Starting phenix.real_space_refine on Fri Feb 16 17:22:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i1u_35122/02_2024/8i1u_35122_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i1u_35122/02_2024/8i1u_35122.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i1u_35122/02_2024/8i1u_35122.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i1u_35122/02_2024/8i1u_35122.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i1u_35122/02_2024/8i1u_35122_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i1u_35122/02_2024/8i1u_35122_updated.pdb" } resolution = 3.24 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= -0.002 sd= 0.346 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Al 16 5.89 5 P 32 5.49 5 Mg 16 5.21 5 S 404 5.16 5 C 42296 2.51 5 N 11751 2.21 5 O 13066 1.98 5 F 48 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 424": "OE1" <-> "OE2" Residue "A GLU 434": "OE1" <-> "OE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B GLU 216": "OE1" <-> "OE2" Residue "B GLU 437": "OE1" <-> "OE2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C GLU 114": "OE1" <-> "OE2" Residue "C GLU 336": "OE1" <-> "OE2" Residue "C GLU 473": "OE1" <-> "OE2" Residue "C GLU 497": "OE1" <-> "OE2" Residue "D GLU 278": "OE1" <-> "OE2" Residue "D GLU 329": "OE1" <-> "OE2" Residue "E GLU 200": "OE1" <-> "OE2" Residue "E GLU 283": "OE1" <-> "OE2" Residue "E GLU 375": "OE1" <-> "OE2" Residue "E GLU 476": "OE1" <-> "OE2" Residue "F GLU 101": "OE1" <-> "OE2" Residue "F GLU 142": "OE1" <-> "OE2" Residue "F GLU 240": "OE1" <-> "OE2" Residue "F GLU 276": "OE1" <-> "OE2" Residue "G GLU 114": "OE1" <-> "OE2" Residue "G GLU 261": "OE1" <-> "OE2" Residue "G GLU 317": "OE1" <-> "OE2" Residue "H GLU 38": "OE1" <-> "OE2" Residue "H GLU 133": "OE1" <-> "OE2" Residue "H TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 134": "OE1" <-> "OE2" Residue "I GLU 360": "OE1" <-> "OE2" Residue "J GLU 197": "OE1" <-> "OE2" Residue "J PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 321": "OE1" <-> "OE2" Residue "J PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 364": "OE1" <-> "OE2" Residue "M GLU 119": "OE1" <-> "OE2" Residue "M GLU 329": "OE1" <-> "OE2" Residue "M GLU 436": "OE1" <-> "OE2" Residue "M GLU 456": "OE1" <-> "OE2" Residue "N GLU 195": "OE1" <-> "OE2" Residue "N PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 308": "OE1" <-> "OE2" Residue "N GLU 357": "OE1" <-> "OE2" Residue "O GLU 379": "OE1" <-> "OE2" Residue "O GLU 494": "OE1" <-> "OE2" Residue "P GLU 17": "OE1" <-> "OE2" Residue "Q GLU 62": "OE1" <-> "OE2" Residue "Q PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 105": "OE1" <-> "OE2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 67629 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4041 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 13, 'TRANS': 518} Chain: "B" Number of atoms: 3898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3898 Classifications: {'peptide': 518} Link IDs: {'PTRANS': 9, 'TRANS': 508} Chain: "C" Number of atoms: 4055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4055 Classifications: {'peptide': 522} Link IDs: {'PTRANS': 16, 'TRANS': 505} Chain: "D" Number of atoms: 3908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3908 Classifications: {'peptide': 518} Link IDs: {'PTRANS': 14, 'TRANS': 503} Chain: "E" Number of atoms: 4050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4050 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 18, 'TRANS': 506} Chain: "F" Number of atoms: 4028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4028 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 14, 'TRANS': 511} Chain: "G" Number of atoms: 4002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4002 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 14, 'TRANS': 506} Chain: "H" Number of atoms: 4029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4029 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "I" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4041 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 13, 'TRANS': 518} Chain: "J" Number of atoms: 3924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 3924 Classifications: {'peptide': 522} Link IDs: {'PTRANS': 10, 'TRANS': 511} Chain: "K" Number of atoms: 4073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4073 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 16, 'TRANS': 507} Chain: "L" Number of atoms: 3919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 3919 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 14, 'TRANS': 504} Chain: "M" Number of atoms: 4050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4050 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 18, 'TRANS': 506} Chain: "N" Number of atoms: 4023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4023 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "O" Number of atoms: 3995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3995 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 14, 'TRANS': 505} Chain: "P" Number of atoms: 4029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4029 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "Q" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1519 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 179} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1533 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 180} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 27.23, per 1000 atoms: 0.40 Number of scatterers: 67629 At special positions: 0 Unit cell: (177.12, 178.2, 178.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 404 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 13066 8.00 N 11751 7.00 C 42296 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 Atom "HETATM67235 O3A ADP D 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67491 O3A ADP L 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67331 O3A ADP G 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 21.53 Conformation dependent library (CDL) restraints added in 9.0 seconds 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16350 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 324 helices and 108 sheets defined 50.3% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.38 Creating SS restraints... Processing helix chain 'A' and resid 15 through 35 removed outlier: 4.322A pdb=" N SER A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N SER A 35 " --> pdb=" O ILE A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 70 through 85 removed outlier: 4.007A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 110 removed outlier: 3.571A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 135 Processing helix chain 'A' and resid 147 through 156 Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 165 through 178 removed outlier: 4.365A pdb=" N ASN A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET A 171 " --> pdb=" O PHE A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 257 through 280 removed outlier: 3.968A pdb=" N ASP A 261 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN A 262 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ILE A 270 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 313 through 323 Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 382 through 404 Processing helix chain 'A' and resid 414 through 428 removed outlier: 3.967A pdb=" N ASN A 425 " --> pdb=" O ILE A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 455 removed outlier: 4.287A pdb=" N ILE A 448 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Proline residue: A 449 - end of helix Processing helix chain 'A' and resid 461 through 464 No H-bonds generated for 'chain 'A' and resid 461 through 464' Processing helix chain 'A' and resid 467 through 476 removed outlier: 3.991A pdb=" N PHE A 470 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N HIS A 471 " --> pdb=" O ARG A 468 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL A 476 " --> pdb=" O GLU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 484 removed outlier: 4.937A pdb=" N ASN A 482 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 501 No H-bonds generated for 'chain 'A' and resid 498 through 501' Processing helix chain 'A' and resid 507 through 525 Processing helix chain 'B' and resid 22 through 42 removed outlier: 4.235A pdb=" N SER B 41 " --> pdb=" O ASP B 37 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N THR B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 59 No H-bonds generated for 'chain 'B' and resid 57 through 59' Processing helix chain 'B' and resid 67 through 73 Processing helix chain 'B' and resid 79 through 94 Processing helix chain 'B' and resid 99 through 119 removed outlier: 3.540A pdb=" N LYS B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 143 Processing helix chain 'B' and resid 153 through 167 Processing helix chain 'B' and resid 171 through 190 removed outlier: 6.172A pdb=" N ASP B 177 " --> pdb=" O HIS B 174 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N THR B 180 " --> pdb=" O ASP B 177 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS B 181 " --> pdb=" O HIS B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 198 No H-bonds generated for 'chain 'B' and resid 196 through 198' Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 261 through 285 removed outlier: 3.890A pdb=" N HIS B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 317 through 327 Processing helix chain 'B' and resid 380 through 402 Processing helix chain 'B' and resid 412 through 427 removed outlier: 3.574A pdb=" N ARG B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 454 removed outlier: 3.576A pdb=" N ALA B 433 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL B 434 " --> pdb=" O LYS B 431 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 446 " --> pdb=" O LEU B 443 " (cutoff:3.500A) Proline residue: B 447 - end of helix removed outlier: 3.515A pdb=" N ASN B 453 " --> pdb=" O ILE B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 471 Processing helix chain 'B' and resid 488 through 491 No H-bonds generated for 'chain 'B' and resid 488 through 491' Processing helix chain 'B' and resid 497 through 515 Processing helix chain 'C' and resid 20 through 36 Processing helix chain 'C' and resid 38 through 40 No H-bonds generated for 'chain 'C' and resid 38 through 40' Processing helix chain 'C' and resid 63 through 69 removed outlier: 4.815A pdb=" N GLU C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 90 Processing helix chain 'C' and resid 95 through 114 removed outlier: 3.869A pdb=" N HIS C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 139 Processing helix chain 'C' and resid 149 through 160 Processing helix chain 'C' and resid 164 through 182 removed outlier: 3.955A pdb=" N ARG C 167 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N SER C 170 " --> pdb=" O ARG C 167 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N CYS C 173 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 No H-bonds generated for 'chain 'C' and resid 195 through 198' Processing helix chain 'C' and resid 209 through 211 No H-bonds generated for 'chain 'C' and resid 209 through 211' Processing helix chain 'C' and resid 264 through 283 Processing helix chain 'C' and resid 298 through 307 Processing helix chain 'C' and resid 317 through 327 Processing helix chain 'C' and resid 335 through 337 No H-bonds generated for 'chain 'C' and resid 335 through 337' Processing helix chain 'C' and resid 381 through 403 Processing helix chain 'C' and resid 413 through 426 Processing helix chain 'C' and resid 432 through 455 removed outlier: 4.007A pdb=" N TRP C 435 " --> pdb=" O VAL C 432 " (cutoff:3.500A) Proline residue: C 436 - end of helix removed outlier: 3.707A pdb=" N ILE C 447 " --> pdb=" O LEU C 444 " (cutoff:3.500A) Proline residue: C 448 - end of helix Processing helix chain 'C' and resid 459 through 471 Processing helix chain 'C' and resid 490 through 493 No H-bonds generated for 'chain 'C' and resid 490 through 493' Processing helix chain 'C' and resid 499 through 517 Processing helix chain 'D' and resid 29 through 49 removed outlier: 3.586A pdb=" N ILE D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 80 Processing helix chain 'D' and resid 86 through 101 Processing helix chain 'D' and resid 108 through 125 removed outlier: 4.347A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU D 123 " --> pdb=" O SER D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 151 removed outlier: 3.589A pdb=" N GLU D 146 " --> pdb=" O GLU D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 172 Processing helix chain 'D' and resid 175 through 182 removed outlier: 4.428A pdb=" N GLN D 178 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N SER D 181 " --> pdb=" O GLN D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 192 removed outlier: 3.776A pdb=" N VAL D 191 " --> pdb=" O SER D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 269 through 293 removed outlier: 4.166A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR D 293 " --> pdb=" O GLN D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 319 Processing helix chain 'D' and resid 330 through 340 removed outlier: 4.403A pdb=" N GLU D 334 " --> pdb=" O GLU D 331 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE D 340 " --> pdb=" O CYS D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 350 No H-bonds generated for 'chain 'D' and resid 348 through 350' Processing helix chain 'D' and resid 353 through 355 No H-bonds generated for 'chain 'D' and resid 353 through 355' Processing helix chain 'D' and resid 395 through 417 Processing helix chain 'D' and resid 427 through 442 removed outlier: 3.879A pdb=" N THR D 442 " --> pdb=" O GLU D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 456 Processing helix chain 'D' and resid 460 through 468 Processing helix chain 'D' and resid 473 through 485 Processing helix chain 'D' and resid 504 through 506 No H-bonds generated for 'chain 'D' and resid 504 through 506' Processing helix chain 'D' and resid 512 through 530 Processing helix chain 'E' and resid 31 through 50 removed outlier: 4.397A pdb=" N THR E 50 " --> pdb=" O ASN E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 79 Processing helix chain 'E' and resid 86 through 101 Processing helix chain 'E' and resid 106 through 126 removed outlier: 3.599A pdb=" N VAL E 110 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG E 126 " --> pdb=" O GLN E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 150 Processing helix chain 'E' and resid 163 through 173 Processing helix chain 'E' and resid 177 through 180 Processing helix chain 'E' and resid 184 through 196 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 219 through 221 No H-bonds generated for 'chain 'E' and resid 219 through 221' Processing helix chain 'E' and resid 271 through 295 removed outlier: 4.008A pdb=" N THR E 295 " --> pdb=" O GLN E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 316 removed outlier: 3.995A pdb=" N LEU E 313 " --> pdb=" O GLU E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 337 Processing helix chain 'E' and resid 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 392 through 415 Processing helix chain 'E' and resid 424 through 437 Processing helix chain 'E' and resid 443 through 466 Proline residue: E 459 - end of helix Processing helix chain 'E' and resid 470 through 484 Processing helix chain 'E' and resid 501 through 504 No H-bonds generated for 'chain 'E' and resid 501 through 504' Processing helix chain 'E' and resid 510 through 529 Processing helix chain 'F' and resid 3 through 7 Processing helix chain 'F' and resid 16 through 36 removed outlier: 4.697A pdb=" N THR F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 66 Processing helix chain 'F' and resid 72 through 87 Processing helix chain 'F' and resid 93 through 110 Processing helix chain 'F' and resid 116 through 137 Processing helix chain 'F' and resid 145 through 159 removed outlier: 3.766A pdb=" N THR F 158 " --> pdb=" O THR F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 178 removed outlier: 3.568A pdb=" N ALA F 178 " --> pdb=" O ASP F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 190 No H-bonds generated for 'chain 'F' and resid 188 through 190' Processing helix chain 'F' and resid 201 through 203 No H-bonds generated for 'chain 'F' and resid 201 through 203' Processing helix chain 'F' and resid 253 through 282 removed outlier: 4.395A pdb=" N PHE F 266 " --> pdb=" O ALA F 262 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ILE