Starting phenix.real_space_refine on Sun Mar 24 02:36:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vcf_31890/03_2024/7vcf_31890_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vcf_31890/03_2024/7vcf_31890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vcf_31890/03_2024/7vcf_31890.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vcf_31890/03_2024/7vcf_31890.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vcf_31890/03_2024/7vcf_31890_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vcf_31890/03_2024/7vcf_31890_updated.pdb" } resolution = 2.5 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= 0.037 sd= 0.144 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 33 5.49 5 Mg 2 5.21 5 S 139 5.16 5 C 25298 2.51 5 N 6868 2.21 5 O 7286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 136": "NH1" <-> "NH2" Residue "A ARG 375": "NH1" <-> "NH2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A ARG 421": "NH1" <-> "NH2" Residue "A ARG 469": "NH1" <-> "NH2" Residue "A PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 620": "NH1" <-> "NH2" Residue "A ARG 662": "NH1" <-> "NH2" Residue "A ARG 735": "NH1" <-> "NH2" Residue "A ARG 744": "NH1" <-> "NH2" Residue "A ARG 752": "NH1" <-> "NH2" Residue "A ARG 819": "NH1" <-> "NH2" Residue "A ARG 839": "NH1" <-> "NH2" Residue "A PHE 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 865": "NH1" <-> "NH2" Residue "A ARG 871": "NH1" <-> "NH2" Residue "A PHE 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 876": "OE1" <-> "OE2" Residue "A ARG 920": "NH1" <-> "NH2" Residue "A ARG 1076": "NH1" <-> "NH2" Residue "A GLU 1090": "OE1" <-> "OE2" Residue "A GLU 1096": "OE1" <-> "OE2" Residue "A ARG 1236": "NH1" <-> "NH2" Residue "A ARG 1251": "NH1" <-> "NH2" Residue "A PHE 1254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1400": "OE1" <-> "OE2" Residue "A GLU 1414": "OE1" <-> "OE2" Residue "A ARG 1429": "NH1" <-> "NH2" Residue "A ARG 1459": "NH1" <-> "NH2" Residue "A ARG 1599": "NH1" <-> "NH2" Residue "A GLU 1625": "OE1" <-> "OE2" Residue "A ARG 1664": "NH1" <-> "NH2" Residue "A ARG 1715": "NH1" <-> "NH2" Residue "A ARG 1720": "NH1" <-> "NH2" Residue "A GLU 1793": "OE1" <-> "OE2" Residue "A ARG 1797": "NH1" <-> "NH2" Residue "A ARG 1852": "NH1" <-> "NH2" Residue "A GLU 1921": "OE1" <-> "OE2" Residue "B ARG 162": "NH1" <-> "NH2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B ARG 204": "NH1" <-> "NH2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "B GLU 263": "OE1" <-> "OE2" Residue "B GLU 268": "OE1" <-> "OE2" Residue "B ARG 286": "NH1" <-> "NH2" Residue "B ASP 310": "OD1" <-> "OD2" Residue "B GLU 320": "OE1" <-> "OE2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B ARG 365": "NH1" <-> "NH2" Residue "B ARG 437": "NH1" <-> "NH2" Residue "B ARG 501": "NH1" <-> "NH2" Residue "B ARG 522": "NH1" <-> "NH2" Residue "B ARG 583": "NH1" <-> "NH2" Residue "B GLU 649": "OE1" <-> "OE2" Residue "B ARG 757": "NH1" <-> "NH2" Residue "C ARG 261": "NH1" <-> "NH2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "C ARG 344": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C GLU 374": "OE1" <-> "OE2" Residue "C ARG 386": "NH1" <-> "NH2" Residue "C GLU 424": "OE1" <-> "OE2" Residue "C ARG 436": "NH1" <-> "NH2" Residue "C ARG 442": "NH1" <-> "NH2" Residue "F GLU 538": "OE1" <-> "OE2" Residue "F GLU 554": "OE1" <-> "OE2" Residue "F GLU 562": "OE1" <-> "OE2" Residue "F GLU 567": "OE1" <-> "OE2" Residue "F GLU 570": "OE1" <-> "OE2" Residue "F ARG 593": "NH1" <-> "NH2" Residue "F ARG 600": "NH1" <-> "NH2" Residue "F GLU 623": "OE1" <-> "OE2" Residue "F GLU 643": "OE1" <-> "OE2" Residue "F GLU 672": "OE1" <-> "OE2" Residue "F PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 706": "OE1" <-> "OE2" Residue "F ARG 787": "NH1" <-> "NH2" Residue "F PHE 846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 862": "NH1" <-> "NH2" Residue "G ARG 342": "NH1" <-> "NH2" Residue "G GLU 361": "OE1" <-> "OE2" Residue "G ARG 362": "NH1" <-> "NH2" Residue "G ARG 381": "NH1" <-> "NH2" Residue "H GLU 83": "OE1" <-> "OE2" Residue "H ARG 131": "NH1" <-> "NH2" Residue "H GLU 157": "OE1" <-> "OE2" Residue "H PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 6": "OE1" <-> "OE2" Residue "I GLU 8": "OE1" <-> "OE2" Residue "I GLU 55": "OE1" <-> "OE2" Residue "I GLU 189": "OE1" <-> "OE2" Residue "I GLU 205": "OE1" <-> "OE2" Residue "I GLU 337": "OE1" <-> "OE2" Residue "I GLU 357": "OE1" <-> "OE2" Residue "K GLU 56": "OE1" <-> "OE2" Residue "K ARG 72": "NH1" <-> "NH2" Residue "K GLU 88": "OE1" <-> "OE2" Residue "M GLU 