (mtm) cc_final: 0.8937 (mtm) REVERT: E 257 ASN cc_start: 0.9033 (t0) cc_final: 0.8645 (t0) REVERT: E 458 TYR cc_start: 0.9276 (t80) cc_final: 0.9026 (t80) REVERT: E 459 MET cc_start: 0.9112 (mmp) cc_final: 0.8906 (mmm) REVERT: F 64 MET cc_start: 0.9107 (mmp) cc_final: 0.8675 (mmp) REVERT: F 97 ASN cc_start: 0.8576 (m110) cc_final: 0.8024 (m110) REVERT: F 201 MET cc_start: 0.9651 (mmp) cc_final: 0.9208 (mmp) REVERT: F 257 ASN cc_start: 0.9432 (m110) cc_final: 0.9004 (m110) REVERT: F 459 MET cc_start: 0.8963 (mmm) cc_final: 0.8660 (mmm) REVERT: G 49 GLN cc_start: 0.8074 (mm110) cc_final: 0.7807 (mm110) REVERT: G 102 GLN cc_start: 0.9321 (mp10) cc_final: 0.8990 (mp10) REVERT: G 154 MET cc_start: 0.9114 (mpp) cc_final: 0.8640 (mpp) REVERT: H 70 ILE cc_start: 0.6487 (tt) cc_final: 0.6261 (tt) REVERT: S 1 MET cc_start: 0.7313 (ppp) cc_final: 0.7054 (ppp) REVERT: S 50 MET cc_start: 0.7425 (pmm) cc_final: 0.7020 (pmm) REVERT: S 70 PHE cc_start: 0.9389 (m-80) cc_final: 0.9095 (t80) REVERT: T 9 TYR cc_start: 0.6159 (m-80) cc_final: 0.5883 (m-80) REVERT: T 67 MET cc_start: 0.6347 (tpt) cc_final: 0.5877 (tpp) REVERT: R 61 THR cc_start: 0.6892 (p) cc_final: 0.6595 (p) REVERT: X 88 MET cc_start: 0.8588 (mpp) cc_final: 0.6938 (mpp) REVERT: X 162 GLU cc_start: 0.9457 (mm-30) cc_final: 0.8883 (mt-10) REVERT: 6 16 LEU cc_start: 0.9360 (mm) cc_final: 0.8839 (pp) REVERT: 6 90 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6839 (mm-30) REVERT: U 28 VAL cc_start: 0.8200 (t) cc_final: 0.7628 (t) REVERT: U 48 LEU cc_start: 0.9047 (mt) cc_final: 0.8844 (pt) outliers start: 2 outliers final: 0 residues processed: 641 average time/residue: 0.5082 time to fit residues: 527.2072 Evaluate side-chains 430 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 430 time to evaluate : 3.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 420 optimal weight: 9.9990 chunk 377 optimal weight: 7.9990 chunk 209 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 254 optimal weight: 9.9990 chunk 201 optimal weight: 9.9990 chunk 390 optimal weight: 30.0000 chunk 151 optimal weight: 9.9990 chunk 237 optimal weight: 10.0000 chunk 290 optimal weight: 8.9990 chunk 452 optimal weight: 0.0970 overall best weight: 5.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 HIS ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 ASN B 217 GLN C 245 GLN ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN D 221 GLN E 365 GLN ** F 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 385 GLN H 78 GLN H 98 GLN H 111 ASN ** S 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 35 ASN ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 39409 Z= 0.297 Angle : 0.666 9.724 53398 Z= 0.347 Chirality : 0.043 0.336 6322 Planarity : 0.005 0.059 6814 Dihedral : 6.828 124.225 5556 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 19.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.89 % Favored : 93.93 % Rotamer: Outliers : 0.12 % Allowed : 6.44 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.12), residues: 5042 helix: 0.66 (0.10), residues: 2620 sheet: -0.89 (0.24), residues: 493 loop : -1.34 (0.15), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 6 79 HIS 0.010 0.001 HIS U 29 PHE 0.029 0.002 PHE R 64 TYR 0.032 0.002 TYR Z 72 ARG 0.010 0.001 ARG X 176 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 553 time to evaluate : 5.007 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: 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: 8 10 MET cc_start: 0.3422 (mtp) cc_final: 0.2867 (mtp) REVERT: 8 20 MET cc_start: 0.3688 (tmm) cc_final: 0.3230 (ppp) REVERT: 8 27 PHE cc_start: 0.7753 (m-80) cc_final: 0.6989 (m-80) REVERT: Y 11 ARG cc_start: 0.8290 (mmp80) cc_final: 0.7944 (mmp-170) REVERT: Y 97 ARG cc_start: 0.8420 (tpm170) cc_final: 0.7708 (tpm170) REVERT: Y 101 PHE cc_start: 0.8793 (m-10) cc_final: 0.8428 (m-10) REVERT: Y 108 PHE cc_start: 0.9204 (t80) cc_final: 0.8796 (t80) REVERT: Y 112 ASN cc_start: 0.8109 (m-40) cc_final: 0.7653 (m-40) REVERT: A 64 MET cc_start: 0.8720 (tmm) cc_final: 0.8510 (tmm) REVERT: A 67 ASN cc_start: 0.8283 (t0) cc_final: 0.8019 (t0) REVERT: A 183 ASP cc_start: 0.9219 (m-30) cc_final: 0.8962 (m-30) REVERT: A 203 CYS cc_start: 0.9242 (m) cc_final: 0.8864 (m) REVERT: A 272 ASP cc_start: 0.8615 (m-30) cc_final: 0.8212 (m-30) REVERT: A 351 GLN cc_start: 0.9574 (pm20) cc_final: 0.9348 (pm20) REVERT: B 56 GLU cc_start: 0.8760 (mp0) cc_final: 0.8553 (mp0) REVERT: B 64 MET cc_start: 0.9467 (ttt) cc_final: 0.9166 (ttm) REVERT: B 228 MET cc_start: 0.8832 (ppp) cc_final: 0.8198 (tpp) REVERT: B 272 ASP cc_start: 0.8938 (t70) cc_final: 0.8468 (t0) REVERT: B 275 LYS cc_start: 0.9727 (mtmt) cc_final: 0.9270 (mtmm) REVERT: B 371 LEU cc_start: 0.9739 (mt) cc_final: 0.9289 (tt) REVERT: B 378 SER cc_start: 0.9035 (t) cc_final: 0.8829 (p) REVERT: C 69 GLU cc_start: 0.8461 (mp0) cc_final: 0.7983 (mp0) REVERT: C 307 LEU cc_start: 0.9727 (tp) cc_final: 0.9321 (tp) REVERT: D 173 ASN cc_start: 0.9333 (m110) cc_final: 0.9092 (m110) REVERT: D 197 LEU cc_start: 0.9832 (tt) cc_final: 0.9556 (tt) REVERT: D 201 MET cc_start: 0.9675 (mmp) cc_final: 0.9245 (mmm) REVERT: D 237 LEU cc_start: 0.9799 (tp) cc_final: 0.9520 (tp) REVERT: D 257 ASN cc_start: 0.9289 (t0) cc_final: 0.8947 (t0) REVERT: D 271 LEU cc_start: 0.9570 (mt) cc_final: 0.9284 (mt) REVERT: D 459 MET cc_start: 0.9113 (mmp) cc_final: 0.8867 (mmm) REVERT: E 257 ASN cc_start: 0.9105 (t0) cc_final: 0.8687 (t0) REVERT: E 382 LYS cc_start: 0.9806 (ttmm) cc_final: 0.9510 (tppp) REVERT: F 64 MET cc_start: 0.9104 (mmp) cc_final: 0.8618 (mmp) REVERT: F 97 ASN cc_start: 0.8581 (m110) cc_final: 0.8056 (m110) REVERT: F 134 LEU cc_start: 0.9336 (mt) cc_final: 0.9050 (mt) REVERT: F 201 MET cc_start: 0.9743 (mmp) cc_final: 0.9388 (mmm) REVERT: F 257 ASN cc_start: 0.9528 (m110) cc_final: 0.9187 (m110) REVERT: G 102 GLN cc_start: 0.9284 (mp10) cc_final: 0.8947 (mp10) REVERT: G 154 MET cc_start: 0.9195 (mpp) cc_final: 0.8692 (mpp) REVERT: S 50 MET cc_start: 0.7063 (pmm) cc_final: 0.6821 (pmm) REVERT: T 48 PHE cc_start: 0.6540 (m-10) cc_final: 0.6037 (m-10) REVERT: T 67 MET cc_start: 0.6483 (tpt) cc_final: 0.6153 (tpt) REVERT: T 70 PHE cc_start: 0.6707 (m-80) cc_final: 0.6159 (m-80) REVERT: K 1 MET cc_start: 0.6305 (pmm) cc_final: 0.5257 (tmm) REVERT: X 88 MET cc_start: 0.8866 (mpp) cc_final: 0.8591 (mpp) REVERT: X 135 TYR cc_start: 0.8322 (t80) cc_final: 0.8100 (t80) REVERT: X 162 GLU cc_start: 0.9445 (mm-30) cc_final: 0.9128 (mt-10) REVERT: X 220 MET cc_start: 0.8507 (ppp) cc_final: 0.8230 (ppp) REVERT: Z 171 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8238 (pp30) REVERT: 7 18 SER cc_start: 0.8740 (m) cc_final: 0.8507 (p) REVERT: 6 9 ARG cc_start: 0.8030 (ttt180) cc_final: 0.7554 (ptt180) REVERT: U 28 VAL cc_start: 0.8452 (t) cc_final: 0.7936 (t) outliers start: 5 outliers final: 0 residues processed: 558 average time/residue: 0.4619 time to fit residues: 421.1877 Evaluate side-chains 391 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 390 time to evaluate : 5.