F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE F 274 " --> pdb=" O ARG F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 308 removed outlier: 3.632A pdb=" N GLU F 308 " --> pdb=" O ALA F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 327 removed outlier: 4.113A pdb=" N GLU F 322 " --> pdb=" O ARG F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 343 No H-bonds generated for 'chain 'F' and resid 341 through 343' Processing helix chain 'F' and resid 381 through 403 Processing helix chain 'F' and resid 413 through 425 Processing helix chain 'F' and resid 432 through 455 Proline residue: F 448 - end of helix removed outlier: 4.037A pdb=" N ASN F 454 " --> pdb=" O LEU F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 459 through 472 Processing helix chain 'F' and resid 489 through 492 No H-bonds generated for 'chain 'F' and resid 489 through 492' Processing helix chain 'F' and resid 498 through 516 removed outlier: 3.920A pdb=" N THR F 509 " --> pdb=" O LEU F 505 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 35 removed outlier: 3.747A pdb=" N ALA G 35 " --> pdb=" O VAL G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' Processing helix chain 'G' and resid 62 through 68 Processing helix chain 'G' and resid 74 through 89 Processing helix chain 'G' and resid 94 through 112 Proline residue: G 110 - end of helix Processing helix chain 'G' and resid 118 through 139 Processing helix chain 'G' and resid 149 through 163 Processing helix chain 'G' and resid 169 through 185 removed outlier: 5.747A pdb=" N ALA G 173 " --> pdb=" O GLN G 170 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ALA G 176 " --> pdb=" O ALA G 173 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LYS G 177 " --> pdb=" O PHE G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 195 Processing helix chain 'G' and resid 205 through 207 No H-bonds generated for 'chain 'G' and resid 205 through 207' Processing helix chain 'G' and resid 260 through 283 Processing helix chain 'G' and resid 297 through 305 Processing helix chain 'G' and resid 316 through 326 Processing helix chain 'G' and resid 334 through 336 No H-bonds generated for 'chain 'G' and resid 334 through 336' Processing helix chain 'G' and resid 379 through 401 removed outlier: 4.240A pdb=" N LYS G 401 " --> pdb=" O ARG G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 411 through 425 removed outlier: 3.905A pdb=" N ARG G 425 " --> pdb=" O ARG G 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 430 through 452 removed outlier: 3.627A pdb=" N GLU G 443 " --> pdb=" O ALA G 439 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE G 444 " --> pdb=" O LYS G 440 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ILE G 445 " --> pdb=" O ALA G 441 " (cutoff:3.500A) Proline residue: G 446 - end of helix Processing helix chain 'G' and resid 457 through 469 Processing helix chain 'G' and resid 496 through 514 Processing helix chain 'H' and resid 11 through 14 No H-bonds generated for 'chain 'H' and resid 11 through 14' Processing helix chain 'H' and resid 25 through 46 removed outlier: 4.098A pdb=" N TYR H 30 " --> pdb=" O GLU H 26 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ARG H 31 " --> pdb=" O GLU H 27 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN H 32 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR H 43 " --> pdb=" O LEU H 39 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR H 45 " --> pdb=" O GLN H 41 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ALA H 46 " --> pdb=" O THR H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 75 Processing helix chain 'H' and resid 81 through 96 Processing helix chain 'H' and resid 101 through 121 Processing helix chain 'H' and resid 125 through 146 Proline residue: H 144 - end of helix Processing helix chain 'H' and resid 157 through 168 removed outlier: 4.258A pdb=" N THR H 166 " --> pdb=" O SER H 162 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER H 167 " --> pdb=" O LEU H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 188 Processing helix chain 'H' and resid 212 through 214 No H-bonds generated for 'chain 'H' and resid 212 through 214' Processing helix chain 'H' and resid 262 through 286 removed outlier: 4.617A pdb=" N SER H 269 " --> pdb=" O LEU H 265 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LYS H 270 " --> pdb=" O MET H 266 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR H 286 " --> pdb=" O ALA H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 299 through 307 Processing helix chain 'H' and resid 318 through 328 Processing helix chain 'H' and resid 382 through 403 Processing helix chain 'H' and resid 414 through 427 Processing helix chain 'H' and resid 435 through 456 removed outlier: 3.767A pdb=" N PHE H 441 " --> pdb=" O ALA H 437 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA H 442 " --> pdb=" O ILE H 438 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU H 443 " --> pdb=" O LYS H 439 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE H 448 " --> pdb=" O ALA H 444 " (cutoff:3.500A) Proline residue: H 449 - end of helix removed outlier: 3.602A pdb=" N SER H 456 " --> pdb=" O LEU H 452 " (cutoff:3.500A) Processing helix chain 'H' and resid 460 through 473 Processing helix chain 'H' and resid 501 through 519 Processing helix chain 'I' and resid 15 through 35 removed outlier: 4.141A pdb=" N SER I 34 " --> pdb=" O ASN I 30 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N SER I 35 " --> pdb=" O ILE I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 64 Processing helix chain 'I' and resid 70 through 85 removed outlier: 4.238A pdb=" N LEU I 75 " --> pdb=" O ALA I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 110 removed outlier: 3.698A pdb=" N VAL I 94 " --> pdb=" O THR I 90 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN I 110 " --> pdb=" O GLU I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 135 Processing helix chain 'I' and resid 147 through 156 Processing helix chain 'I' and resid 163 through 178 removed outlier: 4.329A pdb=" N ASP I 166 " --> pdb=" O ILE I 163 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA I 169 " --> pdb=" O ASP I 166 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASN I 170 " --> pdb=" O PHE I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 207 No H-bonds generated for 'chain 'I' and resid 205 through 207' Processing helix chain 'I' and resid 257 through 280 removed outlier: 4.969A pdb=" N ASP I 261 " --> pdb=" O GLU I 258 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLN I 262 " --> pdb=" O LYS I 259 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ILE I 270 " --> pdb=" O GLU I 267 " (cutoff:3.500A) Processing helix chain 'I' and resid 294 through 302 Processing helix chain 'I' and resid 313 through 323 Processing helix chain 'I' and resid 342 through 344 No H-bonds generated for 'chain 'I' and resid 342 through 344' Processing helix chain 'I' and resid 382 through 404 Processing helix chain 'I' and resid 414 through 425 Processing helix chain 'I' and resid 433 through 455 removed outlier: 4.637A pdb=" N ILE I 448 " --> pdb=" O LEU I 445 " (cutoff:3.500A) Proline residue: I 449 - end of helix Processing helix chain 'I' and resid 460 through 476 Processing helix chain 'I' and resid 478 through 484 removed outlier: 4.806A pdb=" N ASN I 482 " --> pdb=" O GLU I 479 " (cutoff:3.500A) Processing helix chain 'I' and resid 498 through 501 No H-bonds generated for 'chain 'I' and resid 498 through 501' Processing helix chain 'I' and resid 507 through 525 Processing helix chain 'J' and resid 22 through 40 Processing helix chain 'J' and resid 57 through 59 No H-bonds generated for 'chain 'J' and resid 57 through 59' Processing helix chain 'J' and resid 67 through 73 Processing helix chain 'J' and resid 79 through 94 Processing helix chain 'J' and resid 99 through 119 removed outlier: 3.681A pdb=" N LYS J 119 " --> pdb=" O SER J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 144 Processing helix chain 'J' and resid 153 through 167 Processing helix chain 'J' and resid 171 through 189 removed outlier: 6.305A pdb=" N ASP J 177 " --> pdb=" O HIS J 174 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N THR J 180 " --> pdb=" O ASP J 177 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS J 181 " --> pdb=" O HIS J 178 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 198 No H-bonds generated for 'chain 'J' and resid 196 through 198' Processing helix chain 'J' and resid 209 through 211 No H-bonds generated for 'chain 'J' and resid 209 through 211' Processing helix chain 'J' and resid 261 through 285 removed outlier: 4.006A pdb=" N HIS J 285 " --> pdb=" O ARG J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 298 through 307 Processing helix chain 'J' and resid 317 through 327 Processing helix chain 'J' and resid 380 through 402 Processing helix chain 'J' and resid 412 through 427 removed outlier: 3.724A pdb=" N ARG J 427 " --> pdb=" O GLN J 423 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 454 removed outlier: 3.545A pdb=" N VAL J 434 " --> pdb=" O LYS J 431 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU J 446 " --> pdb=" O LEU J 443 " (cutoff:3.500A) Proline residue: J 447 - end of helix Processing helix chain 'J' and resid 458 through 471 Processing helix chain 'J' and resid 488 through 491 No H-bonds generated for 'chain 'J' and resid 488 through 491' Processing helix chain 'J' and resid 497 through 515 Processing helix chain 'K' and resid 20 through 36 Processing helix chain 'K' and resid 38 through 40 No H-bonds generated for 'chain 'K' and resid 38 through 40' Processing helix chain 'K' and resid 63 through 69 removed outlier: 4.460A pdb=" N GLU K 69 " --> pdb=" O ALA K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 90 Processing helix chain 'K' and resid 95 through 114 removed outlier: 4.121A pdb=" N HIS K 111 " --> pdb=" O SER K 107 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE K 112 " --> pdb=" O VAL K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 119 through 139 Processing helix chain 'K' and resid 149 through 160 Processing helix chain 'K' and resid 164 through 183 removed outlier: 4.410A pdb=" N ARG K 167 " --> pdb=" O ALA K 164 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N SER K 170 " --> pdb=" O ARG K 167 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N CYS K 173 " --> pdb=" O SER K 170 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL K 183 " --> pdb=" O VAL K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 209 through 211 No H-bonds generated for 'chain 'K' and resid 209 through 211' Processing helix chain 'K' and resid 264 through 285 removed outlier: 4.506A pdb=" N LEU K 285 " --> pdb=" O ASP K 281 " (cutoff:3.500A) Processing helix chain 'K' and resid 298 through 307 removed outlier: 3.547A pdb=" N ALA K 307 " --> pdb=" O TYR K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 317 through 327 Processing helix chain 'K' and resid 335 through 337 No H-bonds generated for 'chain 'K' and resid 335 through 337' Processing helix chain 'K' and resid 381 through 403 Processing helix chain 'K' and resid 413 through 426 Processing helix chain 'K' and resid 433 through 455 removed outlier: 4.180A pdb=" N GLU K 445 " --> pdb=" O ALA K 441 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL K 446 " --> pdb=" O GLN K 442 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE K 447 " --> pdb=" O ALA K 443 " (cutoff:3.500A) Proline residue: K 448 - end of helix Processing helix chain 'K' and resid 459 through 471 removed outlier: 3.977A pdb=" N THR K 471 " --> pdb=" O ARG K 467 " (cutoff:3.500A) Processing helix chain 'K' and resid 490 through 493 No H-bonds generated for 'chain 'K' and resid 490 through 493' Processing helix chain 'K' and resid 499 through 517 Processing helix chain 'L' and resid 29 through 48 removed outlier: 3.566A pdb=" N ILE L 48 " --> pdb=" O VAL L 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 80 Processing helix chain 'L' and resid 86 through 101 Processing helix chain 'L' and resid 106 through 126 removed outlier: 4.182A pdb=" N VAL L 110 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS L 122 " --> pdb=" O ASP L 118 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU L 123 " --> pdb=" O SER L 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 151 removed outlier: 3.536A pdb=" N GLU L 146 " --> pdb=" O GLU L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 172 Processing helix chain 'L' and resid 175 through 192 removed outlier: 4.484A pdb=" N GLN L 178 " --> pdb=" O VAL L 175 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N SER L 181 " --> pdb=" O GLN L 178 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU L 183 " --> pdb=" O SER L 180 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N SER L 184 " --> pdb=" O SER L 181 " (cutoff:3.500A) Proline residue: L 185 - end of helix removed outlier: 3.627A pdb=" N ALA L 190 " --> pdb=" O SER L 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 205 through 207 No H-bonds generated for 'chain 'L' and resid 205 through 207' Processing helix chain 'L' and resid 218 through 220 No H-bonds generated for 'chain 'L' and resid 218 through 220' Processing helix chain 'L' and resid 269 through 293 removed outlier: 4.167A pdb=" N ASP L 273 " --> pdb=" O TYR L 269 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR L 293 " --> pdb=" O GLN L 289 " (cutoff:3.500A) Processing helix chain 'L' and resid 311 through 319 Processing helix chain 'L' and resid 330 through 340 removed outlier: 3.652A pdb=" N ILE L 333 " --> pdb=" O ARG L 330 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU L 334 " --> pdb=" O GLU L 331 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE L 340 " --> pdb=" O CYS L 337 " (cutoff:3.500A) Processing helix chain 'L' and resid 353 through 355 No H-bonds generated for 'chain 'L' and resid 353 through 355' Processing helix chain 'L' and resid 395 through 417 Processing helix chain 'L' and resid 427 through 442 removed outlier: 3.925A pdb=" N THR L 442 " --> pdb=" O GLU L 438 " (cutoff:3.500A) Processing helix chain 'L' and resid 447 through 457 Processing helix chain 'L' and resid 459 through 468 Processing helix chain 'L' and resid 473 through 485 Processing helix chain 'L' and resid 504 through 506 No H-bonds generated for 'chain 'L' and resid 504 through 506' Processing helix chain 'L' and resid 512 through 531 removed outlier: 3.850A pdb=" N LYS L 531 " --> pdb=" O ARG L 527 " (cutoff:3.500A) Processing helix chain 'M' and resid 31 through 49 Processing helix chain 'M' and resid 74 through 80 Processing helix chain 'M' and resid 86 through 101 Processing helix chain 'M' and resid 106 through 126 removed outlier: 3.847A pdb=" N VAL M 110 " --> pdb=" O THR M 106 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG M 126 " --> pdb=" O GLN M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 151 Processing helix chain 'M' and resid 163 through 173 Processing helix chain 'M' and resid 177 through 180 Processing helix chain 'M' and resid 184 through 196 Processing helix chain 'M' and resid 206 through 208 No H-bonds generated for 'chain 'M' and resid 206 through 208' Processing helix chain 'M' and resid 219 through 221 No H-bonds generated for 'chain 'M' and resid 219 through 221' Processing helix chain 'M' and resid 271 through 295 removed outlier: 4.147A pdb=" N THR M 295 " --> pdb=" O GLN M 291 " (cutoff:3.500A) Processing helix chain 'M' and resid 308 through 316 Processing helix chain 'M' and resid 327 through 337 Processing helix chain 'M' and resid 345 through 347 No H-bonds generated for 'chain 'M' and resid 345 through 347' Processing helix chain 'M' and resid 350 through 352 No H-bonds generated for 'chain 'M' and resid 350 through 352' Processing helix chain 'M' and resid 392 through 415 Processing helix chain 'M' and resid 424 through 438 Processing helix chain 'M' and resid 445 through 466 removed outlier: 4.639A pdb=" N ILE M 458 " --> pdb=" O ALA M 454 " (cutoff:3.500A) Proline residue: M 459 - end of helix Processing helix chain 'M' and resid 470 through 483 Processing helix chain 'M' and resid 510 through 529 Processing helix chain 'N' and resid 16 through 36 removed outlier: 4.540A pdb=" N THR N 36 " --> pdb=" O ASP N 32 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 66 Processing helix chain 'N' and resid 72 through 87 Processing helix chain 'N' and resid 93 through 110 Processing helix chain 'N' and resid 116 through 137 Processing helix chain 'N' and resid 145 