26": "OE1" <-> "OE2" Residue "M GLU 69": "OE1" <-> "OE2" Residue "M GLU 75": "OE1" <-> "OE2" Residue "M GLU 99": "OE1" <-> "OE2" Residue "M ARG 115": "NH1" <-> "NH2" Residue "O ARG 146": "NH1" <-> "NH2" Residue "O GLU 189": "OE1" <-> "OE2" Residue "O GLU 215": "OE1" <-> "OE2" Residue "O GLU 226": "OE1" <-> "OE2" Residue "O GLU 252": "OE1" <-> "OE2" Residue "O ARG 253": "NH1" <-> "NH2" Residue "O GLU 266": "OE1" <-> "OE2" Residue "O ARG 271": "NH1" <-> "NH2" Residue "O GLU 291": "OE1" <-> "OE2" Residue "O ARG 294": "NH1" <-> "NH2" Residue "O ARG 295": "NH1" <-> "NH2" Residue "O GLU 308": "OE1" <-> "OE2" Residue "O ARG 321": "NH1" <-> "NH2" Residue "Q GLU 82": "OE1" <-> "OE2" Residue "Q ARG 141": "NH1" <-> "NH2" Residue "Q TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 212": "NH1" <-> "NH2" Residue "Q ARG 222": "NH1" <-> "NH2" Residue "Q ARG 227": "NH1" <-> "NH2" Residue "T GLU 19": "OE1" <-> "OE2" Residue "T GLU 27": "OE1" <-> "OE2" Residue "T GLU 43": "OE1" <-> "OE2" Residue "T GLU 48": "OE1" <-> "OE2" Residue "T ARG 52": "NH1" <-> "NH2" Residue "T ARG 61": "NH1" <-> "NH2" Residue "T ARG 69": "NH1" <-> "NH2" Residue "T GLU 85": "OE1" <-> "OE2" Residue "T GLU 111": "OE1" <-> "OE2" Residue "T GLU 177": "OE1" <-> "OE2" Residue "T GLU 193": "OE1" <-> "OE2" Residue "T GLU 208": "OE1" <-> "OE2" Residue "T GLU 213": "OE1" <-> "OE2" Residue "T ARG 225": "NH1" <-> "NH2" Residue "T ARG 233": "NH1" <-> "NH2" Residue "T GLU 234": "OE1" <-> "OE2" Residue "T ARG 277": "NH1" <-> "NH2" Residue "T GLU 289": "OE1" <-> "OE2" Residue "T GLU 343": "OE1" <-> "OE2" Residue "T TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 400": "NH1" <-> "NH2" Residue "T ARG 401": "NH1" <-> "NH2" Residue "T GLU 411": "OE1" <-> "OE2" Residue "T GLU 426": "OE1" <-> "OE2" Residue "T GLU 428": "OE1" <-> "OE2" Residue "T GLU 431": "OE1" <-> "OE2" Residue "T GLU 444": "OE1" <-> "OE2" Residue "T ARG 448": "NH1" <-> "NH2" Residue "T PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 500": "NH1" <-> "NH2" Residue "T ARG 545": "NH1" <-> "NH2" Residue "T GLU 553": "OE1" <-> "OE2" Residue "T GLU 560": "OE1" <-> "OE2" Residue "T GLU 562": "OE1" <-> "OE2" Residue "T GLU 595": "OE1" <-> "OE2" Residue "T GLU 605": "OE1" <-> "OE2" Residue "T ARG 607": "NH1" <-> "NH2" Residue "T GLU 645": "OE1" <-> "OE2" Residue "T GLU 647": "OE1" <-> "OE2" Residue "T ARG 676": "NH1" <-> "NH2" Residue "T ARG 696": "NH1" <-> "NH2" Residue "T ARG 743": "NH1" <-> "NH2" Residue "T ARG 753": "NH1" <-> "NH2" Residue "T GLU 799": "OE1" <-> "OE2" Residue "T GLU 838": "OE1" <-> "OE2" Residue "T ARG 840": "NH1" <-> "NH2" Residue "T ARG 846": "NH1" <-> "NH2" Residue "T ARG 856": "NH1" <-> "NH2" Residue "W GLU 122": "OE1" <-> "OE2" Residue "W GLU 129": "OE1" <-> "OE2" Residue "W GLU 142": "OE1" <-> "OE2" Residue "W GLU 152": "OE1" <-> "OE2" Residue "W TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 252": "OE1" <-> "OE2" Residue "W GLU 255": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 39626 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 12577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1496, 12577 Classifications: {'peptide': 1496} Link IDs: {'PTRANS': 57, 'TRANS': 1438} Chain breaks: 14 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 5142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5142 Classifications: {'peptide': 651} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 619} Chain breaks: 1 Chain: "C" Number of atoms: 1728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1728 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 9, 'TRANS': 207} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 529 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 6, 'TRANS': 62} Chain: "F" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3139 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 378} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 612 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 65} Chain: "H" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 861 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'TPO:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2751 Classifications: {'peptide': 363} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain: "K" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 549 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "M" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 939 Classifications: {'peptide': 115} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 105} Chain: "N" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 