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 251 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 376 optimal weight: 5.9990 chunk 307 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 453 optimal weight: 6.9990 chunk 489 optimal weight: 0.5980 chunk 403 optimal weight: 0.9980 chunk 449 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 363 optimal weight: 5.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 39409 Z= 0.217 Angle : 0.625 9.994 53398 Z= 0.319 Chirality : 0.043 0.347 6322 Planarity : 0.005 0.053 6814 Dihedral : 6.725 120.817 5556 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.55 % Favored : 94.27 % Rotamer: Outliers : 0.02 % Allowed : 4.37 % Favored : 95.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.12), residues: 5042 helix: 0.55 (0.10), residues: 2633 sheet: -0.85 (0.24), residues: 491 loop : -1.28 (0.15), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP X 126 HIS 0.009 0.001 HIS Z 148 PHE 0.024 0.001 PHE N 30 TYR 0.028 0.001 TYR Z 72 ARG 0.009 0.000 ARG P 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 552 time to evaluate : 4.793 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: 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: 8 10 MET cc_start: 0.3380 (mtp) cc_final: 0.2743 (mtp) REVERT: 8 27 PHE cc_start: 0.7753 (m-80) cc_final: 0.7286 (m-80) REVERT: Y 11 ARG cc_start: 0.8295 (mmp80) cc_final: 0.7912 (mmp-170) REVERT: Y 97 ARG cc_start: 0.8392 (tpm170) cc_final: 0.7570 (tpm170) REVERT: Y 108 PHE cc_start: 0.9216 (t80) cc_final: 0.8808 (t80) REVERT: Y 112 ASN cc_start: 0.8254 (m-40) cc_final: 0.7753 (m-40) REVERT: A 67 ASN cc_start: 0.8247 (t0) cc_final: 0.7992 (t0) REVERT: A 183 ASP cc_start: 0.9207 (m-30) cc_final: 0.8927 (m-30) REVERT: A 203 CYS cc_start: 0.9102 (m) cc_final: 0.8733 (m) REVERT: A 272 ASP cc_start: 0.8612 (m-30) cc_final: 0.8198 (m-30) REVERT: A 351 GLN cc_start: 0.9560 (pm20) cc_final: 0.9338 (pm20) REVERT: A 357 GLU cc_start: 0.9503 (tp30) cc_final: 0.9222 (tp30) REVERT: B 56 GLU cc_start: 0.8828 (mp0) cc_final: 0.8552 (mp0) REVERT: B 64 MET cc_start: 0.9443 (ttt) cc_final: 0.9239 (ttm) REVERT: B 228 MET cc_start: 0.8814 (ppp) cc_final: 0.8129 (tpp) REVERT: B 272 ASP cc_start: 0.8941 (t70) cc_final: 0.8667 (t0) REVERT: B 275 LYS cc_start: 0.9710 (mtmt) cc_final: 0.9313 (mtmm) REVERT: B 299 ASP cc_start: 0.8302 (p0) cc_final: 0.7972 (p0) REVERT: B 371 LEU cc_start: 0.9734 (mt) cc_final: 0.9192 (tt) REVERT: B 378 SER cc_start: 0.9013 (t) cc_final: 0.8708 (p) REVERT: C 69 GLU cc_start: 0.8553 (mp0) cc_final: 0.8025 (mp0) REVERT: C 307 LEU cc_start: 0.9716 (tp) cc_final: 0.9235 (tp) REVERT: D 197 LEU cc_start: 0.9840 (tt) cc_final: 0.9574 (tt) REVERT: D 201 MET cc_start: 0.9664 (mmp) cc_final: 0.9203 (mmm) REVERT: D 237 LEU cc_start: 0.9752 (tp) cc_final: 0.9442 (tp) REVERT: D 257 ASN cc_start: 0.9320 (t0) cc_final: 0.8929 (t0) REVERT: D 263 GLN cc_start: 0.9180 (tm-30) cc_final: 0.8899 (tm-30) REVERT: D 271 LEU cc_start: 0.9591 (mt) cc_final: 0.9235 (mt) REVERT: D 459 MET cc_start: 0.9154 (mmp) cc_final: 0.8905 (mmm) REVERT: E 257 ASN cc_start: 0.9117 (t0) cc_final: 0.8647 (t0) REVERT: F 64 MET cc_start: 0.9055 (mmp) cc_final: 0.8570 (mmp) REVERT: F 97 ASN cc_start: 0.8687 (m110) cc_final: 0.8179 (m110) REVERT: F 134 LEU cc_start: 0.9350 (mt) cc_final: 0.9055 (mt) REVERT: F 201 MET cc_start: 0.9735 (mmp) cc_final: 0.9356 (mmm) REVERT: F 257 ASN cc_start: 0.9491 (m110) cc_final: 0.9157 (m110) REVERT: G 102 GLN cc_start: 0.9288 (mp10) cc_final: 0.8949 (mp10) REVERT: G 154 MET cc_start: 0.9166 (mpp) cc_final: 0.8662 (mpp) REVERT: S 50 MET cc_start: 0.7276 (pmm) cc_final: 0.7028 (pmm) REVERT: T 48 PHE cc_start: 0.6314 (m-10) cc_final: 0.5735 (m-10) REVERT: T 67 MET cc_start: 0.6537 (tpt) cc_final: 0.6180 (tpt) REVERT: T 70 PHE cc_start: 0.6707 (m-80) cc_final: 0.6167 (m-10) REVERT: K 1 MET cc_start: 0.6337 (pmm) cc_final: 0.6087 (pmm) REVERT: M 50 MET cc_start: 0.3200 (OUTLIER) cc_final: 0.2590 (mmm) REVERT: X 88 MET cc_start: 0.8870 (mpp) cc_final: 0.8628 (mpp) REVERT: X 162 GLU cc_start: 0.9432 (mm-30) cc_final: 0.8711 (mt-10) REVERT: X 176 ARG cc_start: 0.8494 (pmt-80) cc_final: 0.8217 (pmt-80) REVERT: Z 90 ASP cc_start: 0.9245 (m-30) cc_final: 0.8914 (m-30) REVERT: Z 155 ASP cc_start: 0.9187 (m-30) cc_final: 0.8859 (m-30) REVERT: 7 18 SER cc_start: 0.8739 (m) cc_final: 0.8498 (p) REVERT: U 28 VAL cc_start: 0.8487 (t) cc_final: 0.7971 (t) outliers start: 1 outliers final: 0 residues processed: 552 average time/residue: 0.5078 time to fit residues: 461.0778 Evaluate side-chains 398 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 397 time to evaluate : 4.