through 159 Processing helix chain 'N' and resid 162 through 177 Processing helix chain 'N' and resid 201 through 203 No H-bonds generated for 'chain 'N' and resid 201 through 203' Processing helix chain 'N' and resid 253 through 282 removed outlier: 4.247A pdb=" N PHE N 266 " --> pdb=" O ALA N 262 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ILE N 267 " --> pdb=" O GLU N 263 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE N 274 " --> pdb=" O ARG N 270 " (cutoff:3.500A) Processing helix chain 'N' and resid 299 through 308 removed outlier: 3.905A pdb=" N GLU N 308 " --> pdb=" O ALA N 304 " (cutoff:3.500A) Processing helix chain 'N' and resid 318 through 327 removed outlier: 4.016A pdb=" N GLU N 322 " --> pdb=" O ARG N 318 " (cutoff:3.500A) Processing helix chain 'N' and resid 341 through 343 No H-bonds generated for 'chain 'N' and resid 341 through 343' Processing helix chain 'N' and resid 381 through 403 Processing helix chain 'N' and resid 413 through 428 Proline residue: N 427 - end of helix Processing helix chain 'N' and resid 432 through 455 Proline residue: N 448 - end of helix removed outlier: 3.728A pdb=" N ASN N 454 " --> pdb=" O LEU N 451 " (cutoff:3.500A) Processing helix chain 'N' and resid 459 through 469 Processing helix chain 'N' and resid 489 through 492 No H-bonds generated for 'chain 'N' and resid 489 through 492' Processing helix chain 'N' and resid 498 through 516 removed outlier: 3.826A pdb=" N THR N 509 " --> pdb=" O LEU N 505 " (cutoff:3.500A) Processing helix chain 'O' and resid 19 through 36 removed outlier: 3.890A pdb=" N ALA O 35 " --> pdb=" O VAL O 31 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL O 36 " --> pdb=" O ILE O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 68 Processing helix chain 'O' and resid 74 through 89 Processing helix chain 'O' and resid 94 through 113 removed outlier: 3.655A pdb=" N THR O 98 " --> pdb=" O THR O 94 " (cutoff:3.500A) Proline residue: O 110 - end of helix Processing helix chain 'O' and resid 118 through 139 Processing helix chain 'O' and resid 148 through 163 Processing helix chain 'O' and resid 172 through 184 removed outlier: 3.806A pdb=" N LYS O 177 " --> pdb=" O ALA O 173 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N MET O 178 " --> pdb=" O PHE O 174 " (cutoff:3.500A) Processing helix chain 'O' and resid 192 through 194 No H-bonds generated for 'chain 'O' and resid 192 through 194' Processing helix chain 'O' and resid 205 through 207 No H-bonds generated for 'chain 'O' and resid 205 through 207' Processing helix chain 'O' and resid 260 through 283 Processing helix chain 'O' and resid 297 through 306 removed outlier: 3.642A pdb=" N ARG O 306 " --> pdb=" O TYR O 302 " (cutoff:3.500A) Processing helix chain 'O' and resid 316 through 326 Processing helix chain 'O' and resid 379 through 399 Processing helix chain 'O' and resid 411 through 426 removed outlier: 4.061A pdb=" N ARG O 425 " --> pdb=" O ARG O 421 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N THR O 426 " --> pdb=" O ASP O 422 " (cutoff:3.500A) Processing helix chain 'O' and resid 431 through 452 removed outlier: 4.355A pdb=" N ILE O 444 " --> pdb=" O LYS O 440 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ILE O 445 " --> pdb=" O ALA O 441 " (cutoff:3.500A) Proline residue: O 446 - end of helix Processing helix chain 'O' and resid 457 through 469 Processing helix chain 'O' and resid 496 through 514 Processing helix chain 'P' and resid 11 through 14 No H-bonds generated for 'chain 'P' and resid 11 through 14' Processing helix chain 'P' and resid 25 through 46 removed outlier: 4.472A pdb=" N TYR P 30 " --> pdb=" O GLU P 26 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ARG P 31 " --> pdb=" O GLU P 27 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR P 43 " --> pdb=" O LEU P 39 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N THR P 45 " --> pdb=" O GLN P 41 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ALA P 46 " --> pdb=" O THR P 42 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 74 Processing helix chain 'P' and resid 81 through 96 Processing helix chain 'P' and resid 101 through 121 Processing helix chain 'P' and resid 125 through 146 Proline residue: P 144 - end of helix Processing helix chain 'P' and resid 157 through 168 removed outlier: 3.919A pdb=" N THR P 166 " --> pdb=" O SER P 162 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER P 167 " --> pdb=" O LEU P 163 " (cutoff:3.500A) Processing helix chain 'P' and resid 177 through 190 removed outlier: 3.638A pdb=" N SER P 189 " --> pdb=" O GLN P 185 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE P 190 " --> pdb=" O ALA P 186 " (cutoff:3.500A) Processing helix chain 'P' and resid 212 through 214 No H-bonds generated for 'chain 'P' and resid 212 through 214' Processing helix chain 'P' and resid 262 through 286 removed outlier: 4.735A pdb=" N SER P 269 " --> pdb=" O LEU P 265 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS P 270 " --> pdb=" O MET P 266 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR P 286 " --> pdb=" O ALA P 282 " (cutoff:3.500A) Processing helix chain 'P' and resid 299 through 307 Processing helix chain 'P' and resid 318 through 328 Processing helix chain 'P' and resid 341 through 343 No H-bonds generated for 'chain 'P' and resid 341 through 343' Processing helix chain 'P' and resid 382 through 403 Processing helix chain 'P' and resid 414 through 428 Processing helix chain 'P' and resid 433 through 456 removed outlier: 3.986A pdb=" N TYR P 436 " --> pdb=" O LEU P 433 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA P 442 " --> pdb=" O LYS P 439 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE P 445 " --> pdb=" O ALA P 442 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE P 448 " --> pdb=" O PHE P 445 " (cutoff:3.500A) Proline residue: P 449 - end of helix Processing helix chain 'P' and resid 460 through 471 Processing helix chain 'P' and resid 501 through 520 Processing helix chain 'Q' and resid 30 through 34 removed outlier: 3.787A pdb=" N GLU Q 34 " --> pdb=" O GLU Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 50 No H-bonds generated for 'chain 'Q' and resid 48 through 50' Processing helix chain 'Q' and resid 56 through 59 No H-bonds generated for 'chain 'Q' and resid 56 through 59' Processing helix chain 'Q' and resid 68 through 87 removed outlier: 3.918A pdb=" N LEU Q 87 " --> pdb=" O LYS Q 83 " (cutoff:3.500A) Processing helix chain 'Q' and resid 99 through 107 removed outlier: 5.142A pdb=" N VAL Q 103 " --> pdb=" O LYS Q 100 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN Q 104 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR Q 107 " --> pdb=" O GLN Q 104 " (cutoff:3.500A) Processing helix chain 'Q' and resid 125 through 140 removed outlier: 3.707A pdb=" N ARG Q 139 " --> pdb=" O SER Q 135 " (cutoff:3.500A) Processing helix chain 'Q' and resid 160 through 162 No H-bonds generated for 'chain 'Q' and resid 160 through 162' Processing helix chain 'Q' and resid 190 through 198 Processing helix chain 'Q' and resid 208 through 210 No H-bonds generated for 'chain 'Q' and resid 208 through 210' Processing helix chain 'R' and resid 32 through 42 Processing helix chain 'R' and resid 55 through 59 Processing helix chain 'R' and resid 65 through 88 removed outlier: 3.659A pdb=" N GLU R 68 " --> pdb=" O GLU R 65 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ARG R 69 " --> pdb=" O GLU R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 107 removed outlier: 4.531A pdb=" N VAL R 103 " --> pdb=" O GLY R 99 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N GLN R 104 " --> pdb=" O LYS R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 140 removed outlier: 3.547A pdb=" N SER R 135 " --> pdb=" O ASN R 131 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY R 136 " --> pdb=" O GLN R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 154 No H-bonds generated for 'chain 'R' and resid 151 through 154' Processing helix chain 'R' and resid 181 through 184 No H-bonds generated for 'chain 'R' and resid 181 through 184' Processing helix chain 'R' and resid 193 through 201 removed outlier: 4.673A pdb=" N SER R 201 " --> pdb=" O LYS R 197 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 9 through 13 Processing sheet with id= B, first strand: chain 'A' and resid 43 through 46 Processing sheet with id= C, first strand: chain 'A' and resid 180 through 182 Processing sheet with id= D, first strand: chain 'A' and resid 196 through 200 removed outlier: 4.198A pdb=" N ASN A 196 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 346 through 348 removed outlier: 7.052A pdb=" N VAL A 285 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU A 237 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU A 287 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N MET A 306 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N THR A 288 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL A 308 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 350 through 355 Processing sheet with id= G, first strand: chain 'A' and resid 408 through 410 Processing sheet with id= H, first strand: chain 'A' and resid 486 through 489 Processing sheet with id= I, first strand: chain 'B' and resid 17 through 19 Processing sheet with id= J, first strand: chain 'B' and resid 50 through 53 Processing sheet with id= K, first strand: chain 'B' and resid 199 through 203 removed outlier: 6.604A pdb=" N CYS B 371 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE B 202 " --> pdb=" O CYS B 371 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE B 373 " --> pdb=" O ILE B 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 217 through 220 Processing sheet with id= M, first strand: chain 'B' and resid 237 through 239 removed outlier: 6.431A pdb=" N CYS B 289 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N MET B 310 " --> pdb=" O PHE B 290 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'B' and resid 406 through 408 Processing sheet with id= O, first strand: chain 'B' and resid 476 through 479 Processing sheet with id= P, first strand: chain 'C' and resid 15 through 18 Processing sheet with id= Q, first strand: chain 'C' and resid 48 through 51 Processing sheet with id= R, first strand: chain 'C' and resid 199 through 204 removed outlier: 6.379A pdb=" N CYS C 372 " --> pdb=" O ARG C 200 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N GLU C 202 " --> pdb=" O CYS C 372 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ILE C 374 " --> pdb=" O GLU C 202 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE C 204 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU C 376 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR C 373 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 238 through 241 removed outlier: 6.453A pdb=" N VAL C 289 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU C 241 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE C 291 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N THR C 310 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR C 292 " --> pdb=" O THR C 310 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE C 312 " --> pdb=" O THR C 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'C' and resid 351 through 355 Processing sheet with id= U, first strand: chain 'C' and resid 407 through 409 Processing sheet with id= V, first strand: chain 'C' and resid 478 through 481 Processing sheet with id= W, first strand: chain 'D' and resid 59 through 62 Processing sheet with id= X, first strand: chain 'D' and resid 208 through 212 removed outlier: 7.175A pdb=" N VAL D 386 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N VAL D 211 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE D 388 " --> pdb=" O VAL D 211 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 227 through 229 Processing sheet with id= Z, first strand: chain 'D' and resid 357 through 359 removed outlier: 7.126A pdb=" N VAL D 297 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ILE D 249 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU D 299 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N MET D 323 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ILE D 300 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE D 325 " --> pdb=" O ILE D 300 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 421 through 423 Processing sheet with id= AB, first strand: chain 'D' and resid 491 through 494 Processing sheet with id= AC, first strand: chain 'E' and resid 26 through 29 Processing sheet with id= AD, first strand: chain 'E' and resid 59 through 62 Processing sheet with id= AE, first strand: chain 'E' and resid 209 through 215 removed outlier: 7.648A pdb=" N VAL E 383 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLU E 212 " --> pdb=" O VAL E 383 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE E 385 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LYS E 214 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE E 387 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'E' and resid 228 through 230 Processing sheet with id= AG, first strand: chain 'E' and resid 354 through 356 removed outlier: 7.277A pdb=" N LEU E 299 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LEU E 251 " --> pdb=" O LEU E 299 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE E 301 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N CYS E 302 " --> pdb=" O PRO E 320 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL E 322 " --> pdb=" O CYS E 302 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'E' and resid 418 through 420 Processing sheet with id= AI, first strand: chain 'F' and resid 12 through 14 Processing sheet with id= AJ, first strand: chain 'F' and resid 45 through 48 Processing sheet with id= AK, first strand: chain 'F' and resid 192 through 197 Processing sheet with id= AL, first strand: chain 'F' and resid 210 through 212 Processing sheet with id= AM, first strand: chain 'F' and resid 345 through 347 removed outlier: 6.635A pdb=" N GLY F 288 " --> pdb=" O TYR F 229 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N LEU F 231 " --> pdb=" O GLY F 288 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL F 290 " --> pdb=" O LEU F 231 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N CYS F 233 " --> pdb=" O VAL F 290 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE F 292 " --> pdb=" O CYS F 233 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL F 311 " --> pdb=" O VAL F 291 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ASN F 293 " --> pdb=" O VAL F 311 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU F 313 " --> pdb=" O ASN F 293 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'F' and resid 477 through 479 Processing sheet with id= AO, first strand: chain 'G' and resid 47 through 50 Processing sheet with id= AP, first strand: chain 'G' and resid 197 through 201 removed outlier: 5.643A pdb=" N PHE G 372 " --> pdb=" O LYS G 198 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL G 200 " --> pdb=" O PHE G 372 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU G 374 " --> pdb=" O VAL G 200 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'G' and resid 214 through 217 Processing sheet with id= AR, first strand: chain 'G' and resid 237 through 240 removed outlier: 6.647A pdb=" N VAL G 288 " --> pdb=" O ALA G 238 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LEU G 240 " --> pdb=" O VAL G 288 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU G 290 " --> pdb=" O LEU G 240 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE G 309 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N SER G 291 " --> pdb=" O PHE G 309 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA G 311 " --> pdb=" O SER G 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= AR Processing sheet with id= AS, first strand: chain 'G' and resid 405 through 407 Processing sheet with id= AT, first strand: chain 'G' and resid 475 through 478 Processing sheet with id= AU, first strand: chain 'H' and resid 20 through 23 Processing sheet with id= AV, first strand: chain 'H' and resid 54 through 57 Processing sheet with id= AW, first strand: chain 'H' and resid 202 through 208 removed outlier: 6.414A pdb=" N SER H 373 " --> pdb=" O ARG H 203 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N CYS H 205 " --> pdb=" O SER H 373 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE H 375 " --> pdb=" O CYS H 205 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE H 207 " --> pdb=" O