155 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "O" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1572 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 8, 'TRANS': 186} Chain: "Q" Number of atoms: 1244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1244 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 14, 'TRANS': 134} Chain: "T" Number of atoms: 6185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 763, 6185 Classifications: {'peptide': 763} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 716} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Planarities with less than four sites: {'TPO:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "W" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1398 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 10, 'TRANS': 153} Chain: "A" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 241 Unusual residues: {'IHP': 1, 'LMG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 21375 SG CYS F 704 42.771 118.321 45.317 1.00 46.03 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1 IHP A2005 " occ=0.50 ... (34 atoms not shown) pdb=" P6 IHP A2005 " occ=0.50 Time building chain proxies: 20.66, per 1000 atoms: 0.52 Number of scatterers: 39626 At special positions: 0 Unit cell: (129.353, 178.268, 227.183, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 139 16.00 P 33 15.00 Mg 2 11.99 O 7286 8.00 N 6868 7.00 C 25298 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS T 376 " - pdb=" SG CYS T 720 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.60 Conformation dependent library (CDL) restraints added in 6.7 seconds 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9038 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 171 helices and 11 sheets defined 41.5% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.41 Creating SS restraints... Processing helix chain 'A' and resid 9 through 24 removed outlier: 3.788A pdb=" N ILE A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 54 Processing helix chain 'A' and resid 72 through 74 No H-bonds generated for 'chain 'A' and resid 72 through 74' Processing helix chain 'A' and resid 77 through 79 No H-bonds generated for 'chain 'A' and resid 77 through 79' Processing helix chain 'A' and resid 106 through 122 Processing helix chain 'A' and resid 128 through 138 Processing helix chain 'A' and resid 142 through 165 Processing helix chain 'A' and resid 168 through 176 Proline residue: A 173 - end of helix Processing helix chain 'A' and resid 178 through 198 removed outlier: 3.827A pdb=" N LYS A 198 " --> pdb=" O TRP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 221 removed outlier: 3.815A pdb=" N ILE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 221 " --> pdb=" O PHE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 251 through 281 Processing helix chain 'A' and resid 283 through 292 removed outlier: 3.778A pdb=" N ILE A 287 " --> pdb=" O PRO A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 321 Processing helix chain 'A' and resid 329 through 337 removed outlier: 4.221A pdb=" N ASN A 335 " --> pdb=" O TYR A 331 " (cutoff:3.500A) Proline residue: A 336 - end of helix Processing helix chain 'A' and resid 344 through 346 No H-bonds generated for 'chain 'A' and resid 344 through 346' Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 374 through 376 No H-bonds generated for 'chain 'A' and resid 374 through 376' Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 412 through 416 Processing helix chain 'A' and resid 418 through 429 removed outlier: 3.641A pdb=" N ARG A 425 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG A 426 " --> pdb=" O PHE A 422 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LYS A 427 " --> pdb=" O TRP A 423 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N MET A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ARG A 429 " --> pdb=" O ARG A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 479 Processing helix chain 'A' and resid 483 through 486 No H-bonds generated for 'chain 'A' and resid 483 through 486' Processing helix chain 'A' and resid 540 through 543 No H-bonds generated for 'chain 'A' and resid 540 through 543' Processing helix chain 'A' and resid 560 through 583 Processing helix chain 'A' and resid 602 through 610 Processing helix chain 'A' and resid 617 through 633 Processing helix chain 'A' and resid 642 through 645 No H-bonds generated for 'chain 'A' and resid 642 through 645' Processing helix chain 'A' and resid 653 through 667 Processing helix chain 