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 447 optimal weight: 20.0000 chunk 340 optimal weight: 30.0000 chunk 235 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 216 optimal weight: 5.9990 chunk 304 optimal weight: 3.9990 chunk 454 optimal weight: 20.0000 chunk 481 optimal weight: 5.9990 chunk 237 optimal weight: 7.9990 chunk 430 optimal weight: 50.0000 chunk 129 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 ASN D 399 GLN E 52 GLN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 39409 Z= 0.291 Angle : 0.657 9.264 53398 Z= 0.337 Chirality : 0.043 0.334 6322 Planarity : 0.005 0.080 6814 Dihedral : 6.621 115.994 5556 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.29 % Favored : 93.55 % Rotamer: Outliers : 0.07 % Allowed : 5.49 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.12), residues: 5042 helix: 0.49 (0.10), residues: 2637 sheet: -0.75 (0.24), residues: 505 loop : -1.22 (0.15), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP X 126 HIS 0.008 0.001 HIS Z 148 PHE 0.025 0.002 PHE R 64 TYR 0.031 0.002 TYR X 166 ARG 0.009 0.001 ARG B 166 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 520 time to evaluate : 4.422 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 27 PHE cc_start: 0.7898 (m-80) cc_final: 0.7156 (m-10) REVERT: Y 11 ARG cc_start: 0.8399 (mmp80) cc_final: 0.8020 (mmp-170) REVERT: Y 68 ASN cc_start: 0.9563 (m110) cc_final: 0.9280 (m110) REVERT: Y 97 ARG cc_start: 0.8509 (tpm170) cc_final: 0.7499 (tpm170) REVERT: Y 108 PHE cc_start: 0.9222 (t80) cc_final: 0.8832 (t80) REVERT: Y 112 ASN cc_start: 0.7960 (m-40) cc_final: 0.7582 (m-40) REVERT: A 67 ASN cc_start: 0.8430 (t0) cc_final: 0.8005 (t0) REVERT: A 183 ASP cc_start: 0.9258 (m-30) cc_final: 0.9007 (m-30) REVERT: A 203 CYS cc_start: 0.9084 (m) cc_final: 0.8718 (m) REVERT: A 272 ASP cc_start: 0.8687 (m-30) cc_final: 0.8256 (m-30) REVERT: A 351 GLN cc_start: 0.9558 (pm20) cc_final: 0.9326 (pm20) REVERT: A 357 GLU cc_start: 0.9457 (tp30) cc_final: 0.9156 (tp30) REVERT: B 56 GLU cc_start: 0.8828 (mp0) cc_final: 0.8523 (mp0) REVERT: B 64 MET cc_start: 0.9491 (ttt) cc_final: 0.9145 (tpp) REVERT: B 228 MET cc_start: 0.8834 (ppp) cc_final: 0.8042 (tpp) REVERT: B 272 ASP cc_start: 0.8924 (t70) cc_final: 0.8565 (t0) REVERT: B 275 LYS cc_start: 0.9701 (mtmt) cc_final: 0.9463 (mtmt) REVERT: B 299 ASP cc_start: 0.8550 (p0) cc_final: 0.8088 (p0) REVERT: B 371 LEU cc_start: 0.9746 (mt) cc_final: 0.9216 (tt) REVERT: B 378 SER cc_start: 0.9069 (t) cc_final: 0.8861 (p) REVERT: B 399 TYR cc_start: 0.9265 (m-10) cc_final: 0.9062 (m-80) REVERT: B 467 GLU cc_start: 0.9342 (pt0) cc_final: 0.9059 (pp20) REVERT: C 69 GLU cc_start: 0.8645 (mp0) cc_final: 0.8118 (mp0) REVERT: C 270 TYR cc_start: 0.8868 (m-10) cc_final: 0.8577 (m-10) REVERT: C 307 LEU cc_start: 0.9723 (tp) cc_final: 0.9212 (tp) REVERT: D 197 LEU cc_start: 0.9834 (tt) cc_final: 0.9580 (tt) REVERT: D 201 MET cc_start: 0.9672 (mmp) cc_final: 0.9240 (mmm) REVERT: D 237 LEU cc_start: 0.9769 (tp) cc_final: 0.9473 (tp) REVERT: D 257 ASN cc_start: 0.9346 (t0) cc_final: 0.8907 (t0) REVERT: D 271 LEU cc_start: 0.9596 (mt) cc_final: 0.9207 (mt) REVERT: D 311 TYR cc_start: 0.9263 (t80) cc_final: 0.9027 (t80) REVERT: D 459 MET cc_start: 0.9179 (mmp) cc_final: 0.8932 (mmm) REVERT: E 201 MET cc_start: 0.9478 (mtp) cc_final: 0.9216 (mtp) REVERT: E 257 ASN cc_start: 0.9226 (t0) cc_final: 0.8733 (t0) REVERT: E 288 ASP cc_start: 0.9386 (m-30) cc_final: 0.9141 (m-30) REVERT: F 64 MET cc_start: 0.9116 (mmp) cc_final: 0.8636 (mmp) REVERT: F 97 ASN cc_start: 0.8667 (m110) cc_final: 0.8153 (m110) REVERT: F 201 MET cc_start: 0.9752 (mmp) cc_final: 0.9513 (mmp) REVERT: F 257 ASN cc_start: 0.9495 (m110) cc_final: 0.9178 (m110) REVERT: F 281 TYR cc_start: 0.9097 (m-80) cc_final: 0.8843 (m-80) REVERT: G 154 MET cc_start: 0.9223 (mpp) cc_final: 0.8661 (mpp) REVERT: T 48 PHE cc_start: 0.6480 (m-10) cc_final: 0.5939 (m-10) REVERT: T 67 MET cc_start: 0.6705 (tpt) cc_final: 0.6423 (tpt) REVERT: T 70 PHE cc_start: 0.6640 (m-80) cc_final: 0.6183 (m-10) REVERT: K 1 MET cc_start: 0.6269 (pmm) cc_final: 0.4964 (tmm) REVERT: X 70 MET cc_start: 0.9172 (tpp) cc_final: 0.8955 (tpp) REVERT: X 85 TYR cc_start: 0.8232 (m-10) cc_final: 0.8005 (m-10) REVERT: X 88 MET cc_start: 0.8892 (mpp) cc_final: 0.8604 (mmt) REVERT: X 162 GLU cc_start: 0.9422 (mm-30) cc_final: 0.9022 (mt-10) REVERT: 7 166 ARG cc_start: 0.6229 (ptt-90) cc_final: 0.5823 (ptt180) REVERT: 6 90 GLU cc_start: 0.6864 (mm-30) cc_final: 0.6659 (mm-30) outliers start: 3 outliers final: 0 residues processed: 523 average time/residue: 0.5137 time to fit residues: 441.4515 Evaluate side-chains 389 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 389 time to evaluate : 3.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 400 optimal weight: 4.9990 chunk 273 optimal weight: 0.0070 chunk 6 optimal weight: 8.9990 chunk 358 optimal weight: 50.0000 chunk 198 optimal weight: 4.9990 chunk 410 optimal weight: 5.9990 chunk 332 optimal weight: 0.0170 chunk 0 optimal weight: 20.0000 chunk 245 optimal weight: 1.9990 chunk 432 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 overall best weight: 2.4042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 ASN ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN E 478 ASN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 14 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 39409 Z= 0.193 Angle : 0.616 9.637 53398 Z= 0.314 Chirality : 0.043 0.341 6322 Planarity : 0.004 0.070 6814 Dihedral : 6.448 113.236 5556 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.87 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.12), residues: 5042 helix: 0.56 (0.10), residues: 2628 sheet: -0.66 (0.23), residues: 514 loop : -1.19 (0.15), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 126 HIS 0.009 0.001 HIS Z 148 PHE 0.023 0.001 PHE R 64 TYR 0.021 0.001 TYR Z 72 ARG 0.007 0.000 ARG O 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 541 time to evaluate : 4.586 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: 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: 8 20 MET cc_start: 0.4518 (ppp) cc_final: 0.4204 (tmm) REVERT: 8 27 PHE cc_start: 0.7831 (m-80) cc_final: 0.7128 (m-10) REVERT: Y 11 ARG cc_start: 0.8386 (mmp80) cc_final: 0.7986 (mmp-170) REVERT: Y 68 ASN cc_start: 0.9543 (m110) cc_final: 0.9247 (m110) REVERT: Y 103 LYS cc_start: 0.9420 (tmtt) cc_final: 0.9147 (tptm) REVERT: Y 107 ASP cc_start: 0.9476 (m-30) cc_final: 0.9229 (m-30) REVERT: Y 108 PHE cc_start: 0.9198 (t80) cc_final: 0.8770 (t80) REVERT: Y 112 ASN cc_start: 0.8007 (m-40) cc_final: 0.7561 (m110) REVERT: A 67 ASN cc_start: 0.8349 (t0) cc_final: 0.8114 (t0) REVERT: A 183 ASP cc_start: 0.9234 (m-30) cc_final: 0.8953 (m-30) REVERT: A 203 CYS cc_start: 0.9084 (m) cc_final: 0.8690 (m) REVERT: A 272 ASP cc_start: 0.8628 (m-30) cc_final: 0.8210 (m-30) REVERT: A 351 GLN cc_start: 0.9562 (pm20) cc_final: 0.9328 (pm20) REVERT: A 357 GLU cc_start: 0.9451 (tp30) cc_final: 0.9164 (tp30) REVERT: B 56 GLU cc_start: 0.8826 (mp0) cc_final: 0.8473 (mp0) REVERT: B 226 ASP cc_start: 0.8938 (t0) cc_final: 0.8272 (t0) REVERT: B 228 MET cc_start: 0.8784 (ppp) cc_final: 0.8033 (tpp) REVERT: B 272 ASP cc_start: 0.8892 (t70) cc_final: 0.8499 (t0) REVERT: B 275 LYS cc_start: 0.9686 (mtmt) cc_final: 0.9439 (mtmt) REVERT: B 299 ASP cc_start: 0.8510 (p0) cc_final: 0.8037 (p0) REVERT: B 378 SER cc_start: 0.9001 (t) cc_final: 0.8735 (p) REVERT: B 470 PHE cc_start: 0.9403 (t80) cc_final: 0.9188 (t80) REVERT: C 69 GLU cc_start: 0.8665 (mp0) cc_final: 0.8137 (mp0) REVERT: C 270 TYR cc_start: 0.8884 (m-10) cc_final: 0.8508 (m-10) REVERT: C 307 LEU cc_start: 0.9704 (tp) cc_final: 0.9277 (tp) REVERT: D 197 LEU cc_start: 0.9836 (tt) cc_final: 0.9591 (tt) REVERT: D 201 MET cc_start: 0.9657 (mmp) cc_final: 0.9209 (mmm) REVERT: D 237 LEU cc_start: 0.9767 (tp) cc_final: 0.9461 (tp) REVERT: D 257 ASN cc_start: 0.9340 (t0) cc_final: 0.8878 (t0) REVERT: D 263 GLN cc_start: 0.9162 (tm-30) cc_final: 0.8891 (tm-30) REVERT: D 271 LEU cc_start: 0.9574 (mt) cc_final: 0.9220 (mt) REVERT: D 311 TYR cc_start: 0.9274 (t80) cc_final: 0.9037 (t80) REVERT: D 393 MET cc_start: 0.9069 (tpt) cc_final: 0.8618 (tpp) REVERT: D 459 MET cc_start: 0.9162 (mmp) cc_final: 0.8933 (mmm) REVERT: E 257 ASN cc_start: 0.9207 (t0) cc_final: 0.8713 (t0) REVERT: E 288 ASP cc_start: 0.9394 (m-30) cc_final: 0.9125 (m-30) REVERT: F 64 MET cc_start: 0.8998 (mmp) cc_final: 0.8578 (mmp) REVERT: F 97 ASN cc_start: 0.8684 (m110) cc_final: 0.8170 (m110) REVERT: F 134 LEU cc_start: 0.9383 (mt) cc_final: 0.9085 (mt) REVERT: F 201 MET cc_start: 0.9725 (mmp) cc_final: 0.9495 (mmp) REVERT: F 257 ASN cc_start: 0.9439 (m110) cc_final: 0.9139 (m110) REVERT: F 281 TYR cc_start: 0.9134 (m-80) cc_final: 0.8797 (m-80) REVERT: F 308 GLN cc_start: 0.8926 (pm20) cc_final: 0.8714 (pm20) REVERT: F 459 MET cc_start: 0.9127 (mmm) cc_final: 0.8538 (mmm) REVERT: G 102 GLN cc_start: 0.9495 (mp10) cc_final: 0.9135 (mp10) REVERT: G 116 MET cc_start: 0.9403 (mpp) cc_final: 0.9189 (mpp) REVERT: G 154 MET cc_start: 0.9215 (mpp) cc_final: 0.8649 (mpp) REVERT: T 48 PHE cc_start: 0.6532 (m-10) cc_final: 0.6072 (m-10) REVERT: T 67 MET cc_start: 0.6708 (tpt) cc_final: 0.6192 (tpp) REVERT: T 70 PHE cc_start: 0.6673 (m-80) cc_final: 0.6158 (m-10) REVERT: K 1 MET cc_start: 0.6224 (pmm) cc_final: 0.4937 (tmm) REVERT: M 59 GLU cc_start: 0.6089 (mp0) cc_final: 0.5453 (mp0) REVERT: Q 50 MET cc_start: 0.3338 (mmm) cc_final: 0.2685 (mmm) REVERT: X 162 GLU cc_start: 0.9460 (mm-30) cc_final: 0.9198 (tp30) REVERT: Z 155 ASP cc_start: 0.9268 (m-30) cc_final: 0.8953 (m-30) REVERT: 7 40 ARG cc_start: 0.9198 (mtp-110) cc_final: 0.8919 (tmt170) REVERT: 7 166 ARG cc_start: 0.6172 (ptt-90) cc_final: 0.5732 (ptt180) REVERT: U 28 VAL cc_start: 0.8545 (t) cc_final: 0.8220 (t) outliers start: 0 outliers final: 0 residues processed: 541 average time/residue: 0.4904 time to fit residues: 436.3731 Evaluate side-chains 403 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 403 time to evaluate : 4.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 161 optimal weight: 4.9990 chunk 433 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 282 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 481 optimal weight: 0.4980 chunk 399 optimal weight: 20.0000 chunk 223 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 159 optimal weight: 0.0980 chunk 252 optimal weight: 5.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 HIS E 379 GLN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 14 ASN U 29 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 39409 Z= 0.206 Angle : 0.622 8.953 53398 Z= 0.316 Chirality : 0.043 0.352 6322 Planarity : 0.004 0.067 6814 Dihedral : 6.329 109.385 5556 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.23 % Favored : 93.61 % Rotamer: Outliers : 0.05 % Allowed : 2.31 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.12), residues: 5042 helix: 0.58 (0.10), residues: 2614 sheet: -0.63 (0.23), residues: 515 loop : -1.17 (0.15), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 126 HIS 0.009 0.001 HIS Z 148 PHE 0.032 0.001 PHE G 165 TYR 0.022 0.001 TYR G 212 ARG 0.005 0.000 ARG R 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 528 time to evaluate : 4.152 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 20 MET cc_start: 0.4859 (ppp) cc_final: 0.4382 (tmm) REVERT: 8 27 PHE cc_start: 0.7882 (m-80) cc_final: 0.7283 (m-80) REVERT: Y 11 ARG cc_start: 0.8399 (mmp80) cc_final: 0.8021 (mmp-170) REVERT: Y 68 ASN cc_start: 0.9548 (m110) cc_final: 0.9283 (m110) REVERT: Y 82 ASP cc_start: 0.8551 (m-30) cc_final: 0.8334 (m-30) REVERT: Y 97 ARG cc_start: 0.8562 (tpm170) cc_final: 0.8270 (tpm170) REVERT: Y 103 LYS cc_start: 0.9456 (tmtt) cc_final: 0.9161 (tptm) REVERT: Y 108 PHE cc_start: 0.9209 (t80) cc_final: 0.8829 (t80) REVERT: Y 112 ASN cc_start: 0.8079 (m-40) cc_final: 0.7685 (m-40) REVERT: A 67 ASN cc_start: 0.8372 (t0) cc_final: 0.8146 (t0) REVERT: A 183 ASP cc_start: 0.9218 (m-30) cc_final: 0.8951 (m-30) REVERT: A 203 CYS cc_start: 0.9072 (m) cc_final: 0.8694 (m) REVERT: A 272 ASP cc_start: 0.8603 (m-30) cc_final: 0.8192 (m-30) REVERT: A 351 GLN cc_start: 0.9563 (pm20) cc_final: 0.9340 (pm20) REVERT: A 357 GLU cc_start: 0.9439 (tp30) cc_final: 0.9152 (tp30) REVERT: B 56 GLU cc_start: 0.8833 (mp0) cc_final: 0.8456 (mp0) REVERT: B 64 MET cc_start: 0.9612 (ttm) cc_final: 0.9117 (tpp) REVERT: B 226 ASP cc_start: 0.8947 (t0) cc_final: 0.8301 (t0) REVERT: B 272 ASP cc_start: 0.8865 (t70) cc_final: 0.8503 (t0) REVERT: B 275 LYS cc_start: 0.9670 (mtmt) cc_final: 0.9376 (mtmt) REVERT: B 299 ASP cc_start: 0.8557 (p0) cc_final: 0.8178 (p0) REVERT: B 345 ILE cc_start: 0.9771 (tp) cc_final: 0.9559 (pt) REVERT: B 361 LYS cc_start: 0.9609 (mmmt) cc_final: 0.9195 (mmmt) REVERT: B 378 SER cc_start: 0.8960 (t) cc_final: 0.8686 (p) REVERT: B 399 TYR cc_start: 0.9009 (m-80) cc_final: 0.8794 (m-80) REVERT: B 470 PHE cc_start: 0.9473 (t80) cc_final: 0.9153 (t80) REVERT: B 471 LEU cc_start: 0.9656 (tt) cc_final: 0.9368 (pp) REVERT: C 69 GLU cc_start: 0.8703 (mp0) cc_final: 0.8173 (mp0) REVERT: C 270 TYR cc_start: 0.8822 (m-10) cc_final: 0.8425 (m-10) REVERT: C 307 LEU cc_start: 0.9695 (tp) cc_final: 0.9239 (tp) REVERT: D 197 LEU cc_start: 0.9835 (tt) cc_final: 0.9598 (tt) REVERT: D 201 MET cc_start: 0.9676 (mmp) cc_final: 