ILE H 375 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU H 377 " --> pdb=" O ILE H 207 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'H' and resid 345 through 347 removed outlier: 7.006A pdb=" N VAL H 290 " --> pdb=" O ALA H 240 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N TYR H 242 " --> pdb=" O VAL H 290 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL H 292 " --> pdb=" O TYR H 242 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N MET H 311 " --> pdb=" O VAL H 291 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N THR H 293 " --> pdb=" O MET H 311 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL H 313 " --> pdb=" O THR H 293 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'H' and resid 351 through 354 Processing sheet with id= AZ, first strand: chain 'H' and resid 478 through 480 Processing sheet with id= BA, first strand: chain 'I' and resid 9 through 13 Processing sheet with id= BB, first strand: chain 'I' and resid 43 through 46 Processing sheet with id= BC, first strand: chain 'I' and resid 180 through 182 Processing sheet with id= BD, first strand: chain 'I' and resid 196 through 200 Processing sheet with id= BE, first strand: chain 'I' and resid 346 through 348 removed outlier: 7.045A pdb=" N VAL I 285 " --> pdb=" O ALA I 235 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LEU I 237 " --> pdb=" O VAL I 285 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU I 287 " --> pdb=" O LEU I 237 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N MET I 306 " --> pdb=" O ILE I 286 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N THR I 288 " --> pdb=" O MET I 306 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL I 308 " --> pdb=" O THR I 288 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'I' and resid 350 through 355 Processing sheet with id= BG, first strand: chain 'I' and resid 408 through 410 Processing sheet with id= BH, first strand: chain 'I' and resid 486 through 489 Processing sheet with id= BI, first strand: chain 'J' and resid 17 through 19 Processing sheet with id= BJ, first strand: chain 'J' and resid 50 through 53 Processing sheet with id= BK, first strand: chain 'J' and resid 199 through 203 removed outlier: 6.902A pdb=" N CYS J 371 " --> pdb=" O HIS J 200 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ILE J 202 " --> pdb=" O CYS J 371 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE J 373 " --> pdb=" O ILE J 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= BK Processing sheet with id= BL, first strand: chain 'J' and resid 217 through 220 Processing sheet with id= BM, first strand: chain 'J' and resid 237 through 239 removed outlier: 6.319A pdb=" N CYS J 289 " --> pdb=" O LEU J 238 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N MET J 310 " --> pdb=" O PHE J 290 " (cutoff:3.500A) No H-bonds generated for sheet with id= BM Processing sheet with id= BN, first strand: chain 'J' and resid 406 through 408 Processing sheet with id= BO, first strand: chain 'J' and resid 476 through 479 Processing sheet with id= BP, first strand: chain 'K' and resid 15 through 18 Processing sheet with id= BQ, first strand: chain 'K' and resid 48 through 51 Processing sheet with id= BR, first strand: chain 'K' and resid 199 through 204 removed outlier: 6.347A pdb=" N CYS K 372 " --> pdb=" O ARG K 200 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N GLU K 202 " --> pdb=" O CYS K 372 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE K 374 " --> pdb=" O GLU K 202 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE K 204 " --> pdb=" O ILE K 374 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU K 376 " --> pdb=" O ILE K 204 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR K 373 " --> pdb=" O LEU K 215 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'K' and resid 238 through 241 removed outlier: 6.405A pdb=" N VAL K 289 " --> pdb=" O VAL K 239 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LEU K 241 " --> pdb=" O VAL K 289 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE K 291 " --> pdb=" O LEU K 241 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR K 310 " --> pdb=" O VAL K 290 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N THR K 292 " --> pdb=" O THR K 310 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE K 312 " --> pdb=" O THR K 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= BS Processing sheet with id= BT, first strand: chain 'K' and resid 351 through 355 Processing sheet with id= BU, first strand: chain 'K' and resid 407 through 409 Processing sheet with id= BV, first strand: chain 'K' and resid 478 through 481 Processing sheet with id= BW, first strand: chain 'L' and resid 59 through 62 Processing sheet with id= BX, first strand: chain 'L' and resid 208 through 212 removed outlier: 7.184A pdb=" N VAL L 386 " --> pdb=" O LYS L 209 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N VAL L 211 " --> pdb=" O VAL L 386 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE L 388 " --> pdb=" O VAL L 211 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'L' and resid 227 through 229 Processing sheet with id= BZ, first strand: chain 'L' and resid 357 through 359 removed outlier: 7.160A pdb=" N VAL L 297 " --> pdb=" O GLY L 247 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ILE L 249 " --> pdb=" O VAL L 297 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU L 299 " --> pdb=" O ILE L 249 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N MET L 323 " --> pdb=" O LEU L 298 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ILE L 300 " --> pdb=" O MET L 323 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE L 325 " --> pdb=" O ILE L 300 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'L' and resid 421 through 423 Processing sheet with id= CB, first strand: chain 'L' and resid 491 through 494 Processing sheet with id= CC, first strand: chain 'M' and resid 26 through 28 Processing sheet with id= CD, first strand: chain 'M' and resid 59 through 62 Processing sheet with id= CE, first strand: chain 'M' and resid 212 through 215 removed outlier: 3.700A pdb=" N GLY M 389 " --> pdb=" O LYS M 214 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'M' and resid 227 through 230 Processing sheet with id= CG, first strand: chain 'M' and resid 354 through 356 removed outlier: 7.355A pdb=" N LEU M 299 " --> pdb=" O ALA M 249 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU M 251 " --> pdb=" O LEU M 299 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE M 301 " --> pdb=" O LEU M 251 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N CYS M 302 " --> pdb=" O PRO M 320 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL M 322 " --> pdb=" O CYS M 302 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'N' and resid 12 through 14 Processing sheet with id= CI, first strand: chain 'N' and resid 45 through 48 Processing sheet with id= CJ, first strand: chain 'N' and resid 192 through 197 Processing sheet with id= CK, first strand: chain 'N' and resid 210 through 212 Processing sheet with id= CL, first strand: chain 'N' and resid 345 through 347 removed outlier: 6.636A pdb=" N VAL N 311 " --> pdb=" O VAL N 291 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ASN N 293 " --> pdb=" O VAL N 311 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU N 313 " --> pdb=" O ASN N 293 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain 'N' and resid 407 through 409 Processing sheet with id= CN, first strand: chain 'N' and resid 477 through 479 Processing sheet with id= CO, first strand: chain 'O' and resid 14 through 17 Processing sheet with id= CP, first strand: chain 'O' and resid 47 through 50 Processing sheet with id= CQ, first strand: chain 'O' and resid 195 through 201 removed outlier: 6.665A pdb=" N CYS O 370 " --> pdb=" O GLY O 196 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N LYS O 198 " --> pdb=" O CYS O 370 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N PHE O 372 " --> pdb=" O LYS O 198 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL O 200 " --> pdb=" O PHE O 372 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU O 374 " --> pdb=" O VAL O 200 " (cutoff:3.500A) Processing sheet with id= CR, first strand: chain 'O' and resid 214 through 217 Processing sheet with id= CS, first strand: chain 'O' and resid 237 through 240 removed outlier: 7.217A pdb=" N VAL O 288 " --> pdb=" O ALA O 238 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N LEU O 240 " --> pdb=" O VAL O 288 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU O 290 " --> pdb=" O LEU O 240 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N PHE O 309 " --> pdb=" O VAL O 289 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N SER O 291 " --> pdb=" O PHE O 309 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA O 311 " --> pdb=" O SER O 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= CS Processing sheet with id= CT, first strand: chain 'O' and resid 405 through 407 Processing sheet with id= CU, first strand: chain 'O' and resid 475 through 478 Processing sheet with id= CV, first strand: chain 'P' and resid 19 through 23 Processing sheet with id= CW, first strand: chain 'P' and resid 54 through 57 Processing sheet with id= CX, first strand: chain 'P' and resid 202 through 208 removed outlier: 6.749A pdb=" N SER P 373 " --> pdb=" O ARG P 203 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N CYS P 205 " --> pdb=" O SER P 373 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE P 375 " --> pdb=" O CYS P 205 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ILE P 207 " --> pdb=" O ILE P 375 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU P 377 " --> pdb=" O ILE P 207 " (cutoff:3.500A) Processing sheet with id= CY, first strand: chain 'P' and resid 239 through 242 removed outlier: 6.497A pdb=" N VAL P 290 " --> pdb=" O ALA P 240 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N TYR P 242 " --> pdb=" O VAL P 290 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL P 292 " --> pdb=" O TYR P 242 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N MET P 311 " --> pdb=" O VAL P 291 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N THR P 293 " --> pdb=" O MET P 311 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL P 313 " --> pdb=" O THR P 293 " (cutoff:3.500A) No H-bonds generated for sheet with id= CY Processing sheet with id= CZ, first strand: chain 'P' and resid 351 through 354 Processing sheet with id= DA, first strand: chain 'P' and resid 408 through 410 Processing sheet with id= DB, first strand: chain 'P' and resid 478 through 480 Processing sheet with id= DC, first strand: chain 'Q' and resid 147 through 150 removed outlier: 3.866A pdb=" N ALA Q 176 " --> pdb=" O VAL Q 168 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N LEU Q 170 " --> pdb=" O ILE Q 174 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE Q 174 " --> pdb=" O LEU Q 170 " (cutoff:3.500A) Processing sheet with id= DD, first strand: chain 'R' and resid 118 through 120 3397 hydrogen bonds defined for protein. 8919 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: 28.96 Time building geometry restraints manager: 23.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 14256 1.33 - 1.45: 13168 1.45 - 1.57: 40237 1.57 - 1.69: 48 1.69 - 1.82: 716 Bond restraints: 68425 Sorted by residual: bond pdb=" F2 AF3 A 603 " pdb="AL AF3 A 603 " ideal model delta sigma weight residual 1.637 1.705 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" F2 AF3 K 603 " pdb="AL AF3 K 603 " ideal model delta sigma weight residual 1.637 1.705 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" F2 AF3 B 603 " pdb="AL AF3 B 603 " ideal model delta sigma weight residual 1.637 1.705 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" F2 AF3 L 603 " pdb="AL AF3 L 603 " ideal model delta sigma weight residual 1.637 1.704 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" F2 AF3 C 603 " pdb="AL AF3 C 603 " ideal model delta sigma weight residual 1.637 1.704 -0.067 2.00e-02 2.50e+03 1.13e+01 ... (remaining 68420 not shown) Histogram of bond angle deviations from ideal: 97.74 - 105.51: 1090 105.51 - 113.27: 39779 113.27 - 121.04: 33387 121.04 - 128.81: 17840 128.81 - 136.58: 300 Bond angle restraints: 92396 Sorted by residual: angle pdb=" N PRO R 215 " pdb=" CA PRO R 215 " pdb=" CB PRO R 215 " ideal model delta sigma weight residual 103.00 110.52 -7.52 1.10e+00 8.26e-01 4.67e+01 angle pdb=" CA PRO O 110 " pdb=" N PRO O 110 " pdb=" CD PRO O 110 " ideal model delta sigma weight residual 112.00 106.42 5.58 1.40e+00 5.10e-01 1.59e+01 angle pdb=" C THR M 442 " pdb=" N LEU M 443 " pdb=" CA LEU M 443 " ideal model delta sigma weight residual 121.54 128.72 -7.18 1.91e+00 2.74e-01 1.41e+01 angle pdb=" N VAL O 183 " pdb=" CA VAL O 183 " pdb=" C VAL O 183 " ideal model delta sigma weight residual 113.39 108.19 5.20 1.47e+00 4.63e-01 1.25e+01 angle pdb=" N SER J 333 " pdb=" CA SER J 333 " pdb=" C SER J 333 " ideal model delta sigma weight residual 114.56 110.27 4.29 1.27e+00 6.20e-01 1.14e+01 ... (remaining 92391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 41425 35.43 - 70.87: 776 70.87 - 106.30: 94 106.30 - 141.74: 17 141.74 - 177.17: 5 Dihedral angle restraints: 42317 sinusoidal: 17078 harmonic: 25239 Sorted by residual: dihedral pdb=" O2A ADP C 601 " pdb=" O3A ADP C 601 " pdb=" PA ADP C 601 " pdb=" PB ADP C 601 " ideal model delta sinusoidal sigma weight residual -60.00 117.17 -177.17 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " pdb=" PA ADP A 601 " ideal model delta sinusoidal sigma weight residual 300.00 149.93 150.06 1 2.00e+01 2.50e-03 4.48e+01 dihedral pdb=" O1B ADP J 601 " pdb=" O3A ADP J 601 " pdb=" PB ADP J 601 " pdb=" PA ADP J 601 " ideal model delta sinusoidal sigma weight residual -60.00 87.19 -147.19 1 2.00e+01 2.50e-03 4.42e+01 ... (remaining 42314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 8496 0.049 - 0.098: 1976 0.098 - 0.147: 504 0.147 - 0.196: 17 0.196 - 0.245: 5 Chirality restraints: 10998 Sorted by residual: chirality pdb=" CB ILE K 460 " pdb=" CA ILE K 460 " pdb=" CG1 ILE K 460 " pdb=" CG2 ILE K 460 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA PRO R 215 " pdb=" N PRO R 215 " pdb=" C PRO R 215 " pdb=" CB PRO R 215 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB ILE Q 124 " pdb=" CA ILE Q 124 " pdb=" CG1 ILE Q 124 " pdb=" CG2 ILE Q 124 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 10995 not shown) Planarity restraints: 11789 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS O 109 " -0.080 5.00e-02 4.00e+02 1.18e-01 2.24e+01 pdb=" N PRO O 110 " 0.204 5.00e-02 4.00e+02 pdb=" CA PRO O 110 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO O 110 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 441 " -0.019 2.00e-02 2.50e+03 1.78e-02 5.55e+00 pdb=" CG PHE H 441 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE H 441 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE H 441 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE H 441 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE H 441 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE H 441 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS N 426 " -0.035 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO N 427 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO N 427 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO N 427 " -0.030 5.00e-02 4.00e+02 ... (remaining 11786 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 440 2.48 - 3.09: 49123 3.09 - 3.69: 103376 3.69 - 4.30: 148607 4.30 - 4.90: 251187 Nonbonded interactions: 552733 Sorted by model distance: nonbonded pdb="MG MG P 602 " pdb="AL AF3 P 603 " model vdw 1.879 1.890 nonbonded pdb="MG MG P 602 " pdb=" F3 AF3 P 603 " model vdw 1.889 2.120 nonbonded pdb="MG MG P 602 " pdb=" F2 AF3 P 603 " model vdw 1.893 2.120 nonbonded pdb=" O1B ADP H 601 " pdb="MG MG H 602 " model vdw 1.918 2.170 nonbonded pdb="MG MG H 602 " pdb=" F2 AF3 H 603 " model vdw 1.949 2.120 ... (remaining 552728 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'I' } ncs_group { reference = chain 'B' selection = (chain 'J' and (resid 9 through 526 or resid 601 through 603)) } ncs_group { reference = chain 'C' selection = (chain 'K' and (resid 6 through 527 or resid 601 through 603)) } ncs_group { reference = chain 'D' selection = (chain 'L' and (resid 21 through 538 or resid 601 through 603)) } ncs_group { reference = chain 'E' selection = chain 'M' } ncs_group { reference = (chain 'F' and (resid 3 through 527 or resid 601 through 603)) selection = chain 'N' } ncs_group { reference = (chain 'G' and (resid 6 through 525 or resid 601 through 603)) selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = (chain 'R' and (resid 28 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 214)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 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: 0.080 Extract box with map and model: 9.240 Check model and map are aligned: 0.730 Set scattering table: 0.470 Process input model: 145.350 Find NCS groups from input model: 6.610 Set up NCS constraints: 0.680 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 167.