'A' and resid 681 through 700 removed outlier: 4.651A pdb=" N TYR A 699 " --> pdb=" O ARG A 695 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TYR A 700 " --> pdb=" O LYS A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 723 Processing helix chain 'A' and resid 732 through 738 Processing helix chain 'A' and resid 815 through 834 removed outlier: 3.831A pdb=" N TYR A 834 " --> pdb=" O GLN A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 838 No H-bonds generated for 'chain 'A' and resid 836 through 838' Processing helix chain 'A' and resid 840 through 852 removed outlier: 3.761A pdb=" N ASN A 851 " --> pdb=" O ASP A 847 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG A 852 " --> pdb=" O ALA A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 857 No H-bonds generated for 'chain 'A' and resid 855 through 857' Processing helix chain 'A' and resid 861 through 881 removed outlier: 4.166A pdb=" N LEU A 881 " --> pdb=" O HIS A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 886 Processing helix chain 'A' and resid 893 through 896 No H-bonds generated for 'chain 'A' and resid 893 through 896' Processing helix chain 'A' and resid 903 through 905 No H-bonds generated for 'chain 'A' and resid 903 through 905' Processing helix chain 'A' and resid 916 through 919 No H-bonds generated for 'chain 'A' and resid 916 through 919' Processing helix chain 'A' and resid 955 through 958 Processing helix chain 'A' and resid 968 through 980 Processing helix chain 'A' and resid 1047 through 1062 Processing helix chain 'A' and resid 1066 through 1103 removed outlier: 4.407A pdb=" N LYS A1079 " --> pdb=" O HIS A1075 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ARG A1080 " --> pdb=" O ARG A1076 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TRP A1101 " --> pdb=" O LYS A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1142 Processing helix chain 'A' and resid 1156 through 1180 Processing helix chain 'A' and resid 1232 through 1248 removed outlier: 3.894A pdb=" N VAL A1241 " --> pdb=" O THR A1237 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LYS A1246 " --> pdb=" O ILE A1242 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N SER A1247 " --> pdb=" O THR A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1261 Processing helix chain 'A' and resid 1398 through 1411 removed outlier: 3.785A pdb=" N GLN A1402 " --> pdb=" O LYS A1398 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLN A1410 " --> pdb=" O ASN A1406 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG A1411 " --> pdb=" O LEU A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1431 through 1435 Processing helix chain 'A' and resid 1439 through 1447 Processing helix chain 'A' and resid 1454 through 1489 removed outlier: 5.230A pdb=" N LEU A1483 " --> pdb=" O TRP A1479 " (cutoff:3.500A) Proline residue: A1484 - end of helix Processing helix chain 'A' and resid 1625 through 1630 Processing helix chain 'A' and resid 1640 through 1645 removed outlier: 5.912A pdb=" N PHE A1645 " --> pdb=" O ASN A1641 " (cutoff:3.500A) Processing helix chain 'A' and resid 1647 through 1653 Processing helix chain 'A' and resid 1691 through 1693 No H-bonds generated for 'chain 'A' and resid 1691 through 1693' Processing helix chain 'A' and resid 1699 through 1718 removed outlier: 3.672A pdb=" N LYS A1703 " --> pdb=" O SER A1699 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN A1704 " --> pdb=" O SER A1700 " (cutoff:3.500A) Processing helix chain 'A' and resid 1721 through 1724 No H-bonds generated for 'chain 'A' and resid 1721 through 1724' Processing helix chain 'A' and resid 1746 through 1752 removed outlier: 4.147A pdb=" N ILE A1749 " --> pdb=" O SER A1746 " (cutoff:3.500A) Processing helix chain 'A' and resid 1759 through 1761 No H-bonds generated for 'chain 'A' and resid 1759 through 1761' Processing helix chain 'A' and resid 1774 through 1786 Processing helix chain 'A' and resid 1804 through 1806 No H-bonds generated for 'chain 'A' and resid 1804 through 1806' Processing helix chain 'A' and resid 1956 through 1970 Processing helix chain 'A' and resid 1974 through 1988 removed outlier: 5.025A pdb=" N THR A1978 " --> pdb=" O GLN A1975 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL A1981 " --> pdb=" O THR A1978 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 186 removed outlier: 3.844A pdb=" N LEU B 186 " --> pdb=" O GLU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 210 Processing helix chain 'B' and resid 259 through 268 removed outlier: 3.729A pdb=" N GLU