0.9209 (mmm) REVERT: D 237 LEU cc_start: 0.9764 (tp) cc_final: 0.9473 (tp) REVERT: D 257 ASN cc_start: 0.9356 (t0) cc_final: 0.8853 (t0) REVERT: D 263 GLN cc_start: 0.9216 (tm-30) cc_final: 0.8935 (tm-30) REVERT: D 271 LEU cc_start: 0.9557 (mt) cc_final: 0.9196 (mt) REVERT: D 311 TYR cc_start: 0.9283 (t80) cc_final: 0.9008 (t80) REVERT: D 459 MET cc_start: 0.9146 (mmp) cc_final: 0.8908 (mmm) REVERT: E 257 ASN cc_start: 0.9205 (t0) cc_final: 0.8700 (t0) REVERT: E 288 ASP cc_start: 0.9362 (m-30) cc_final: 0.9112 (m-30) REVERT: E 289 MET cc_start: 0.9520 (ttp) cc_final: 0.9267 (ttp) REVERT: F 64 MET cc_start: 0.9004 (mmp) cc_final: 0.8587 (mmp) REVERT: F 97 ASN cc_start: 0.8723 (m110) cc_final: 0.8239 (m110) REVERT: F 201 MET cc_start: 0.9721 (mmp) cc_final: 0.9472 (mmp) REVERT: F 257 ASN cc_start: 0.9445 (m110) cc_final: 0.9159 (m110) REVERT: F 281 TYR cc_start: 0.9143 (m-80) cc_final: 0.8761 (m-80) REVERT: G 116 MET cc_start: 0.9356 (mpp) cc_final: 0.9048 (mpp) REVERT: G 154 MET cc_start: 0.9242 (mpp) cc_final: 0.8672 (mpp) REVERT: T 48 PHE cc_start: 0.6539 (m-10) cc_final: 0.6248 (m-80) REVERT: T 67 MET cc_start: 0.6694 (tpt) cc_final: 0.6186 (tpp) REVERT: T 70 PHE cc_start: 0.6542 (m-80) cc_final: 0.6040 (m-10) REVERT: K 1 MET cc_start: 0.6096 (pmm) cc_final: 0.4988 (tmm) REVERT: Q 50 MET cc_start: 0.3416 (mmm) cc_final: 0.2919 (mmm) REVERT: X 162 GLU cc_start: 0.9462 (mm-30) cc_final: 0.9208 (tp30) REVERT: X 167 PHE cc_start: 0.9170 (m-80) cc_final: 0.8843 (m-10) REVERT: X 220 MET cc_start: 0.8616 (ppp) cc_final: 0.8387 (ppp) REVERT: Z 155 ASP cc_start: 0.9282 (m-30) cc_final: 0.8965 (m-30) REVERT: 7 40 ARG cc_start: 0.9252 (mtp-110) cc_final: 0.8906 (tmt170) REVERT: 7 166 ARG cc_start: 0.6232 (ptt-90) cc_final: 0.5894 (ptt180) REVERT: 6 90 GLU cc_start: 0.6823 (mm-30) cc_final: 0.6591 (mm-30) REVERT: U 28 VAL cc_start: 0.8669 (t) cc_final: 0.8126 (t) outliers start: 2 outliers final: 1 residues processed: 530 average time/residue: 0.5292 time to fit residues: 463.1251 Evaluate side-chains 396 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 395 time to evaluate : 4.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 464 optimal weight: 0.0000 chunk 54 optimal weight: 10.0000 chunk 274 optimal weight: 10.0000 chunk 351 optimal weight: 20.0000 chunk 272 optimal weight: 5.9990 chunk 405 optimal weight: 6.9990 chunk 269 optimal weight: 5.9990 chunk 479 optimal weight: 20.0000 chunk 300 optimal weight: 0.9980 chunk 292 optimal weight: 0.9990 chunk 221 optimal weight: 0.0570 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 GLN ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 HIS ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 39409 Z= 0.177 Angle : 0.618 9.138 53398 Z= 0.312 Chirality : 0.044 0.348 6322 Planarity : 0.004 0.054 6814 Dihedral : 6.214 105.922 5556 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.83 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.12), residues: 5042 helix: 0.54 (0.10), residues: 2646 sheet: -0.46 (0.23), residues: 499 loop : -1.17 (0.15), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP X 126 HIS 0.009 0.001 HIS Z 148 PHE 0.021 0.001 PHE R 64 TYR 0.022 0.001 TYR Z 72 ARG 0.005 0.000 ARG 7 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 531 time to evaluate : 4.238 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: 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: 8 20 MET cc_start: 0.5059 (ppp) cc_final: 0.4811 (tmm) REVERT: 8 27 PHE cc_start: 0.7908 (m-80) cc_final: 0.7353 (m-80) REVERT: Y 11 ARG cc_start: 0.8399 (mmp80) cc_final: 0.8042 (mmp-170) REVERT: Y 68 ASN cc_start: 0.9527 (m110) cc_final: 0.9243 (m110) REVERT: Y 82 ASP cc_start: 0.8589 (m-30) cc_final: 0.8372 (m-30) REVERT: Y 97 ARG cc_start: 0.8575 (tpm170) cc_final: 0.8244 (tpm170) REVERT: Y 103 LYS cc_start: 0.9473 (tmtt) cc_final: 0.9197 (tptm) REVERT: Y 107 ASP cc_start: 0.9489 (m-30) cc_final: 0.9246 (m-30) REVERT: Y 108 PHE cc_start: 0.9202 (t80) cc_final: 0.8827 (t80) REVERT: Y 112 ASN cc_start: 0.8130 (m-40) cc_final: 0.7745 (m-40) REVERT: A 67 ASN cc_start: 0.8300 (t0) cc_final: 0.7925 (t0) REVERT: A 183 ASP cc_start: 0.9218 (m-30) cc_final: 0.8932 (m-30) REVERT: A 203 CYS cc_start: 0.9052 (m) cc_final: 0.8689 (m) REVERT: A 351 GLN cc_start: 0.9574 (pm20) cc_final: 0.9347 (pm20) REVERT: A 357 GLU cc_start: 0.9430 (tp30) cc_final: 0.9147 (tp30) REVERT: B 64 MET cc_start: 0.9608 (ttm) cc_final: 0.8520 (tmm) REVERT: B 226 ASP cc_start: 0.8931 (t0) cc_final: 0.8318 (t0) REVERT: B 272 ASP cc_start: 0.8861 (t70) cc_final: 0.8554 (t0) REVERT: B 275 LYS cc_start: 0.9663 (mtmt) cc_final: 0.9275 (mtmt) REVERT: B 299 ASP cc_start: 0.8466 (p0) cc_final: 0.7997 (p0) REVERT: B 345 ILE cc_start: 0.9759 (tp) cc_final: 0.9557 (pt) REVERT: B 361 LYS cc_start: 0.9612 (mmmt) cc_final: 0.9188 (mmmt) REVERT: B 378 SER cc_start: 0.8954 (t) cc_final: 0.8642 (p) REVERT: B 470 PHE cc_start: 0.9468 (t80) cc_final: 0.9112 (t80) REVERT: B 471 LEU cc_start: 0.9657 (tt) cc_final: 0.9359 (pp) REVERT: C 69 GLU cc_start: 0.8700 (mp0) cc_final: 0.8156 (mp0) REVERT: C 270 TYR cc_start: 0.8771 (m-10) cc_final: 0.8369 (m-10) REVERT: C 307 LEU cc_start: 0.9696 (tp) cc_final: 0.9221 (tp) REVERT: D 197 LEU cc_start: 0.9828 (tt) cc_final: 0.9596 (tt) REVERT: D 201 MET cc_start: 0.9620 (mmp) cc_final: 0.9144 (mmm) REVERT: D 237 LEU cc_start: 0.9762 (tp) cc_final: 0.9471 (tp) REVERT: D 257 ASN cc_start: 0.9323 (t0) cc_final: 0.8820 (t0) REVERT: D 263 GLN cc_start: 0.9202 (tm-30) cc_final: 0.8907 (tm-30) REVERT: D 271 LEU cc_start: 0.9564 (mt) cc_final: 0.9192 (mt) REVERT: D 311 TYR cc_start: 0.9266 (t80) cc_final: 0.8966 (t80) REVERT: D 393 MET cc_start: 0.9025 (tpt) cc_final: 0.8596 (tpp) REVERT: D 459 MET cc_start: 0.9095 (mmp) cc_final: 0.8848 (mmm) REVERT: E 120 ASP cc_start: 0.9100 (p0) cc_final: 0.8836 (p0) REVERT: E 201 MET cc_start: 0.9391 (mtp) cc_final: 0.9024 (mtp) REVERT: E 257 ASN cc_start: 0.9166 (t0) cc_final: 0.8843 (t0) REVERT: E 288 ASP cc_start: 0.9372 (m-30) cc_final: 0.9106 (m-30) REVERT: F 64 MET cc_start: 0.8999 (mmp) cc_final: 0.8570 (mmp) REVERT: F 97 ASN cc_start: 0.8726 (m110) cc_final: 0.8272 (m110) REVERT: F 189 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7464 (tm-30) REVERT: F 201 MET cc_start: 