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 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 : 0.004 0.068 68425 Z= 0.256 Angle : 0.630 9.600 92396 Z= 0.315 Chirality : 0.044 0.245 10998 Planarity : 0.004 0.118 11789 Dihedral : 15.392 177.169 25967 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.82 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.09), residues: 8727 helix: 1.23 (0.08), residues: 4428 sheet: -0.54 (0.17), residues: 1071 loop : -1.32 (0.11), residues: 3228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Q 196 HIS 0.009 0.001 HIS N 71 PHE 0.042 0.001 PHE H 441 TYR 0.022 0.001 TYR A 121 ARG 0.014 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1134 residues out of total 7331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1134 time to evaluate : 5.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 ASP cc_start: 0.6741 (t0) cc_final: 0.6469 (t0) REVERT: B 452 ASP cc_start: 0.8555 (m-30) cc_final: 0.8353 (m-30) REVERT: D 503 ILE cc_start: 0.8080 (mm) cc_final: 0.7788 (mm) REVERT: G 48 LEU cc_start: 0.8232 (tt) cc_final: 0.7995 (tt) REVERT: G 330 ILE cc_start: 0.8988 (mm) cc_final: 0.8770 (mm) REVERT: G 455 PHE cc_start: 0.7334 (m-10) cc_final: 0.6630 (m-10) REVERT: I 115 THR cc_start: 0.8853 (m) cc_final: 0.8647 (m) REVERT: J 251 ILE cc_start: 0.8199 (mt) cc_final: 0.7998 (mt) REVERT: K 305 MET cc_start: 0.7612 (ttm) cc_final: 0.7402 (ttm) REVERT: M 28 LEU cc_start: 0.7935 (mp) cc_final: 0.7659 (mp) REVERT: P 34 GLN cc_start: 0.8107 (tp40) cc_final: 0.7697 (tp-100) REVERT: P 156 ASP cc_start: 0.7250 (t70) cc_final: 0.6925 (t70) REVERT: P 247 ASP cc_start: 0.7582 (t70) cc_final: 0.7357 (t70) REVERT: P 358 THR cc_start: 0.8600 (p) cc_final: 0.8313 (p) REVERT: P 436 TYR cc_start: 0.8188 (m-10) cc_final: 0.7888 (m-10) outliers start: 0 outliers final: 0 residues processed: 1134 average time/residue: 0.6215 time to fit residues: 1210.1255 Evaluate side-chains 924 residues out of total 7331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 924 time to evaluate : 5.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 867 random chunks: chunk 732 optimal weight: 3.9990 chunk 657 optimal weight: 9.9990 chunk 364 optimal weight: 0.9990 chunk 224 optimal weight: 6.9990 chunk 443 optimal weight: 10.0000 chunk 351 optimal weight: 9.9990 chunk 679 optimal weight: 7.9990 chunk 262 optimal weight: 0.0670 chunk 413 optimal weight: 4.9990 chunk 505 optimal weight: 0.8980 chunk 787 optimal weight: 1.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN A 475 GLN B 314 HIS ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 497 ASN I 217 ASN I 534 HIS ** J 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 453 ASN K 301 GLN K 320 ASN ** N 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 346 HIS N 514 ASN O 151 GLN ** P 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 34 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.0518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 68425 Z= 0.194 Angle : 0.574 8.943 92396 Z= 0.281 Chirality : 0.042 0.211 10998 Planarity : 0.004 0.075 11789 Dihedral : 7.985 167.710 9484 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.59 % Favored : 94.36 % Rotamer: Outliers : 1.09 % Allowed : 9.60 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.09), residues: 8727 helix: 1.34 (0.08), residues: 4417 sheet: -0.49 (0.16), residues: 1101 loop : -1.27 (0.11), residues: 3209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP I 485 HIS 0.007 0.001 HIS N 71 PHE 0.027 0.001 PHE H 441 TYR 0.015 0.001 TYR N 239 ARG 0.006 0.000 ARG F 523 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1083 residues out of total 7331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1003 time to evaluate : 5.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 437 TYR cc_start: 0.7493 (t80) cc_final: 0.7288 (t80) REVERT: D 503 ILE cc_start: 0.8073 (mm) cc_final: 0.7815 (mm) REVERT: F 308 GLU cc_start: 0.6038 (mm-30) cc_final: 0.5623 (mm-30) REVERT: G 48 LEU cc_start: 0.8243 (tt) cc_final: 0.7985 (tt) REVERT: G 320 LYS cc_start: 0.7694 (mptt) cc_final: 0.6807 (mptt) REVERT: G 330 ILE cc_start: 0.9009 (mm) cc_final: 0.8806 (mm) REVERT: H 230 ASP cc_start: 0.7030 (m-30) cc_final: 0.6769 (m-30) REVERT: K 305 MET cc_start: 0.7832 (ttm) cc_final: 0.7590 (ttm) REVERT: P 34 GLN cc_start: 0.8110 (tp-100) cc_final: 0.7657 (tp-100) REVERT: P 247 ASP cc_start: 0.7626 (t70) cc_final: 0.7338 (t70) REVERT: P 358 THR cc_start: 0.8559 (p) cc_final: 0.8351 (p) REVERT: P 436 TYR cc_start: 0.8168 (m-10) cc_final: 0.7867 (m-10) REVERT: Q 51 MET cc_start: 0.6032 (mtt) cc_final: 0.5697 (mtm) REVERT: Q 86 LYS cc_start: 0.4731 (mmpt) cc_final: 0.4439 (mmtt) REVERT: Q 179 ILE cc_start: 0.6782 (mm) cc_final: 0.6540 (mt) outliers start: 80 outliers final: 61 residues processed: 1045 average time/residue: 0.6836 time to fit residues: 1240.1967 Evaluate side-chains 990 residues out of total 7331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 929 time to evaluate : 5.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 317 GLU Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain H residue 498 LEU Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain I residue 344 MET Chi-restraints excluded: chain I residue 415 VAL Chi-restraints excluded: chain J residue 289 CYS Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 364 THR Chi-restraints excluded: chain K residue 516 LEU Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 456 ASP Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 493 CYS Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain N residue 213 ASP Chi-restraints excluded: chain N residue 302 LEU Chi-restraints excluded: chain N residue 354 THR Chi-restraints excluded: chain N residue 371 SER Chi-restraints excluded: chain O residue 17 GLN Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain O residue 183 VAL Chi-restraints excluded: chain O residue 242 VAL Chi-restraints excluded: chain O residue 334 VAL Chi-restraints excluded: chain O residue 362 THR Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain O residue 515 SER Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 166 THR Chi-restraints excluded: chain P residue 204 VAL Chi-restraints excluded: chain R residue 71 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 867 random chunks: chunk 437 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 655 optimal weight: 10.0000 chunk 536 optimal weight: 0.4980 chunk 217 optimal weight: 9.9990 chunk 788 optimal weight: 9.9990 chunk 852 optimal weight: 9.9990 chunk 702 optimal weight: 7.9990 chunk 782 optimal weight: 7.9990 chunk 268 optimal weight: 0.9980 chunk 632 optimal weight: 0.1980 overall best weight: 3.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN C 470 HIS ** E 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 460 GLN ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 501 ASN H 289 ASN I 393 HIS I 534 HIS ** J 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 320 ASN L 484 HIS M 316 GLN M 504 GLN N 346 HIS N 514 ASN O 151 GLN ** P 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 68425 Z= 0.329 Angle : 0.628 9.736 92396 Z= 0.309 Chirality : 0.045 0.182 10998 Planarity : 0.004 0.067 11789 Dihedral : 7.928 149.028 9484 Min Nonbonded Distance : 1.688 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.22 % Favored : 93.72 % Rotamer: Outliers : 2.05 % Allowed : 13.91 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.09), residues: 8727 helix: 1.20 (0.08), residues: 4408 sheet: -0.49 (0.16), residues: 1099 loop : -1.36 (0.11), residues: 3220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP I 485 HIS 0.007 0.001 HIS N 71 PHE 0.032 0.002 PHE H 441 TYR 0.023 0.002 TYR M 420 ARG 0.006 0.000 ARG Q 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1114 residues out of total 7331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 964 time to evaluate : 5.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 246 GLU cc_start: 0.6459 (OUTLIER) cc_final: 0.6107 (pt0) REVERT: C 293 GLU cc_start: 0.7156 (tt0) cc_final: 0.6955 (mt-10) REVERT: C 388 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7739 (tm-30) REVERT: D 57 MET cc_start: 0.8108 (mmm) cc_final: 0.7826 (mmm) REVERT: D 503 ILE cc_start: 0.8078 (mm) cc_final: 0.7834 (mm) REVERT: F 308 GLU cc_start: 0.6098 (mm-30) cc_final: 0.5572 (mm-30) REVERT: G 48 LEU cc_start: 0.8219 (tt) cc_final: 0.7994 (tt) REVERT: G 307 ASP cc_start: 0.7300 (OUTLIER) cc_final: 0.6933 (m-30) REVERT: I 53 THR cc_start: 0.9027 (OUTLIER) cc_final: 0.8783 (p) REVERT: L 320 MET cc_start: 0.7903 (mtt) cc_final: 0.7654 (mtt) REVERT: N 467 GLN cc_start: 0.7497 (OUTLIER) cc_final: 0.7237 (mp10) REVERT: O 194 MET cc_start: 0.7752 (mmp) cc_final: 0.7239 (mmp) REVERT: P 34 GLN cc_start: 0.8218 (tp-100) cc_final: 0.7793 (tp-100) REVERT: P 358 THR cc_start: 0.8500 (p) cc_final: 0.8293 (p) REVERT: P 436 TYR cc_start: 0.8257 (m-10) cc_final: 0.7850 (m-80) REVERT: Q 86 LYS cc_start: 0.4722 (mmpt) cc_final: 0.4473 (mmtt) REVERT: Q 88 LYS cc_start: 0.6387 (tptp) cc_final: 0.5059 (tptt) REVERT: Q 179 ILE cc_start: 0.6830 (mm) cc_final: 0.6614 (mt) outliers start: 150 outliers final: 106 residues processed: 1046 average time/residue: 0.6393 time to fit residues: 1147.5693 Evaluate side-chains 997 residues out of total 7331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 887 time to evaluate : 5.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 307 ASP Chi-restraints excluded: chain G residue 317 GLU Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain H residue 355 VAL Chi-restraints excluded: chain H residue 384 LEU Chi-restraints excluded: chain H residue 498 LEU Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 156 MET Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain I residue 344 MET Chi-restraints excluded: chain I residue 415 VAL Chi-restraints excluded: chain J residue 289 CYS Chi-restraints excluded: chain J residue 379 THR Chi-restraints excluded: chain J residue 396 VAL Chi-restraints excluded: chain J residue 443 LEU Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 201 VAL Chi-restraints excluded: chain K residue 364 THR Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 145 ILE Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 456 ASP Chi-restraints excluded: chain L residue 503 ILE Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 62 VAL Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 408 VAL Chi-restraints excluded: chain M residue 485 MET Chi-restraints excluded: chain M residue 493 CYS Chi-restraints excluded: chain N residue 69 ILE Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain N residue 213 ASP Chi-restraints excluded: chain N residue 214 HIS Chi-restraints excluded: chain N residue 302 LEU Chi-restraints excluded: chain N residue 354 THR Chi-restraints excluded: chain N residue 371 SER Chi-restraints excluded: chain N residue 467 GLN Chi-restraints excluded: chain N residue 479 VAL Chi-restraints excluded: chain N residue 487 MET Chi-restraints excluded: chain O residue 17 GLN Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain O residue 120 ILE Chi-restraints excluded: chain O residue 165 SER Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain O residue 188 ASP Chi-restraints excluded: chain O residue 242 VAL Chi-restraints excluded: chain O residue 329 SER Chi-restraints excluded: chain O residue 334 VAL Chi-restraints excluded: chain O residue 362 THR Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain O residue 515 SER Chi-restraints excluded: chain P residue 72 ILE Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 166 THR Chi-restraints excluded: chain P residue 204 VAL Chi-restraints excluded: chain P residue 381 THR Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain P residue 478 VAL Chi-restraints excluded: chain R residue 71 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 867 random chunks: chunk 779 optimal weight: 3.9990 chunk 593 optimal weight: 10.0000 chunk 409 optimal weight: 0.9990 chunk 87 optimal weight: 0.4980 chunk 376 optimal weight: 10.0000 chunk 529 optimal weight: 4.9990 chunk 791 optimal weight: 5.9990 chunk 838 optimal weight: 8.9990 chunk 413 optimal weight: 0.7980 chunk 750 optimal weight: 6.9990 chunk 225 optimal weight: 4.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 HIS ** E 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 497 ASN ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 501 ASN I 534 HIS ** J 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 510 GLN N 346 HIS O 151 GLN ** P 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 68425 Z= 0.232 Angle : 0.581 8.784 92396 Z= 0.285 Chirality : 0.043 0.159 10998 Planarity : 0.004 0.061 11789 Dihedral : 7.662 141.224 9484 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.81 % Favored : 94.14 % Rotamer: Outliers : 2.35 % Allowed : 16.31 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.09), residues: 8727 helix: 1.29 (0.08), residues: 4408 sheet: -0.51 (0.16), residues: 1074 loop : -1.32 (0.11), residues: 3245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP I 485 HIS 0.010 0.001 HIS C 470 PHE 0.019 0.001 PHE Q 167 TYR 0.020 0.001 TYR M 420 ARG 0.007 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1128 residues out of total 7331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 956 time to evaluate : 5.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 246 GLU cc_start: 0.6362 (OUTLIER) cc_final: 0.6038 (pt0) REVERT: D 458 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7448 (mtm) REVERT: D 503 ILE cc_start: 0.8042 (mm) cc_final: 0.7808 (mm) REVERT: G 48 LEU cc_start: 0.8222 (tt) cc_final: 0.7971 (tt) REVERT: G 307 ASP cc_start: 0.7254 (OUTLIER) cc_final: 0.6838 (m-30) REVERT: H 92 MET cc_start: 0.7836 (tpp) cc_final: 0.7406 (tpp) REVERT: J 202 ILE cc_start: 0.8540 (mt) cc_final: 0.8340 (mt) REVERT: J 488 MET cc_start: 0.8030 (mmt) cc_final: 0.7813 (mmt) REVERT: L 320 MET cc_start: 0.7920 (mtt) cc_final: 0.7713 (mtt) REVERT: M 221 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7376 (m-30) REVERT: N 467 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.7199 (mp10) REVERT: N 522 MET cc_start: 0.8013 (tpp) cc_final: 0.7428 (tpp) REVERT: O 194 MET cc_start: 0.7657 (mmp) cc_final: 0.7273 (mmp) REVERT: P 34 GLN cc_start: 0.8171 (tp-100) cc_final: 0.7744 (tp-100) REVERT: P 436 TYR cc_start: 0.8225 (m-10) cc_final: 0.7824 (m-80) REVERT: Q 86 LYS cc_start: 0.4703 (mmpt) cc_final: 0.4475 (mmtt) REVERT: Q 88 LYS cc_start: 0.6591 (tptp) cc_final: 0.5101 (tptt) REVERT: Q 124 ILE cc_start: 0.2734 (OUTLIER) cc_final: 0.2363 (tp) outliers start: 172 outliers final: 114 residues processed: 1066 average time/residue: 0.6221 time to fit residues: 1137.7213 Evaluate side-chains 1021 residues out of total 7331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 901 time to evaluate : 5.