B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ARG B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.504A pdb=" N ARG B 286 " --> pdb=" O MET B 282 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN B 291 " --> pdb=" O ASN B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 361 removed outlier: 3.746A pdb=" N ILE B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 384 removed outlier: 4.924A pdb=" N CYS B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 439 No H-bonds generated for 'chain 'B' and resid 437 through 439' Processing helix chain 'B' and resid 658 through 662 Processing helix chain 'B' and resid 686 through 688 No H-bonds generated for 'chain 'B' and resid 686 through 688' Processing helix chain 'B' and resid 723 through 726 Processing helix chain 'B' and resid 752 through 755 No H-bonds generated for 'chain 'B' and resid 752 through 755' Processing helix chain 'C' and resid 257 through 279 Proline residue: C 262 - end of helix removed outlier: 3.973A pdb=" N ARG C 278 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 288 Processing helix chain 'C' and resid 291 through 302 removed outlier: 3.813A pdb=" N TYR C 299 " --> pdb=" O ARG C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 323 Processing helix chain 'C' and resid 330 through 363 Processing helix chain 'C' and resid 368 through 378 Processing helix chain 'C' and resid 380 through 386 Processing helix chain 'C' and resid 392 through 396 Processing helix chain 'C' and resid 415 through 425 Processing helix chain 'C' and resid 433 through 446 Processing helix chain 'C' and resid 460 through 466 Processing helix chain 'D' and resid 28 through 35 removed outlier: 3.610A pdb=" N ILE D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 49 removed outlier: 3.647A pdb=" N ASP D 48 " --> pdb=" O ALA D 44 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 81 removed outlier: 3.645A pdb=" N ARG D 63 " --> pdb=" O PRO D 59 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA D 64 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA D 65 " --> pdb=" O GLU D 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 540 Processing helix chain 'F' and resid 567 through 586 removed outlier: 3.662A pdb=" N VAL F 575 " --> pdb=" O SER F 571 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG F 578 " --> pdb=" O HIS F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 589 through 623 removed outlier: 3.611A pdb=" N GLU F 594 " --> pdb=" O TRP F 590 " (cutoff:3.500A) Processing helix chain 'F' and resid 647 through 649 No H-bonds generated for 'chain 'F' and resid 647 through 649' Processing helix chain 'F' and resid 782 through 784 No H-bonds generated for 'chain 'F' and resid 782 through 784' Processing helix chain 'F' and resid 905 through 919 removed outlier: 3.700A pdb=" N TRP F 908 " --> pdb=" O ARG F 905 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU F 909 " --> pdb=" O LEU F 906 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU F 911 " --> pdb=" O TRP F 908 " (cutoff:3.500A) Proline residue: F 913 - end of helix removed outlier: 3.687A pdb=" N ASN F 916 " --> pdb=" O PRO F 913 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR F 917 " --> pdb=" O ALA F 914 " (cutoff:3.500A) Processing helix chain 'F' and resid 922 through 929 Processing helix chain 'G' and resid 330 through 373 removed outlier: 5.400A pdb=" N HIS G 346 " --> pdb=" O ARG G 342 " (cutoff:3.500A) Proline residue: G 347 - end of helix Processing helix chain 'G' and resid 384 through 393 Processing helix chain 'H' and resid 75 through 104 Processing helix chain 'H' and resid 114 through 130 Proline residue: H 125 - end of helix removed outlier: 3.579A pdb=" N TYR H 130 " --> pdb=" O TYR H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 159 Processing helix chain 'I' and resid 20 through 28 Processing helix chain 'I' and resid 96 through 103 Processing helix chain 'I' and resid 223 through 237 Processing helix chain 'I' and resid 239 through 241 No H-bonds generated for 'chain 'I' and resid 239 through 241' Processing helix chain 'I' and resid 244 through 248 Processing helix chain 'I' and resid 252 through 259 Processing helix chain 'K' and resid 27 through 40 removed outlier: 3.906A pdb=" N VAL K 33 " --> pdb=" O VAL K 29 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP K 38 " --> pdb=" O ALA K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 54 Processing helix chain 'K' and resid 79 through 84 removed outlier: 5.193A pdb=" N ASN K 84 " --> pdb=" O SER K 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 