0.9725 (mmp) cc_final: 0.9287 (mmm) REVERT: F 257 ASN cc_start: 0.9426 (m110) cc_final: 0.9164 (m110) REVERT: F 281 TYR cc_start: 0.9175 (m-80) cc_final: 0.8744 (m-80) REVERT: G 154 MET cc_start: 0.9268 (mpp) cc_final: 0.8686 (mpp) REVERT: G 212 TYR cc_start: 0.7928 (t80) cc_final: 0.7456 (t80) REVERT: T 48 PHE cc_start: 0.6233 (m-10) cc_final: 0.5865 (m-80) REVERT: T 67 MET cc_start: 0.6548 (tpt) cc_final: 0.6037 (tpp) REVERT: T 70 PHE cc_start: 0.6508 (m-80) cc_final: 0.6020 (m-10) REVERT: K 1 MET cc_start: 0.6150 (pmm) cc_final: 0.4996 (tmm) REVERT: Q 50 MET cc_start: 0.3554 (mmm) cc_final: 0.3009 (mmm) REVERT: X 104 MET cc_start: 0.4168 (ppp) cc_final: 0.3734 (pmm) REVERT: X 162 GLU cc_start: 0.9449 (mm-30) cc_final: 0.9136 (tp30) REVERT: X 167 PHE cc_start: 0.9171 (m-80) cc_final: 0.8831 (m-10) REVERT: X 220 MET cc_start: 0.8686 (ppp) cc_final: 0.8392 (ppp) REVERT: Z 155 ASP cc_start: 0.9277 (m-30) cc_final: 0.8944 (m-30) REVERT: 7 40 ARG cc_start: 0.9246 (mtp-110) cc_final: 0.8904 (tmt170) REVERT: 7 166 ARG cc_start: 0.6256 (ptt-90) cc_final: 0.5695 (ptt180) REVERT: 6 90 GLU cc_start: 0.6802 (mm-30) cc_final: 0.6558 (mm-30) outliers start: 0 outliers final: 0 residues processed: 531 average time/residue: 0.4977 time to fit residues: 435.7311 Evaluate side-chains 407 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 407 time to evaluate : 4.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 296 optimal weight: 0.6980 chunk 191 optimal weight: 7.9990 chunk 286 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 305 optimal weight: 1.9990 chunk 327 optimal weight: 5.9990 chunk 237 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 377 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 11 ASN ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 HIS ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 39409 Z= 0.178 Angle : 0.622 11.974 53398 Z= 0.314 Chirality : 0.043 0.350 6322 Planarity : 0.004 0.058 6814 Dihedral : 6.152 103.476 5556 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.85 % Favored : 93.99 % Rotamer: Outliers : 0.02 % Allowed : 1.68 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.12), residues: 5042 helix: 0.54 (0.10), residues: 2640 sheet: -0.38 (0.24), residues: 495 loop : -1.11 (0.15), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP X 126 HIS 0.011 0.001 HIS Z 148 PHE 0.018 0.001 PHE R 30 TYR 0.018 0.001 TYR X 241 ARG 0.005 0.000 ARG R 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 521 time to evaluate : 4.558 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: 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: 8 27 PHE cc_start: 0.7923 (m-80) cc_final: 0.7359 (m-80) REVERT: Y 68 ASN cc_start: 0.9550 (m110) cc_final: 0.9264 (m110) REVERT: Y 82 ASP cc_start: 0.8621 (m-30) cc_final: 0.8407 (m-30) REVERT: Y 97 ARG cc_start: 0.8526 (tpm170) cc_final: 0.8224 (tpm170) REVERT: Y 103 LYS cc_start: 0.9494 (tmtt) cc_final: 0.9233 (tptm) REVERT: Y 108 PHE cc_start: 0.9196 (t80) cc_final: 0.8830 (t80) REVERT: Y 112 ASN cc_start: 0.8133 (m-40) cc_final: 0.7748 (m-40) REVERT: A 67 ASN cc_start: 0.8320 (t0) cc_final: 0.7953 (t0) REVERT: A 183 ASP cc_start: 0.9222 (m-30) cc_final: 0.8925 (m-30) REVERT: A 203 CYS cc_start: 0.9052 (m) cc_final: 0.8698 (m) REVERT: A 351 GLN cc_start: 0.9577 (pm20) cc_final: 0.9360 (pm20) REVERT: A 357 GLU cc_start: 0.9420 (tp30) cc_final: 0.9142 (tp30) REVERT: B 56 GLU cc_start: 0.8856 (mp0) cc_final: 0.8472 (mp0) REVERT: B 226 ASP cc_start: 0.8982 (t0) cc_final: 0.8353 (t0) REVERT: B 272 ASP cc_start: 0.8866 (t70) cc_final: 0.8528 (t0) REVERT: B 275 LYS cc_start: 0.9640 (mtmt) cc_final: 0.9245 (mtmt) REVERT: B 299 ASP cc_start: 0.8472 (p0) cc_final: 0.8002 (p0) REVERT: B 361 LYS cc_start: 0.9647 (mmmt) cc_final: 0.9260 (mmmt) REVERT: B 378 SER cc_start: 0.8937 (t) cc_final: 0.8626 (p) REVERT: B 470 PHE cc_start: 0.9474 (t80) cc_final: 0.9136 (t80) REVERT: C 69 GLU cc_start: 0.8696 (mp0) cc_final: 0.8152 (mp0) REVERT: C 270 TYR cc_start: 0.8603 (m-10) cc_final: 0.8259 (m-10) REVERT: C 307 LEU cc_start: 0.9664 (tp) cc_final: 0.9330 (tp) REVERT: D 197 LEU cc_start: 0.9825 (tt) cc_final: 0.9594 (tt) REVERT: D 201 MET cc_start: 0.9630 (mmp) cc_final: 0.9185 (mmm) REVERT: D 237 LEU cc_start: 0.9761 (tp) cc_final: 0.9473 (tp) REVERT: D 257 ASN cc_start: 0.9348 (t0) cc_final: 0.8851 (t0) REVERT: D 263 GLN cc_start: 0.9208 (tm-30) cc_final: 0.8922 (tm-30) REVERT: D 271 LEU cc_start: 0.9553 (mt) cc_final: 0.9185 (mt) REVERT: D 311 TYR cc_start: 0.9273 (t80) cc_final: 0.8949 (t80) REVERT: D 393 MET cc_start: 0.9031 (tpt) cc_final: 0.8559 (tpp) REVERT: D 459 MET cc_start: 0.9128 (mmp) cc_final: 0.8899 (mmm) REVERT: E 120 ASP cc_start: 0.9096 (p0) cc_final: 0.8834 (p0) REVERT: E 257 ASN cc_start: 0.9162 (t0) cc_final: 0.8787 (t0) REVERT: E 288 ASP cc_start: 0.9337 (m-30) cc_final: 0.9082 (m-30) REVERT: F 64 MET cc_start: 0.9001 (mmp) cc_final: 0.8566 (mmp) REVERT: F 97 ASN cc_start: 0.8701 (m110) cc_final: 0.8229 (m110) REVERT: F 189 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7454 (tm-30) REVERT: F 201 MET cc_start: 0.9742 (mmp) cc_final: 0.9370 (mmm) REVERT: F 257 ASN cc_start: 0.9436 (m110) cc_final: 0.9179 (m110) REVERT: F 281 TYR cc_start: 0.9197 (m-80) cc_final: 0.8746 (m-80) REVERT: F 459 MET cc_start: 0.9079 (mmm) cc_final: 0.8798 (tpp) REVERT: G 116 MET cc_start: 0.9369 (mpp) cc_final: 0.9137 (mpp) REVERT: G 154 MET cc_start: 0.9274 (mpp) cc_final: 0.8747 (mpp) REVERT: T 48 PHE cc_start: 0.6127 (m-10) cc_final: 0.5791 (m-80) REVERT: T 67 MET cc_start: 0.6499 (tpt) cc_final: 0.5984 (tpp) REVERT: T 70 PHE cc_start: 0.6557 (m-80) cc_final: 0.6092 (m-10) REVERT: K 1 MET cc_start: 0.6086 (pmm) cc_final: 0.5109 (tmm) REVERT: Q 50 MET cc_start: 0.3320 (mmm) cc_final: 0.2891 (mmm) REVERT: X 70 MET cc_start: 0.9174 (tpp) cc_final: 0.8972 (tpp) REVERT: X 88 MET cc_start: 0.8651 (mpp) cc_final: 0.8436 (mmt) REVERT: X 162 GLU cc_start: 0.9434 (mm-30) cc_final: 0.9112 (tp30) REVERT: X 167 PHE cc_start: 0.9171 (m-80) cc_final: 0.8857 (m-10) REVERT: X 220 MET cc_start: 0.8686 (ppp) cc_final: 0.8410 (ppp) REVERT: Z 155 ASP cc_start: 0.9269 (m-30) cc_final: 0.8935 (m-30) REVERT: 7 40 ARG cc_start: 0.9245 (mtp-110) cc_final: 0.8926 (tmt170) REVERT: 7 166 ARG cc_start: 0.6214 (ptt-90) cc_final: 0.5688 (ptt180) REVERT: 6 90 GLU cc_start: 0.6785 (mm-30) cc_final: 0.6552 (mm-30) REVERT: U 29 HIS cc_start: 0.8032 (t-90) cc_final: 0.7790 (t70) outliers start: 1 outliers final: 1 residues processed: 522 average time/residue: 0.4895 time to fit residues: 421.2088 Evaluate side-chains 404 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 403 time to evaluate : 4.