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 485 MET Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 380 ASN Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 307 ASP Chi-restraints excluded: chain G residue 317 GLU Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain H residue 355 VAL Chi-restraints excluded: chain H residue 498 LEU Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 48 ASP Chi-restraints excluded: chain I residue 156 MET Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain I residue 344 MET Chi-restraints excluded: chain I residue 415 VAL Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 289 CYS Chi-restraints excluded: chain J residue 396 VAL Chi-restraints excluded: chain J residue 414 GLU Chi-restraints excluded: chain K residue 157 ASN Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 364 THR Chi-restraints excluded: chain K residue 446 VAL Chi-restraints excluded: chain K residue 447 ILE Chi-restraints excluded: chain K residue 516 LEU Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 311 ASP Chi-restraints excluded: chain L residue 456 ASP Chi-restraints excluded: chain L residue 503 ILE Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 62 VAL Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 221 ASP Chi-restraints excluded: chain M residue 493 CYS Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain N residue 69 ILE Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain N residue 213 ASP Chi-restraints excluded: chain N residue 214 HIS Chi-restraints excluded: chain N residue 302 LEU Chi-restraints excluded: chain N residue 354 THR Chi-restraints excluded: chain N residue 371 SER Chi-restraints excluded: chain N residue 467 GLN Chi-restraints excluded: chain N residue 487 MET Chi-restraints excluded: chain O residue 17 GLN Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain O residue 120 ILE Chi-restraints excluded: chain O residue 149 VAL Chi-restraints excluded: chain O residue 165 SER Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain O residue 188 ASP Chi-restraints excluded: chain O residue 242 VAL Chi-restraints excluded: chain O residue 329 SER Chi-restraints excluded: chain O residue 334 VAL Chi-restraints excluded: chain O residue 362 THR Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain O residue 515 SER Chi-restraints excluded: chain P residue 65 VAL Chi-restraints excluded: chain P residue 72 ILE Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 166 THR Chi-restraints excluded: chain P residue 204 VAL Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain P residue 478 VAL Chi-restraints excluded: chain P residue 521 VAL Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain R residue 71 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 867 random chunks: chunk 697 optimal weight: 8.9990 chunk 475 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 623 optimal weight: 0.9980 chunk 345 optimal weight: 7.9990 chunk 715 optimal weight: 9.9990 chunk 579 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 427 optimal weight: 8.9990 chunk 752 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 HIS ** E 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 GLN ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 GLN G 501 ASN ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 217 ASN I 393 HIS I 534 HIS ** J 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 510 GLN N 346 HIS O 151 GLN O 228 GLN ** P 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 68425 Z= 0.258 Angle : 0.593 9.950 92396 Z= 0.290 Chirality : 0.043 0.244 10998 Planarity : 0.004 0.057 11789 Dihedral : 7.563 141.080 9484 Min Nonbonded Distance : 1.683 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.15 % Favored : 93.80 % Rotamer: Outliers : 3.00 % Allowed : 17.61 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.09), residues: 8727 helix: 1.27 (0.08), residues: 4411 sheet: -0.55 (0.16), residues: 1078 loop : -1.31 (0.11), residues: 3238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP I 485 HIS 0.011 0.001 HIS C 470 PHE 0.018 0.001 PHE Q 167 TYR 0.021 0.001 TYR M 420 ARG 0.007 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1156 residues out of total 7331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 936 time to evaluate : 5.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8182 (mm) REVERT: C 219 MET cc_start: 0.7525 (tmm) cc_final: 0.7299 (ttp) REVERT: C 246 GLU cc_start: 0.6373 (OUTLIER) cc_final: 0.6061 (pt0) REVERT: D 57 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7960 (mmm) REVERT: D 141 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8194 (tp) REVERT: D 458 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7414 (mtm) REVERT: D 503 ILE cc_start: 0.8048 (mm) cc_final: 0.7823 (mm) REVERT: F 132 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.6727 (mt0) REVERT: F 308 GLU cc_start: 0.5845 (mm-30) cc_final: 0.5566 (mm-30) REVERT: G 48 LEU cc_start: 0.8259 (tt) cc_final: 0.8008 (tt) REVERT: G 307 ASP cc_start: 0.7289 (OUTLIER) cc_final: 0.6867 (m-30) REVERT: H 92 MET cc_start: 0.7853 (tpp) cc_final: 0.7410 (tpp) REVERT: I 53 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8746 (p) REVERT: J 202 ILE cc_start: 0.8570 (mt) cc_final: 0.8351 (mt) REVERT: L 320 MET cc_start: 0.7937 (mtt) cc_final: 0.7727 (mtt) REVERT: M 221 ASP cc_start: 0.7619 (OUTLIER) cc_final: 0.7388 (m-30) REVERT: N 467 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.7257 (mp10) REVERT: O 194 MET cc_start: 0.7645 (mmp) cc_final: 0.7267 (mmp) REVERT: O 318 ASP cc_start: 0.7572 (m-30) cc_final: 0.7318 (m-30) REVERT: P 34 GLN cc_start: 0.8183 (tp-100) cc_final: 0.7723 (tp-100) REVERT: P 436 TYR cc_start: 0.8246 (m-10) cc_final: 0.7834 (m-80) REVERT: P 441 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7638 (m-80) REVERT: Q 86 LYS cc_start: 0.4774 (mmpt) cc_final: 0.4508 (mmtt) REVERT: Q 88 LYS cc_start: 0.6642 (tptp) cc_final: 0.6019 (tmtt) REVERT: Q 124 ILE cc_start: 0.2642 (OUTLIER) cc_final: 0.2279 (tp) REVERT: Q 175 LYS cc_start: 0.4436 (tptm) cc_final: 0.4207 (tptm) REVERT: Q 179 ILE cc_start: 0.6886 (mm) cc_final: 0.6594 (mt) outliers start: 220 outliers final: 156 residues processed: 1083 average time/residue: 0.6228 time to fit residues: 1162.1063 Evaluate side-chains 1073 residues out of total 7331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 905 time to evaluate : 5.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 485 MET Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 132 GLN Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 380 ASN Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 307 ASP Chi-restraints excluded: chain G residue 317 GLU Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain H residue 230 ASP Chi-restraints excluded: chain H residue 355 VAL Chi-restraints excluded: chain H residue 384 LEU Chi-restraints excluded: chain H residue 498 LEU Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 48 ASP Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 156 MET Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 252 VAL Chi-restraints excluded: chain I residue 288 THR Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain I residue 344 MET Chi-restraints excluded: chain I residue 415 VAL Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 289 CYS Chi-restraints excluded: chain J residue 396 VAL Chi-restraints excluded: chain J residue 414 GLU Chi-restraints excluded: chain J residue 443 LEU Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 133 MET Chi-restraints excluded: chain K residue 157 ASN Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 201 VAL Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 446 VAL Chi-restraints excluded: chain K residue 447 ILE Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 120 CYS Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 145 ILE Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 311 ASP Chi-restraints excluded: chain L residue 456 ASP Chi-restraints excluded: chain L residue 503 ILE Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 62 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 151 ILE Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 221 ASP Chi-restraints excluded: chain M residue 307 ASP Chi-restraints excluded: chain M residue 485 MET Chi-restraints excluded: chain M residue 493 CYS Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain N residue 69 ILE Chi-restraints excluded: chain N residue 82 THR Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain N residue 213 ASP Chi-restraints excluded: chain N residue 214 HIS Chi-restraints excluded: chain N residue 302 LEU Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 354 THR Chi-restraints excluded: chain N residue 371 SER Chi-restraints excluded: chain N residue 467 GLN Chi-restraints excluded: chain N residue 479 VAL Chi-restraints excluded: chain N residue 487 MET Chi-restraints excluded: chain O residue 17 GLN Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain O residue 120 ILE Chi-restraints excluded: chain O residue 149 VAL Chi-restraints excluded: chain O residue 165 SER Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain O residue 188 ASP Chi-restraints excluded: chain O residue 242 VAL Chi-restraints excluded: chain O residue 329 SER Chi-restraints excluded: chain O residue 334 VAL Chi-restraints excluded: chain O residue 362 THR Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain O residue 515 SER Chi-restraints excluded: chain P residue 65 VAL Chi-restraints excluded: chain P residue 72 ILE Chi-restraints excluded: chain P residue 76 LEU Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 166 THR Chi-restraints excluded: chain P residue 204 VAL Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain P residue 381 THR Chi-restraints excluded: chain P residue 417 ILE Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain P residue 441 PHE Chi-restraints excluded: chain P residue 478 VAL Chi-restraints excluded: chain P residue 521 VAL Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain R residue 71 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 867 random chunks: chunk 281 optimal weight: 9.9990 chunk 754 optimal weight: 0.9990 chunk 165 optimal weight: 0.8980 chunk 492 optimal weight: 5.9990 chunk 206 optimal weight: 0.8980 chunk 838 optimal weight: 6.9990 chunk 696 optimal weight: 0.6980 chunk 388 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 277 optimal weight: 7.9990 chunk 440 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 GLN ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 HIS D 502 ASN ** E 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 317 ASN F 460 GLN ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 534 HIS ** J 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 510 GLN M 291 GLN N 346 HIS O 151 GLN ** P 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 68425 Z= 0.156 Angle : 0.556 10.544 92396 Z= 0.271 Chirality : 0.041 0.361 10998 Planarity : 0.003 0.054 11789 Dihedral : 7.262 144.461 9484 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.25 % Favored : 94.71 % Rotamer: Outliers : 2.43 % Allowed : 18.71 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.09), residues: 8727 helix: 1.43 (0.08), residues: 4412 sheet: -0.48 (0.17), residues: 1078 loop : -1.20 (0.11), residues: 3237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 485 HIS 0.022 0.001 HIS C 470 PHE 0.019 0.001 PHE Q 167 TYR 0.017 0.001 TYR M 420 ARG 0.006 0.000 ARG K 316 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1191 residues out of total 7331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 1013 time to evaluate : 5.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8123 (mm) REVERT: C 219 MET cc_start: 0.7449 (tmm) cc_final: 0.7230 (ttp) REVERT: C 246 GLU cc_start: 0.6261 (OUTLIER) cc_final: 0.5960 (pt0) REVERT: C 282 ILE cc_start: 0.8603 (tp) cc_final: 0.8326 (tp) REVERT: C 293 GLU cc_start: 0.7257 (tt0) cc_final: 0.6937 (mt-10) REVERT: D 57 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7900 (mmm) REVERT: D 141 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8191 (tp) REVERT: D 458 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7390 (mtm) REVERT: D 503 ILE cc_start: 0.8036 (mm) cc_final: 0.7817 (mm) REVERT: E 231 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7973 (p0) REVERT: F 132 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.6640 (mt0) REVERT: G 48 LEU cc_start: 0.8208 (tt) cc_final: 0.7962 (tt) REVERT: G 307 ASP cc_start: 0.7204 (OUTLIER) cc_final: 0.6978 (m-30) REVERT: H 92 MET cc_start: 0.7744 (tpp) cc_final: 0.7413 (tpp) REVERT: H 509 LYS cc_start: 0.8690 (ttmm) cc_final: 0.8479 (ttmt) REVERT: J 202 ILE cc_start: 0.8569 (mt) cc_final: 0.8351 (mt) REVERT: J 475 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8214 (m) REVERT: K 104 GLU cc_start: 0.6543 (mm-30) cc_final: 0.6163 (tp30) REVERT: M 288 MET cc_start: 0.5894 (ttm) cc_final: 0.5649 (ttp) REVERT: O 331 GLN cc_start: 0.7219 (OUTLIER) cc_final: 0.6846 (mp10) REVERT: P 34 GLN cc_start: 0.8101 (tp-100) cc_final: 0.7590 (tp-100) REVERT: P 436 TYR cc_start: 0.8213 (m-10) cc_final: 0.7820 (m-80) REVERT: P 441 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.7526 (m-80) REVERT: Q 51 MET cc_start: 0.6618 (mtp) cc_final: 0.6323 (mtt) REVERT: Q 86 LYS cc_start: 0.4636 (mmpt) cc_final: 0.4385 (mmtt) REVERT: Q 88 LYS cc_start: 0.6534 (tptp) cc_final: 0.6236 (tptp) REVERT: Q 124 ILE cc_start: 0.2746 (OUTLIER) cc_final: 0.2370 (tp) REVERT: Q 175 LYS cc_start: 0.4415 (tptm) cc_final: 0.4189 (tptm) REVERT: Q 179 ILE cc_start: 0.6787 (mm) cc_final: 0.6514 (mt) outliers start: 178 outliers final: 128 residues processed: 1132 average time/residue: 0.6314 time to fit residues: 1228.5947 Evaluate side-chains 1071 residues out of total 7331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 931 time to evaluate : 5.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 132 GLN Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 380 ASN Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 522 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 307 ASP Chi-restraints excluded: chain G residue 317 GLU Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain H residue 230 ASP Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 252 VAL Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain I residue 415 VAL Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 289 CYS Chi-restraints excluded: chain J residue 414 GLU Chi-restraints excluded: chain J residue 443 LEU Chi-restraints excluded: chain J residue 475 THR Chi-restraints excluded: chain K residue 133 MET Chi-restraints excluded: chain K residue 157 ASN Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 364 THR Chi-restraints excluded: chain K residue 447 ILE Chi-restraints excluded: chain K residue 455 CYS Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain L residue 120 CYS Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 311 ASP Chi-restraints excluded: chain L residue 429 GLU Chi-restraints excluded: chain L residue 443 LEU Chi-restraints excluded: chain L residue 456 ASP Chi-restraints excluded: chain L residue 535 VAL Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 62 VAL Chi-restraints excluded: chain M residue 151 ILE Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 307 ASP Chi-restraints excluded: chain M residue 362 ILE Chi-restraints excluded: chain M residue 372 LEU Chi-restraints excluded: chain M residue 493 CYS Chi-restraints excluded: chain N residue 53 ASP Chi-restraints excluded: chain N residue 65 HIS Chi-restraints excluded: chain N residue 69 ILE Chi-restraints excluded: chain N residue 82 THR Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain N residue 179 ILE Chi-restraints excluded: chain N residue 213 ASP Chi-restraints excluded: chain N residue 214 HIS Chi-restraints excluded: chain N residue 302 LEU Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 354 THR Chi-restraints excluded: chain N residue 371 SER Chi-restraints excluded: chain N residue 479 VAL Chi-restraints excluded: chain N residue 487 MET Chi-restraints excluded: chain O residue 17 GLN Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain O residue 120 ILE Chi-restraints excluded: chain O residue 165 SER Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain O residue 188 ASP Chi-restraints excluded: chain O residue 242 VAL Chi-restraints excluded: chain O residue 331 GLN Chi-restraints excluded: chain O residue 334 VAL Chi-restraints excluded: chain O residue 362 THR Chi-restraints excluded: chain P residue 65 VAL Chi-restraints excluded: chain P residue 72 ILE Chi-restraints excluded: chain P residue 76 LEU Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 166 THR Chi-restraints excluded: chain P residue 204 VAL Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain P residue 381 THR Chi-restraints excluded: chain P residue 401 VAL Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain P residue 441 PHE Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 205 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 867 random chunks: chunk 808 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 477 optimal weight: 0.1980 chunk 612 optimal weight: 4.9990 chunk 474 optimal weight: 0.7980 chunk 706 optimal weight: 7.9990 chunk 468 optimal weight: 7.9990 chunk 835 optimal weight: 5.9990 chunk 522 optimal weight: 0.8980 chunk 509 optimal weight: 0.8980 chunk 385 optimal weight: 7.