43 Processing helix chain 'M' and resid 60 through 77 Processing helix chain 'M' and resid 98 through 101 No H-bonds generated for 'chain 'M' and resid 98 through 101' Processing helix chain 'M' and resid 103 through 116 removed outlier: 3.763A pdb=" N TRP M 111 " --> pdb=" O HIS M 107 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LYS M 112 " --> pdb=" O TRP M 108 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL M 113 " --> pdb=" O LYS M 109 " (cutoff:3.500A) Proline residue: M 114 - end of helix Processing helix chain 'N' and resid 1276 through 1287 removed outlier: 3.637A pdb=" N TYR N1280 " --> pdb=" O ALA N1276 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA N1281 " --> pdb=" O ALA N1277 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR N1287 " --> pdb=" O LEU N1283 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 167 Processing helix chain 'O' and resid 169 through 180 Processing helix chain 'O' and resid 184 through 205 removed outlier: 4.307A pdb=" N GLY O 188 " --> pdb=" O PRO O 184 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU O 189 " --> pdb=" O GLN O 185 " (cutoff:3.500A) Processing helix chain 'O' and resid 214 through 220 removed outlier: 3.775A pdb=" N ALA O 220 " --> pdb=" O GLU O 216 " (cutoff:3.500A) Processing helix chain 'O' and resid 224 through 231 Processing helix chain 'O' and resid 234 through 236 No H-bonds generated for 'chain 'O' and resid 234 through 236' Processing helix chain 'O' and resid 250 through 260 Processing helix chain 'O' and resid 279 through 286 Processing helix chain 'O' and resid 289 through 302 Processing helix chain 'O' and resid 306 through 310 Processing helix chain 'O' and resid 315 through 322 Processing helix chain 'Q' and resid 80 through 93 removed outlier: 3.639A pdb=" N THR Q 93 " --> pdb=" O MET Q 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 105 removed outlier: 4.217A pdb=" N ASN Q 105 " --> pdb=" O PRO Q 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 102 through 105' Processing helix chain 'Q' and resid 127 through 139 Processing helix chain 'Q' and resid 160 through 169 Processing helix chain 'Q' and resid 189 through 191 No H-bonds generated for 'chain 'Q' and resid 189 through 191' Processing helix chain 'Q' and resid 195 through 199 Processing helix chain 'Q' and resid 202 through 214 Processing helix chain 'Q' and resid 216 through 226 Processing helix chain 'T' and resid 16 through 18 No H-bonds generated for 'chain 'T' and resid 16 through 18' Processing helix chain 'T' and resid 33 through 36 No H-bonds generated for 'chain 'T' and resid 33 through 36' Processing helix chain 'T' and resid 47 through 66 Processing helix chain 'T' and resid 79 through 85 Processing helix chain 'T' and resid 156 through 161 Processing helix chain 'T' and resid 175 through 185 Processing helix chain 'T' and resid 206 through 208 No H-bonds generated for 'chain 'T' and resid 206 through 208' Processing helix chain 'T' and resid 215 through 221 Processing helix chain 'T' and resid 231 through 235 Processing helix chain 'T' and resid 272 through 276 Processing helix chain 'T' and resid 383 through 390 Processing helix chain 'T' and resid 395 through 409 removed outlier: 5.754A pdb=" N GLY T 404 " --> pdb=" O ARG T 400 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ALA T 405 " --> pdb=" O ARG T 401 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN T 409 " --> pdb=" O ALA T 405 " (cutoff:3.500A) Processing helix chain 'T' and resid 426 through 438 removed outlier: 3.779A pdb=" N VAL T 429 " --> pdb=" O GLU T 426 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N VAL T 430 " --> pdb=" O ASP T 427 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU T 431 " --> pdb=" O GLU T 428 " (cutoff:3.500A) Processing helix chain 'T' and resid 442 through 460 Processing helix chain 'T' and resid 464 through 481 removed outlier: 3.712A pdb=" N ARG T 481 " --> pdb=" O GLU T 477 " (cutoff:3.500A) Processing helix chain 'T' and resid 516 through 519 No H-bonds generated for 'chain 'T' and resid 516 through 519' Processing helix chain 'T' and resid 547 through 569 Processing helix chain 'T' and resid 582 through 586 Processing helix chain 'T' and resid 590 through 601 Processing helix chain 'T' and resid 604 through 613 Processing helix chain 'T' and resid 644 through 658 removed outlier: 3.663A pdb=" N GLU T 656 " --> pdb=" O ALA T 652 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN T 657 " --> pdb=" O ARG T 653 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA T 658 " --> pdb=" O LEU T 654 " (cutoff:3.500A) Processing helix chain 'T' and resid 662 through 674 Processing helix chain 'T' and resid 722 through 742 removed outlier: 4.662A pdb=" N TRP T 742 " --> pdb=" O ARG T 738 " (cutoff:3.500A) Processing helix chain 'T' and resid 749 through 754 Processing helix chain 'T' and resid 777 through 779 No H-bonds generated for 'chain 'T' and resid 777 through 779' Processing helix chain 'T' and resid 783 through 786 No H-bonds generated for 'chain 'T' and resid 783 through 786' Processing helix chain 'T' and resid 794 through 813 removed outlier: 3.950A pdb=" N MET T 813 " --> pdb=" O ALA T 809 " (cutoff:3.500A) Processing helix chain 'T' and resid 825 through 855 Processing helix chain 'W' and resid 103 through 128 Proline residue: W 116 - end of helix removed outlier: 5.255A pdb=" N GLU W 122 " --> pdb=" O VAL W 118 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LYS W 123 " --> pdb=" O ASP W 119 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR W 124 " --> pdb=" O VAL W 120 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL W 125 " --> pdb=" O THR W 121 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N TYR W 126 " --> pdb=" O GLU W 122 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE W 127 " --> pdb=" O LYS W 123 " (cutoff:3.500A) Processing helix chain 'W' and resid 132 through 138 removed outlier: 4.856A pdb=" N TRP W 136 " --> pdb=" O ALA W 133 " (cutoff:3.500A) Processing helix chain 'W' and resid 142 through 149 removed outlier: 3.553A pdb=" N ASN W 149 " --> pdb=" O GLU W 145 " (cutoff:3.500A) Processing helix chain 'W' and resid 154 through 165 Processing helix chain 'W' and resid 174 through 199 removed outlier: 3.573A pdb=" N ASN W 199 " --> pdb=" O VAL W 195 " (cutoff:3.500A) Processing helix chain 'W' and resid 202 through 205 No H-bonds generated for 'chain 'W' and resid 202 through 205' Processing helix chain 'W' and resid 208 through 234 Processing helix chain 'W' and resid 244 through 256 removed outlier: 4.065A pdb=" N GLN W 256 " --> pdb=" O GLU W 252 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 92 through 94 Processing sheet with id= B, first strand: chain 'B' and resid 166 through 169 removed outlier: 9.001A pdb=" N VAL B 167 " --> pdb=" O GLN B 232 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL B 234 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N GLU B 169 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N TYR B 236 " --> pdb=" O GLU B 169 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 248 through 253 removed outlier: 3.818A pdb=" N PHE B 305 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N THR B 319 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL B 303 " --> pdb=" O THR B 319 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 416 through 421 removed outlier: 11.459A pdb=" N PHE B 478 " --> pdb=" O ASN B 499 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASN B 499 " --> pdb=" O PHE B 478 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL B 480 " --> pdb=" O LEU B 497 " (cutoff:3.500A) removed outlier: 11.882A pdb=" N GLN B 605 " --> pdb=" O GLU B 649 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLU B 649 " --> pdb=" O GLN B 605 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N TYR B 637 " --> pdb=" O GLY B 617 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR B 765 " --> pdb=" O ARG B 781 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 322 through 330 removed outlier: 7.348A pdb=" N VAL B 406 " --> pdb=" O ASP B 324 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL B 326 " --> pdb=" O VAL B 406 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE B 408 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL B 328 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N CYS B 410 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N PHE B 330 " --> pdb=" O CYS B 410 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N GLU B 412 " --> pdb=" O PHE B 330 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP B 389 " --> pdb=" O GLU B 411 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 690 through 692 removed outlier: 3.745A pdb=" N LEU B 692 " --> pdb=" O GLY B 707 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLY B 707 " --> pdb=" O LEU B 692 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 892 through 899 removed outlier: 4.743A pdb=" N MET F 844 " --> pdb=" O VAL F 834 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU F 826 " --> pdb=" O ARG F 852 