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 436 optimal weight: 20.0000 chunk 459 optimal weight: 20.0000 chunk 419 optimal weight: 20.0000 chunk 447 optimal weight: 6.9990 chunk 269 optimal weight: 10.0000 chunk 194 optimal weight: 8.9990 chunk 351 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 404 optimal weight: 30.0000 chunk 423 optimal weight: 7.9990 chunk 445 optimal weight: 40.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 GLN E 328 HIS ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 ASN ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 169 GLN ** Z 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 39409 Z= 0.390 Angle : 0.746 11.183 53398 Z= 0.383 Chirality : 0.045 0.341 6322 Planarity : 0.005 0.070 6814 Dihedral : 6.418 106.973 5556 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 24.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.84 % Favored : 93.00 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.12), residues: 5042 helix: 0.33 (0.10), residues: 2659 sheet: -0.55 (0.23), residues: 522 loop : -1.10 (0.15), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP 6 79 HIS 0.010 0.002 HIS Z 148 PHE 0.035 0.002 PHE B 395 TYR 0.024 0.002 TYR G 212 ARG 0.012 0.001 ARG B 17 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 4.545 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: 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: 8 27 PHE cc_start: 0.7922 (m-80) cc_final: 0.7219 (m-80) REVERT: J 27 MET cc_start: 0.2336 (ppp) cc_final: 0.1972 (ppp) REVERT: Y 13 PHE cc_start: 0.8754 (m-80) cc_final: 0.8408 (m-80) REVERT: Y 68 ASN cc_start: 0.9570 (m110) cc_final: 0.9246 (m110) REVERT: Y 82 ASP cc_start: 0.8606 (m-30) cc_final: 0.8367 (m-30) REVERT: Y 103 LYS cc_start: 0.9588 (tmtt) cc_final: 0.9339 (tptm) REVERT: Y 108 PHE cc_start: 0.9250 (t80) cc_final: 0.8933 (t80) REVERT: Y 112 ASN cc_start: 0.8097 (m-40) cc_final: 0.7625 (m-40) REVERT: A 67 ASN cc_start: 0.8444 (t0) cc_final: 0.8129 (t0) REVERT: A 183 ASP cc_start: 0.9313 (m-30) cc_final: 0.9086 (m-30) REVERT: A 203 CYS cc_start: 0.9051 (m) cc_final: 0.8715 (m) REVERT: A 272 ASP cc_start: 0.8613 (m-30) cc_final: 0.8202 (m-30) REVERT: A 357 GLU cc_start: 0.9458 (tp30) cc_final: 0.9191 (tp30) REVERT: B 56 GLU cc_start: 0.8800 (mp0) cc_final: 0.8443 (mp0) REVERT: B 64 MET cc_start: 0.9526 (ttm) cc_final: 0.9084 (tpp) REVERT: B 226 ASP cc_start: 0.9222 (t0) cc_final: 0.8675 (t0) REVERT: B 228 MET cc_start: 0.8922 (ppp) cc_final: 0.8323 (tpp) REVERT: B 275 LYS cc_start: 0.9730 (mtmt) cc_final: 0.9491 (mtmt) REVERT: B 299 ASP cc_start: 0.8616 (p0) cc_final: 0.8222 (p0) REVERT: B 357 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8515 (tm-30) REVERT: B 361 LYS cc_start: 0.9633 (mmmt) cc_final: 0.9161 (mmmt) REVERT: B 470 PHE cc_start: 0.9524 (t80) cc_final: 0.9130 (t80) REVERT: C 69 GLU cc_start: 0.8571 (mp0) cc_final: 0.8049 (mp0) REVERT: C 124 ASP cc_start: 0.9028 (t70) cc_final: 0.8813 (p0) REVERT: C 270 TYR cc_start: 0.8916 (m-10) cc_final: 0.8431 (m-10) REVERT: C 307 LEU cc_start: 0.9733 (tp) cc_final: 0.9306 (tp) REVERT: D 197 LEU cc_start: 0.9816 (tt) cc_final: 0.9583 (tt) REVERT: D 201 MET cc_start: 0.9701 (mmp) cc_final: 0.9284 (mmm) REVERT: D 257 ASN cc_start: 0.9391 (t0) cc_final: 0.8800 (t0) REVERT: D 271 LEU cc_start: 0.9592 (mt) cc_final: 0.9232 (mt) REVERT: D 311 TYR cc_start: 0.9211 (t80) cc_final: 0.8824 (t80) REVERT: D 393 MET cc_start: 0.9094 (tpt) cc_final: 0.8728 (tpp) REVERT: D 459 MET cc_start: 0.9065 (mmp) cc_final: 0.8781 (mmm) REVERT: E 257 ASN cc_start: 0.9367 (t0) cc_final: 0.8937 (t0) REVERT: F 64 MET cc_start: 0.9041 (mmp) cc_final: 0.8651 (mmp) REVERT: F 97 ASN cc_start: 0.8685 (m110) cc_final: 0.8175 (m110) REVERT: F 172 ASN cc_start: 0.9672 (t0) cc_final: 0.9467 (t0) REVERT: F 201 MET cc_start: 0.9803 (mmp) cc_final: 0.9427 (mmm) REVERT: F 257 ASN cc_start: 0.9520 (m110) cc_final: 0.9275 (m110) REVERT: G 116 MET cc_start: 0.9392 (mpp) cc_final: 0.9188 (mpp) REVERT: G 154 MET cc_start: 0.9320 (mpp) cc_final: 0.8780 (mpp) REVERT: T 67 MET cc_start: 0.6692 (tpt) cc_final: 0.6194 (tpp) REVERT: T 70 PHE cc_start: 0.6640 (m-80) cc_final: 0.6133 (m-10) REVERT: X 70 MET cc_start: 0.9210 (tpp) cc_final: 0.8835 (tpp) REVERT: X 88 MET cc_start: 0.8653 (mpp) cc_final: 0.8280 (mmt) REVERT: X 162 GLU cc_start: 0.9407 (mm-30) cc_final: 0.8890 (mt-10) REVERT: X 167 PHE cc_start: 0.9205 (m-80) cc_final: 0.8906 (m-10) REVERT: X 220 MET cc_start: 0.8674 (ppp) cc_final: 0.8407 (ppp) REVERT: 7 40 ARG cc_start: 0.9280 (mtp-110) cc_final: 0.8966 (tmt170) REVERT: 7 166 ARG cc_start: 0.6264 (ptt-90) cc_final: 0.5851 (ptt180) REVERT: 6 9 ARG cc_start: 0.8114 (ttt180) cc_final: 0.7774 (ttt180) REVERT: 6 90 GLU cc_start: 0.6615 (mm-30) cc_final: 0.6285 (mm-30) outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 0.5010 time to fit residues: 394.9618 Evaluate side-chains 365 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 4.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 293 optimal weight: 1.9990 chunk 472 optimal weight: 10.0000 chunk 288 optimal weight: 9.9990 chunk 224 optimal weight: 7.9990 chunk 328 optimal weight: 6.9990 chunk 496 optimal weight: 30.0000 chunk 456 optimal weight: 8.9990 chunk 395 optimal weight: 5.9990 chunk 41 optimal weight: 0.2980 chunk 305 optimal weight: 0.6980 chunk 242 optimal weight: 4.