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 400 ASN C 470 HIS ** E 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 193 ASN I 534 HIS ** J 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 504 GLN N 346 HIS O 151 GLN ** P 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 68425 Z= 0.192 Angle : 0.568 9.905 92396 Z= 0.276 Chirality : 0.042 0.214 10998 Planarity : 0.003 0.054 11789 Dihedral : 7.176 145.031 9484 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.43 % Favored : 94.52 % Rotamer: Outliers : 2.63 % Allowed : 19.14 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.09), residues: 8727 helix: 1.43 (0.08), residues: 4414 sheet: -0.48 (0.16), residues: 1083 loop : -1.19 (0.11), residues: 3230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP I 485 HIS 0.011 0.001 HIS C 470 PHE 0.019 0.001 PHE Q 167 TYR 0.018 0.001 TYR M 420 ARG 0.007 0.000 ARG F 523 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1145 residues out of total 7331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 952 time to evaluate : 5.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 GLU cc_start: 0.7410 (tm-30) cc_final: 0.7184 (tm-30) REVERT: C 219 MET cc_start: 0.7481 (tmm) cc_final: 0.7257 (ttp) REVERT: C 246 GLU cc_start: 0.6249 (OUTLIER) cc_final: 0.5923 (pt0) REVERT: C 293 GLU cc_start: 0.7290 (tt0) cc_final: 0.6973 (mt-10) REVERT: D 57 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7890 (mmm) REVERT: D 141 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8144 (tp) REVERT: D 458 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7346 (mtm) REVERT: E 231 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7973 (p0) REVERT: F 132 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.6665 (mt0) REVERT: G 48 LEU cc_start: 0.8220 (tt) cc_final: 0.7975 (tt) REVERT: G 307 ASP cc_start: 0.7294 (OUTLIER) cc_final: 0.6941 (m-30) REVERT: H 92 MET cc_start: 0.7850 (tpp) cc_final: 0.7437 (tpp) REVERT: H 509 LYS cc_start: 0.8695 (ttmm) cc_final: 0.8494 (ttmt) REVERT: I 53 THR cc_start: 0.8982 (OUTLIER) cc_final: 0.8697 (p) REVERT: J 202 ILE cc_start: 0.8579 (mt) cc_final: 0.8362 (mt) REVERT: J 475 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8224 (m) REVERT: K 104 GLU cc_start: 0.6574 (mm-30) cc_final: 0.6177 (tp30) REVERT: O 194 MET cc_start: 0.7214 (mmp) cc_final: 0.6981 (mmp) REVERT: O 331 GLN cc_start: 0.7242 (OUTLIER) cc_final: 0.6873 (mp10) REVERT: P 34 GLN cc_start: 0.8140 (tp-100) cc_final: 0.7630 (tp-100) REVERT: P 57 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8279 (mm) REVERT: P 436 TYR cc_start: 0.8151 (m-10) cc_final: 0.7754 (m-80) REVERT: P 441 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7560 (m-80) REVERT: Q 51 MET cc_start: 0.6630 (mtp) cc_final: 0.6368 (mtt) REVERT: Q 124 ILE cc_start: 0.2711 (OUTLIER) cc_final: 0.2285 (tp) REVERT: Q 179 ILE cc_start: 0.6852 (mm) cc_final: 0.6598 (mt) outliers start: 193 outliers final: 157 residues processed: 1088 average time/residue: 0.6461 time to fit residues: 1212.1084 Evaluate side-chains 1085 residues out of total 7331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 915 time to evaluate : 5.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 40 LYS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 132 GLN Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 380 ASN Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 522 MET Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 307 ASP Chi-restraints excluded: chain G residue 317 GLU Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain H residue 230 ASP Chi-restraints excluded: chain H residue 355 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 48 ASP Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 193 ASN Chi-restraints excluded: chain I residue 252 VAL Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain I residue 415 VAL Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 289 CYS Chi-restraints excluded: chain J residue 414 GLU Chi-restraints excluded: chain J residue 443 LEU Chi-restraints excluded: chain J residue 475 THR Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 133 MET Chi-restraints excluded: chain K residue 201 VAL Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 364 THR Chi-restraints excluded: chain K residue 444 LEU Chi-restraints excluded: chain K residue 446 VAL Chi-restraints excluded: chain K residue 447 ILE Chi-restraints excluded: chain K residue 455 CYS Chi-restraints excluded: chain K residue 470 HIS Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain L residue 120 CYS Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 311 ASP Chi-restraints excluded: chain L residue 429 GLU Chi-restraints excluded: chain L residue 443 LEU Chi-restraints excluded: chain L residue 456 ASP Chi-restraints excluded: chain L residue 503 ILE Chi-restraints excluded: chain L residue 535 VAL Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 62 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 151 ILE Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 307 ASP Chi-restraints excluded: chain M residue 362 ILE Chi-restraints excluded: chain M residue 372 LEU Chi-restraints excluded: chain M residue 493 CYS Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 65 HIS Chi-restraints excluded: chain N residue 69 ILE Chi-restraints excluded: chain N residue 82 THR Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain N residue 213 ASP Chi-restraints excluded: chain N residue 214 HIS Chi-restraints excluded: chain N residue 302 LEU Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 354 THR Chi-restraints excluded: chain N residue 371 SER Chi-restraints excluded: chain N residue 479 VAL Chi-restraints excluded: chain N residue 487 MET Chi-restraints excluded: chain O residue 17 GLN Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain O residue 120 ILE Chi-restraints excluded: chain O residue 149 VAL Chi-restraints excluded: chain O residue 165 SER Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain O residue 242 VAL Chi-restraints excluded: chain O residue 329 SER Chi-restraints excluded: chain O residue 331 GLN Chi-restraints excluded: chain O residue 334 VAL Chi-restraints excluded: chain O residue 362 THR Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain P residue 65 VAL Chi-restraints excluded: chain P residue 72 ILE Chi-restraints excluded: chain P residue 76 LEU Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 166 THR Chi-restraints excluded: chain P residue 204 VAL Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain P residue 333 LEU Chi-restraints excluded: chain P residue 355 VAL Chi-restraints excluded: chain P residue 381 THR Chi-restraints excluded: chain P residue 401 VAL Chi-restraints excluded: chain P residue 417 ILE Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain P residue 441 PHE Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 152 THR Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 205 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 867 random chunks: chunk 516 optimal weight: 8.9990 chunk 333 optimal weight: 4.9990 chunk 499 optimal weight: 5.9990 chunk 251 optimal weight: 0.7980 chunk 164 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 chunk 531 optimal weight: 0.7980 chunk 569 optimal weight: 4.9990 chunk 413 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 656 optimal weight: 10.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 470 HIS ** E 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 481 ASN ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 193 ASN ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 534 HIS ** J 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 346 HIS O 151 GLN ** P 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 68425 Z= 0.280 Angle : 0.610 9.430 92396 Z= 0.298 Chirality : 0.044 0.222 10998 Planarity : 0.004 0.054 11789 Dihedral : 7.261 144.346 9484 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.06 % Favored : 93.88 % Rotamer: Outliers : 3.06 % Allowed : 19.21 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.09), residues: 8727 helix: 1.33 (0.08), residues: 4412 sheet: -0.51 (0.16), residues: 1106 loop : -1.27 (0.11), residues: 3209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP I 485 HIS 0.022 0.001 HIS C 470 PHE 0.017 0.001 PHE Q 167 TYR 0.021 0.001 TYR M 420 ARG 0.007 0.000 ARG F 523 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1136 residues out of total 7331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 912 time to evaluate : 5.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 ASP cc_start: 0.7176 (m-30) cc_final: 0.6755 (m-30) REVERT: C 104 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7379 (tm-30) REVERT: C 219 MET cc_start: 0.7523 (tmm) cc_final: 0.7323 (ttp) REVERT: C 246 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.6004 (pt0) REVERT: D 141 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8176 (tp) REVERT: D 458 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7407 (mtm) REVERT: E 231 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.8021 (p0) REVERT: F 132 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.6729 (mt0) REVERT: F 214 HIS cc_start: 0.6934 (OUTLIER) cc_final: 0.6392 (m90) REVERT: G 48 LEU cc_start: 0.8227 (tt) cc_final: 0.7972 (tt) REVERT: G 194 MET cc_start: 0.7406 (mmp) cc_final: 0.7204 (mmp) REVERT: G 307 ASP cc_start: 0.7329 (OUTLIER) cc_final: 0.6967 (m-30) REVERT: G 503 LEU cc_start: 0.8451 (mt) cc_final: 0.8202 (mt) REVERT: H 92 MET cc_start: 0.7887 (tpp) cc_final: 0.7438 (tpp) REVERT: H 292 VAL cc_start: 0.8249 (OUTLIER) cc_final: 0.7976 (t) REVERT: H 311 MET cc_start: 0.7412 (ttm) cc_final: 0.7100 (ttm) REVERT: I 53 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8697 (p) REVERT: J 202 ILE cc_start: 0.8561 (mt) cc_final: 0.8304 (mt) REVERT: J 475 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8248 (m) REVERT: K 104 GLU cc_start: 0.6587 (mm-30) cc_final: 0.6190 (tp30) REVERT: K 416 MET cc_start: 0.8186 (mmt) cc_final: 0.7884 (mmt) REVERT: M 288 MET cc_start: 0.5993 (ttp) cc_final: 0.5617 (ttp) REVERT: N 467 GLN cc_start: 0.7641 (mp10) cc_final: 0.7344 (mt0) REVERT: O 331 GLN cc_start: 0.7242 (OUTLIER) cc_final: 0.6919 (mp10) REVERT: P 34 GLN cc_start: 0.8172 (tp-100) cc_final: 0.7694 (tp-100) REVERT: P 57 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8345 (mm) REVERT: P 436 TYR cc_start: 0.8239 (m-10) cc_final: 0.7832 (m-80) REVERT: P 441 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7710 (m-80) REVERT: Q 124 ILE cc_start: 0.2703 (OUTLIER) cc_final: 0.2295 (tp) REVERT: Q 179 ILE cc_start: 0.6856 (mm) cc_final: 0.6621 (mt) outliers start: 224 outliers final: 183 residues processed: 1064 average time/residue: 0.6399 time to fit residues: 1175.6786 Evaluate side-chains 1095 residues out of total 7331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 898 time to evaluate : 5.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 132 GLN Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 214 HIS Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 380 ASN Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 522 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 307 ASP Chi-restraints excluded: chain G residue 317 GLU Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain H residue 230 ASP Chi-restraints excluded: chain H residue 292 VAL Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 355 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 417 ILE Chi-restraints excluded: chain H residue 458 VAL Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 48 ASP Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 192 VAL Chi-restraints excluded: chain I residue 193 ASN Chi-restraints excluded: chain I residue 252 VAL Chi-restraints excluded: chain I residue 288 THR Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain I residue 415 VAL Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 244 MET Chi-restraints excluded: chain J residue 289 CYS Chi-restraints excluded: chain J residue 294 GLN Chi-restraints excluded: chain J residue 379 THR Chi-restraints excluded: chain J residue 396 VAL Chi-restraints excluded: chain J residue 414 GLU Chi-restraints excluded: chain J residue 443 LEU Chi-restraints excluded: chain J residue 475 THR Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 201 VAL Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 364 THR Chi-restraints excluded: chain K residue 444 LEU Chi-restraints excluded: chain K residue 446 VAL Chi-restraints excluded: chain K residue 447 ILE Chi-restraints excluded: chain K residue 455 CYS Chi-restraints excluded: chain K residue 464 THR Chi-restraints excluded: chain K residue 470 HIS Chi-restraints excluded: chain K residue 471 THR Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 120 CYS Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 311 ASP Chi-restraints excluded: chain L residue 429 GLU Chi-restraints excluded: chain L residue 443 LEU Chi-restraints excluded: chain L residue 456 ASP Chi-restraints excluded: chain L residue 503 ILE Chi-restraints excluded: chain L residue 535 VAL Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 62 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 151 ILE Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 307 ASP Chi-restraints excluded: chain M residue 358 LEU Chi-restraints excluded: chain M residue 362 ILE Chi-restraints excluded: chain M residue 372 LEU Chi-restraints excluded: chain M residue 485 MET Chi-restraints excluded: chain M residue 493 CYS Chi-restraints excluded: chain M residue 509 THR Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 69 ILE Chi-restraints excluded: chain N residue 82 THR Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain N residue 213 ASP Chi-restraints excluded: chain N residue 214 HIS Chi-restraints excluded: chain N residue 302 LEU Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 354 THR Chi-restraints excluded: chain N residue 371 SER Chi-restraints excluded: chain N residue 479 VAL Chi-restraints excluded: chain N residue 487 MET Chi-restraints excluded: chain O residue 17 GLN Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain O residue 120 ILE Chi-restraints excluded: chain O residue 149 VAL Chi-restraints excluded: chain O residue 165 SER Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 242 VAL Chi-restraints excluded: chain O residue 329 SER Chi-restraints excluded: chain O residue 331 GLN Chi-restraints excluded: chain O residue 334 VAL Chi-restraints excluded: chain O residue 362 THR Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain O residue 515 SER Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain P residue 65 VAL Chi-restraints excluded: chain P residue 72 ILE Chi-restraints excluded: chain P residue 76 LEU Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 166 THR Chi-restraints excluded: chain P residue 204 VAL Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain P residue 333 LEU Chi-restraints excluded: chain P residue 355 VAL Chi-restraints excluded: chain P residue 381 THR Chi-restraints excluded: chain P residue 401 VAL Chi-restraints excluded: chain P residue 417 ILE Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain P residue 441 PHE Chi-restraints excluded: chain P residue 478 VAL Chi-restraints excluded: chain P residue 521 VAL Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 152 THR Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 174 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 867 random chunks: chunk 760 optimal weight: 7.9990 chunk 800 optimal weight: 3.9990 chunk 730 optimal weight: 3.9990 chunk 778 optimal weight: 8.9990 chunk 468 optimal weight: 9.9990 chunk 339 optimal weight: 6.9990 chunk 611 optimal weight: 0.9990 chunk 238 optimal weight: 0.9990 chunk 703 optimal weight: 6.9990 chunk 736 optimal weight: 0.7980 chunk 775 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 470 HIS ** E 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 534 HIS ** J 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 346 HIS O 151 GLN ** P 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 68425 Z= 0.231 Angle : 0.593 10.351 92396 Z= 0.289 Chirality : 0.043 0.280 10998 Planarity : 0.004 0.067 11789 Dihedral : 7.178 147.643 9484 Min Nonbonded Distance : 1.687 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.79 % Favored : 94.16 % Rotamer: Outliers : 2.80 % Allowed : 19.75 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.09), residues: 8727 helix: 1.34 (0.08), residues: 4413 sheet: -0.51 (0.16), residues: 1078 loop : -1.25 (0.11), residues: 3236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP I 485 HIS 0.012 0.001 HIS C 470 PHE 0.017 0.001 PHE Q 167 TYR 0.020 0.001 TYR M 420 ARG 0.007 0.000 ARG F 523 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1137 residues out of total 7331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 932 time to evaluate : 5.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 ASP cc_start: 0.7170 (m-30) cc_final: 0.6753 (m-30) REVERT: C 104 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7165 (tm-30) REVERT: C 219 MET cc_start: 0.7488 (tmm) cc_final: 0.7135 (ttt) REVERT: C 246 GLU cc_start: 0.6300 (OUTLIER) cc_final: 0.5971 (pt0) REVERT: D 141 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8171 (tp) REVERT: D 458 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7409 (mtm) REVERT: E 80 MET cc_start: 0.8286 (mtm) cc_final: 0.7661 (mtt) REVERT: E 231 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7995 (p0) REVERT: F 132 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.6706 (mt0) REVERT: G 48 LEU cc_start: 0.8224 (tt) cc_final: 0.7977 (tt) REVERT: G 307 ASP cc_start: 0.7238 (OUTLIER) cc_final: 0.7006 (m-30) REVERT: H 92 MET cc_start: 0.7866 (tpp) cc_final: 0.7422 (tpp) REVERT: H 292 VAL cc_start: 0.8240 (OUTLIER) cc_final: 0.7972 (t) REVERT: I 53 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8685 (p) REVERT: J 202 ILE cc_start: 0.8563 (mt) cc_final: 0.8331 (mt) REVERT: J 321 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6953 (mt-10) REVERT: J 475 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8247 (m) REVERT: K 104 GLU cc_start: 0.6649 (mm-30) cc_final: 0.6237 (tp30) REVERT: L 307 ASP cc_start: 0.6478 (OUTLIER) cc_final: 0.6256 (p0) REVERT: M 221 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7403 (m-30) REVERT: N 467 GLN cc_start: 0.7663 (mp10) cc_final: 0.7399 (mt0) REVERT: O 194 MET cc_start: 0.7226 (mmp) cc_final: 0.6961 (mmp) REVERT: O 228 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8839 (pt0) REVERT: O 331 GLN cc_start: 0.7234 (OUTLIER) cc_final: 0.6917 (mp10) REVERT: P 34 GLN cc_start: 0.8141 (tp-100) cc_final: 0.7664 (tp-100) REVERT: P 436 TYR cc_start: 0.8230 (m-10) cc_final: 0.7825 (m-80) REVERT: P 441 PHE cc_start: 0.8074 (OUTLIER) cc_final: 0.7708 (m-80) REVERT: Q 51 MET cc_start: 0.6027 (mtt) cc_final: 0.5680 (mtm) REVERT: Q 124 ILE cc_start: 0.2703 (OUTLIER) cc_final: 0.2284 (tp) REVERT: Q 179 ILE cc_start: 0.6792 (mm) cc_final: 0.6536 (mt) outliers start: 205 outliers final: 176 residues processed: 1073 average time/residue: 0.6428 time to fit residues: 1192.1710 Evaluate side-chains 1099 residues out of total 7331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 908 time to evaluate : 5.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 132 GLN Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 380 ASN Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 522 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 194 MET Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 307 ASP Chi-restraints excluded: chain G residue 317 GLU Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain H residue 230 ASP Chi-restraints excluded: chain H residue 292 VAL Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 355 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 417 ILE Chi-restraints excluded: chain H residue 458 VAL Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 48 ASP Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 252 VAL Chi-restraints excluded: chain I residue 288 THR Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain I residue 415 VAL Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 289 CYS Chi-restraints excluded: chain J residue 294 GLN Chi-restraints excluded: chain J residue 414 GLU Chi-restraints excluded: chain J residue 443 LEU Chi-restraints excluded: chain J residue 475 THR Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 157 ASN Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 201 VAL Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 364 THR Chi-restraints excluded: chain K residue 444 LEU Chi-restraints excluded: chain K residue 446 VAL Chi-restraints excluded: chain K residue 447 ILE Chi-restraints excluded: chain K residue 455 CYS Chi-restraints excluded: chain K residue 464 THR Chi-restraints excluded: chain K residue 470 HIS Chi-restraints excluded: chain K residue 471 THR Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain L residue 120 CYS Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 307 ASP Chi-restraints excluded: chain L residue 311 ASP Chi-restraints excluded: chain L residue 429 GLU Chi-restraints excluded: chain L residue 456 ASP Chi-restraints excluded: chain L residue 503 ILE Chi-restraints excluded: chain L residue 535 VAL Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 62 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 151 ILE Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 221 ASP Chi-restraints excluded: chain M residue 307 ASP Chi-restraints excluded: chain M residue 358 LEU Chi-restraints excluded: chain M residue 362 ILE Chi-restraints excluded: chain M residue 372 LEU Chi-restraints excluded: chain M residue 485 MET Chi-restraints excluded: chain M residue 493 CYS Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 69 ILE Chi-restraints excluded: chain N residue 82 THR Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain N residue 213 ASP Chi-restraints excluded: chain N residue 214 HIS Chi-restraints excluded: chain N residue 302 LEU Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 354 THR Chi-restraints excluded: chain N residue 371 SER Chi-restraints excluded: chain N residue 479 VAL Chi-restraints excluded: chain N residue 487 MET Chi-restraints excluded: chain O residue 17 GLN Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain O residue 120 ILE Chi-restraints excluded: chain O residue 149 VAL Chi-restraints excluded: chain O residue 165 SER Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 228 GLN Chi-restraints excluded: chain O residue 242 VAL Chi-restraints excluded: chain O residue 329 SER Chi-restraints excluded: chain O residue 331 GLN Chi-restraints excluded: chain O residue 334 VAL Chi-restraints excluded: chain O residue 362 THR Chi-restraints excluded: chain O residue 405 VAL Chi-restraints excluded: chain O residue 515 SER Chi-restraints excluded: chain P residue 65 VAL Chi-restraints excluded: chain P residue 72 ILE Chi-restraints excluded: chain P residue 76 LEU Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 166 THR Chi-restraints excluded: chain P residue 204 VAL Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain P residue 333 LEU Chi-restraints excluded: chain P residue 355 VAL Chi-restraints excluded: chain P residue 381 THR Chi-restraints excluded: chain P residue 401 VAL Chi-restraints excluded: chain P residue 417 ILE Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain P residue 441 PHE Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 152 THR Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 174 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 867 random chunks: chunk 511 optimal weight: 0.8980 chunk 823 optimal weight: 1.9990 chunk 502 optimal weight: 0.9980 chunk 390 optimal weight: 6.9990 chunk 572 optimal weight: 6.9990 chunk 863 optimal weight: 7.9990 chunk 794 optimal weight: 0.0870 chunk 687 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 531 optimal weight: 0.8980 chunk 421 optimal weight: 7.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 HIS ** E 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 193 ASN I 534 HIS ** J 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 453 ASN M 376 GLN N 346 HIS O 151 GLN ** P 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 68425 Z= 0.164 Angle : 0.571 13.785 92396 Z= 0.277 Chirality : 0.042 0.439 10998 Planarity : 0.003 0.058 11789 Dihedral : 6.993 152.597 9484 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.25 % Favored : 94.69 % Rotamer: Outliers : 2.47 % Allowed : 20.16 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.09), residues: 8727 helix: 1.45 (0.08), residues: 4407 sheet: -0.42 (0.17), residues: 1067 loop : -1.18 (0.11), residues: 3253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP I 485 HIS 0.027 0.001 HIS C 470 PHE 0.019 0.001 PHE Q 167 TYR 0.019 0.001 TYR N 239 ARG 0.007 0.000 ARG F 523 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17454 Ramachandran restraints generated. 8727 Oldfield, 0 Emsley, 8727 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1149 residues out of total 7331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 968 time to evaluate : 5.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 GLU cc_start: 0.7387 (tm-30) cc_final: 0.7028 (tm-30) REVERT: C 246 GLU cc_start: 0.6181 (OUTLIER) cc_final: 0.5915 (pt0) REVERT: D 141 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8195 (tp) REVERT: D 320 MET cc_start: 0.7407 (mtt) cc_final: 0.7187 (mtt) REVERT: D 458 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.7376 (mtm) REVERT: E 80 MET cc_start: 0.8239 (mtm) cc_final: 0.7790 (mtt) REVERT: E 231 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.8008 (p0) REVERT: F 132 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.6518 (mp10) REVERT: G 48 LEU cc_start: 0.8203 (tt) cc_final: 0.7957 (tt) REVERT: H 92 MET cc_start: 0.7847 (tpp) cc_final: 0.7441 (tpp) REVERT: H 292 VAL cc_start: 0.8012 (OUTLIER) cc_final: 0.7756 (t) REVERT: I 53 THR cc_start: 0.8971 (OUTLIER) cc_final: 0.8636 (p) REVERT: J 202 ILE cc_start: 0.8558 (mt) cc_final: 0.8330 (mt) REVERT: J 321 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6950 (mt-10) REVERT: J 475 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8239 (m) REVERT: K 104 GLU cc_start: 0.6566 (mm-30) cc_final: 0.6173 (tp30) REVERT: L 307 ASP cc_start: 0.6426 (OUTLIER) cc_final: 0.6213 (p0) REVERT: M 288 MET cc_start: 0.5966 (ttp) cc_final: 0.5575 (ttp) REVERT: N 467 GLN cc_start: 0.7628 (mp10) cc_final: 0.7410 (mt0) REVERT: O 184 MET cc_start: 0.7822 (mmt) cc_final: 0.7498 (mmt) REVERT: O 228 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.8777 (pt0) REVERT: O 331 GLN cc_start: 0.7263 (OUTLIER) cc_final: 0.6926 (mp10) REVERT: P 34 GLN cc_start: 0.8110 (tp-100) cc_final: 0.7598 (tp-100) REVERT: P 436 TYR cc_start: 0.8168 (m-10) cc_final: 0.7771 (m-80) REVERT: P 441 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.7591 (m-80) REVERT: Q 51 MET cc_start: 0.5940 (mtt) cc_final: 0.5575 (mtm) REVERT: Q 124 ILE cc_start: 0.2674 (OUTLIER) cc_final: 0.2256 (tp) REVERT: Q 179 ILE cc_start: 0.6780 (mm) cc_final: 0.6518 (mt) outliers start: 181 outliers final: 155 residues processed: 1093 average time/residue: 0.6401 time to fit residues: 1206.3897 Evaluate side-chains 1101 residues out of total 7331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 933 time to evaluate : 5.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 408 VAL Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 132 GLN Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 380 ASN Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 522 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 194 MET Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 317 GLU Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain H residue 230 ASP Chi-restraints excluded: chain H residue 292 VAL Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 355 VAL Chi-restraints excluded: chain H residue 376 VAL Chi-restraints excluded: chain H residue 458 VAL Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 252 VAL Chi-restraints excluded: chain I residue 288 THR Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain I residue 415 VAL Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 289 CYS Chi-restraints excluded: chain J residue 414 GLU Chi-restraints excluded: chain J residue 443 LEU Chi-restraints excluded: chain J residue 475 THR Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 157 ASN Chi-restraints excluded: chain K residue 201 VAL Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 364 THR Chi-restraints excluded: chain K residue 444 LEU Chi-restraints excluded: chain K residue 447 ILE Chi-restraints excluded: chain K residue 455 CYS Chi-restraints excluded: chain K residue 471 THR Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain L residue 120 CYS Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 223 LEU Chi-restraints excluded: chain L residue 307 ASP Chi-restraints excluded: chain L residue 311 ASP Chi-restraints excluded: chain L residue 429 GLU Chi-restraints excluded: chain L residue 456 ASP Chi-restraints excluded: chain L residue 535 VAL Chi-restraints excluded: chain M residue 62 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain M residue 307 ASP Chi-restraints excluded: chain M residue 358 LEU Chi-restraints excluded: chain M residue 362 ILE Chi-restraints excluded: chain M residue 372 LEU Chi-restraints excluded: chain M residue 493 CYS Chi-restraints excluded: chain M residue 509 THR Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 69 ILE Chi-restraints excluded: chain N residue 82 THR Chi-restraints excluded: chain N residue 118 ILE Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 149 ILE Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain N residue 213 ASP Chi-restraints excluded: chain N residue 214 HIS Chi-restraints excluded: chain N residue 302 LEU Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 354 THR Chi-restraints excluded: chain N residue 371 SER Chi-restraints excluded: chain N residue 479 VAL Chi-restraints excluded: chain N residue 487 MET Chi-restraints excluded: chain O residue 17 GLN Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain O residue 120 ILE Chi-restraints excluded: chain O residue 149 VAL Chi-restraints excluded: chain O residue 165 SER Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 228 GLN Chi-restraints excluded: chain O residue 242 VAL Chi-restraints excluded: chain O residue 329 SER Chi-restraints excluded: chain O residue 331 GLN Chi-restraints excluded: chain O residue 334 VAL Chi-restraints excluded: chain O residue 362 THR Chi-restraints excluded: chain P residue 65 VAL Chi-restraints excluded: chain P residue 72 ILE Chi-restraints excluded: chain P residue 76 LEU Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain P residue 166 THR Chi-restraints excluded: chain P residue 204 VAL Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain P residue 333 LEU Chi-restraints excluded: chain P residue 355 VAL Chi-restraints excluded: chain P residue 381 THR Chi-restraints excluded: chain P residue 401 VAL Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain P residue 441 PHE Chi-restraints excluded: chain P residue 521 VAL Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 152 THR Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 174 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 867 random chunks: chunk 546 optimal weight: 1.9990 chunk 732 optimal weight: 2.9990 chunk 210 optimal weight: 0.7980 chunk 634 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 191 optimal weight: 6.9990 chunk 688 optimal weight: 0.6980 chunk 288 optimal weight: 0.9990 chunk 707 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 126 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 HIS ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 534 HIS ** J 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 453 ASN ** M 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 346 HIS O 151 GLN ** P 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 59 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.144435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.129550 restraints weight = 98879.163| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.88 r_work: 0.3424 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 68425 Z= 0.160 Angle : 0.569 12.988 92396 Z= 0.276 Chirality : 0.042 0.376 10998 Planarity : 0.003 0.054 11789 Dihedral : 6.888 153.953 9484 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.93 % Favored : 95.02 % Rotamer: Outliers : 2.42 % Allowed : 20.30 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.09), residues: 8727 helix: 1.50 (0.08), residues: 4404 sheet: -0.41 (0.16), residues: 1086 loop : -1.14 (0.11), residues: 3237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP I 485 HIS 0.018 0.001 HIS C 470 PHE 0.019 0.001 PHE Q 167 TYR 0.017 0.001 TYR D 282 ARG 0.007 0.000 ARG A 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17751.68 seconds wall clock time: 312 minutes 48.89 seconds (18768.89 seconds total)