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 HIS ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 39409 Z= 0.208 Angle : 0.653 13.906 53398 Z= 0.330 Chirality : 0.044 0.341 6322 Planarity : 0.004 0.051 6814 Dihedral : 6.295 103.993 5556 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.13 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.12), residues: 5042 helix: 0.47 (0.10), residues: 2674 sheet: -0.39 (0.24), residues: 500 loop : -1.00 (0.15), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 6 79 HIS 0.011 0.001 HIS Z 148 PHE 0.029 0.001 PHE B 395 TYR 0.029 0.001 TYR G 212 ARG 0.010 0.000 ARG B 17 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 497 time to evaluate : 4.641 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 27 PHE cc_start: 0.7882 (m-80) cc_final: 0.7252 (m-80) REVERT: J 27 MET cc_start: 0.2285 (ppp) cc_final: 0.1946 (ppp) REVERT: Y 13 PHE cc_start: 0.8665 (m-80) cc_final: 0.8304 (m-80) REVERT: Y 68 ASN cc_start: 0.9592 (m110) cc_final: 0.9228 (m110) REVERT: Y 97 ARG cc_start: 0.8673 (tpm170) cc_final: 0.8380 (tpm170) REVERT: Y 103 LYS cc_start: 0.9565 (tmtt) cc_final: 0.9331 (tptt) REVERT: Y 107 ASP cc_start: 0.9460 (m-30) cc_final: 0.9065 (m-30) REVERT: Y 108 PHE cc_start: 0.9256 (t80) cc_final: 0.8943 (t80) REVERT: Y 112 ASN cc_start: 0.8127 (m-40) cc_final: 0.7680 (m110) REVERT: A 67 ASN cc_start: 0.8326 (t0) cc_final: 0.7969 (t0) REVERT: A 183 ASP cc_start: 0.9251 (m-30) cc_final: 0.9000 (m-30) REVERT: A 203 CYS cc_start: 0.9010 (m) cc_final: 0.8669 (m) REVERT: A 272 ASP cc_start: 0.8594 (m-30) cc_final: 0.8165 (m-30) REVERT: A 351 GLN cc_start: 0.9560 (pm20) cc_final: 0.9314 (pm20) REVERT: A 357 GLU cc_start: 0.9441 (tp30) cc_final: 0.9171 (tp30) REVERT: B 56 GLU cc_start: 0.8782 (mp0) cc_final: 0.8397 (mp0) REVERT: B 64 MET cc_start: 0.9495 (ttm) cc_final: 0.9085 (tpp) REVERT: B 226 ASP cc_start: 0.9209 (t0) cc_final: 0.8676 (t0) REVERT: B 228 MET cc_start: 0.8926 (ppp) cc_final: 0.8351 (tpp) REVERT: B 299 ASP cc_start: 0.8508 (p0) cc_final: 0.7992 (p0) REVERT: B 345 ILE cc_start: 0.9776 (tp) cc_final: 0.9564 (pt) REVERT: B 357 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8429 (tm-30) REVERT: B 361 LYS cc_start: 0.9626 (mmmt) cc_final: 0.9093 (mmmt) REVERT: B 378 SER cc_start: 0.9096 (p) cc_final: 0.8866 (t) REVERT: B 399 TYR cc_start: 0.9325 (m-10) cc_final: 0.9085 (m-80) REVERT: B 462 ARG cc_start: 0.9011 (mtp-110) cc_final: 0.8810 (ttp-110) REVERT: B 470 PHE cc_start: 0.9520 (t80) cc_final: 0.9130 (t80) REVERT: B 471 LEU cc_start: 0.9743 (tt) cc_final: 0.9476 (pp) REVERT: C 69 GLU cc_start: 0.8647 (mp0) cc_final: 0.8091 (mp0) REVERT: C 270 TYR cc_start: 0.8749 (m-10) cc_final: 0.8277 (m-10) REVERT: C 307 LEU cc_start: 0.9714 (tp) cc_final: 0.9364 (tp) REVERT: D 197 LEU cc_start: 0.9814 (tt) cc_final: 0.9572 (tt) REVERT: D 201 MET cc_start: 0.9628 (mmp) cc_final: 0.9190 (mmm) REVERT: D 237 LEU cc_start: 0.9737 (tp) cc_final: 0.9480 (tp) REVERT: D 257 ASN cc_start: 0.9393 (t0) cc_final: 0.8850 (t0) REVERT: D 271 LEU cc_start: 0.9544 (mt) cc_final: 0.9163 (mt) REVERT: D 311 TYR cc_start: 0.9263 (t80) cc_final: 0.8887 (t80) REVERT: D 393 MET cc_start: 0.9049 (tpt) cc_final: 0.8646 (tpp) REVERT: D 459 MET cc_start: 0.9127 (mmp) cc_final: 0.8878 (mmm) REVERT: E 257 ASN cc_start: 0.9273 (t0) cc_final: 0.8867 (t0) REVERT: E 288 ASP cc_start: 0.9364 (m-30) cc_final: 0.9132 (m-30) REVERT: E 393 MET cc_start: 0.9294 (pmm) cc_final: 0.8891 (tpp) REVERT: E 396 LEU cc_start: 0.9631 (mp) cc_final: 0.9211 (mp) REVERT: F 64 MET cc_start: 0.9023 (mmp) cc_final: 0.8643 (mmp) REVERT: F 97 ASN cc_start: 0.8761 (m110) cc_final: 0.8271 (m110) REVERT: F 201 MET cc_start: 0.9775 (mmp) cc_final: 0.9364 (mmm) REVERT: F 257 ASN cc_start: 0.9498 (m110) cc_final: 0.9251 (m110) REVERT: G 102 GLN cc_start: 0.9471 (mp10) cc_final: 0.9226 (mp10) REVERT: G 116 MET cc_start: 0.9350 (mpp) cc_final: 0.9138 (mpp) REVERT: G 154 MET cc_start: 0.9325 (mpp) cc_final: 0.8783 (mpp) REVERT: T 67 MET cc_start: 0.6667 (tpt) cc_final: 0.6158 (tpp) REVERT: T 70 PHE cc_start: 0.6573 (m-80) cc_final: 0.6089 (m-10) REVERT: K 1 MET cc_start: 0.6777 (mpp) cc_final: 0.6253 (tmm) REVERT: R 30 PHE cc_start: 0.7141 (m-10) cc_final: 0.6892 (m-10) REVERT: X 88 MET cc_start: 0.8540 (mpp) cc_final: 0.6549 (mpp) REVERT: X 104 MET cc_start: 0.3266 (ppp) cc_final: 0.2892 (pmm) REVERT: X 162 GLU cc_start: 0.9405 (mm-30) cc_final: 0.8883 (mt-10) REVERT: X 167 PHE cc_start: 0.9171 (m-80) cc_final: 0.8880 (m-10) REVERT: X 220 MET cc_start: 0.8723 (ppp) cc_final: 0.8367 (ppp) REVERT: Z 155 ASP cc_start: 0.9316 (m-30) cc_final: 0.8979 (m-30) REVERT: 7 40 ARG cc_start: 0.9276 (mtp-110) cc_final: 0.8954 (tmt170) REVERT: 7 166 ARG cc_start: 0.6200 (ptt-90) cc_final: 0.5820 (ptt180) REVERT: 6 9 ARG cc_start: 0.8097 (ttt180) cc_final: 0.7622 (ttt180) REVERT: 6 90 GLU cc_start: 0.6583 (mm-30) cc_final: 0.6248 (mm-30) REVERT: U 29 HIS cc_start: 0.8001 (t-90) cc_final: 0.7776 (t70) outliers start: 0 outliers final: 0 residues processed: 497 average time/residue: 0.5049 time to fit residues: 412.0322 Evaluate side-chains 384 residues out of total 4147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 4.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 313 optimal weight: 10.0000 chunk 420 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 364 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 395 optimal weight: 8.9990 chunk 165 optimal weight: 9.9990 chunk 406 optimal weight: 20.0000 chunk 50 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN ** S 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.074079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.048898 restraints weight = 217498.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.048716 restraints weight = 132028.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.049783 restraints weight = 94960.843| |-----------------------------------------------------------------------------| r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 39409 Z= 0.316 Angle : 0.691 10.358 53398 Z= 0.354 Chirality : 0.044 0.327 6322 Planarity : 0.005 0.050 6814 Dihedral : 6.346 104.039 5556 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 21.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.84 % Favored : 93.00 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.12), residues: 5042 helix: 0.37 (0.10), residues: 2675 sheet: -0.38 (0.23), residues: 517 loop : -1.00 (0.15), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP X 126 HIS 0.011 0.001 HIS Z 148 PHE 0.025 0.002 PHE T 48 TYR 0.040 0.002 TYR X 166 ARG 0.010 0.001 ARG B 17 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8325.55 seconds wall clock time: 152 minutes 20.71 seconds (9140.71 seconds total)