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL F 793 " --> pdb=" O ALA F 816 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR F 791 " --> pdb=" O GLN F 818 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY F 772 " --> pdb=" O GLN F 798 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR F 800 " --> pdb=" O HIS F 770 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N HIS F 770 " --> pdb=" O THR F 800 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ASP F 750 " --> pdb=" O LEU F 744 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LEU F 744 " --> pdb=" O ASP F 750 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER F 725 " --> pdb=" O HIS F 733 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR F 735 " --> pdb=" O VAL F 723 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N VAL F 723 " --> pdb=" O THR F 735 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL F 737 " --> pdb=" O SER F 721 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N SER F 721 " --> pdb=" O VAL F 737 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N GLY F 739 " --> pdb=" O HIS F 719 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N HIS F 719 " --> pdb=" O GLY F 739 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N TRP F 741 " --> pdb=" O GLU F 717 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N GLU F 717 " --> pdb=" O TRP F 741 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL F 743 " --> pdb=" O GLN F 715 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLN F 715 " --> pdb=" O VAL F 743 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ARG F 745 " --> pdb=" O CYS F 713 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N CYS F 713 " --> pdb=" O ARG F 745 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LYS F 707 " --> pdb=" O ASN F 678 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N ASN F 678 " --> pdb=" O LYS F 707 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N SER F 665 " --> pdb=" O ASN F 678 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ILE F 680 " --> pdb=" O ILE F 663 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE F 663 " --> pdb=" O ILE F 680 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE F 682 " --> pdb=" O THR F 661 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR F 661 " --> pdb=" O PHE F 682 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'I' and resid 351 through 356 removed outlier: 3.727A pdb=" N GLY I 36 " --> pdb=" O LYS I 74 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY I 60 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL I 69 " --> pdb=" O SER I 85 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N SER I 85 " --> pdb=" O VAL I 69 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ALA I 71 " --> pdb=" O SER I 83 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N SER I 83 " --> pdb=" O ALA I 71 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N LEU I 73 " --> pdb=" O GLY I 81 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N GLY I 81 " --> pdb=" O LEU I 73 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASN I 122 " --> pdb=" O PHE I 118 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA I 334 " --> pdb=" O ARG I 349 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ARG I 349 " --> pdb=" O ALA I 334 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 180 through 182 removed outlier: 3.786A pdb=" N LEU I 187 " --> pdb=" O ASN I 182 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'T' and resid 292 through 297 removed outlier: 4.792A pdb=" N MET T 316 " --> pdb=" O LEU T 307 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N LEU T 352 " --> pdb=" O GLU T 343 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N CYS T 376 " --> pdb=" O GLU T 367 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'T' and resid 491 through 493 1684 hydrogen bonds defined for protein. 4851 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.60 Time building geometry restraints manager: 15.92 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: 9587 1.33 - 1.45: 9377 1.45 - 1.58: 21290 1.58 - 1.70: 97 1.70 - 1.83: 245 Bond restraints: 40596 Sorted by residual: bond pdb=" OG1 TPO H 177 " pdb=" P TPO H 177 " ideal model delta sigma weight residual 1.717 1.578 0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" OG1 TPO H 176 " pdb=" P TPO H 176 " ideal model delta sigma weight residual 1.717 1.583 0.134 2.00e-02 2.50e+03 4.50e+01 bond pdb=" OG1 TPO H 178 " pdb=" P TPO H 178 " ideal model delta sigma weight residual 1.717 1.587 0.130 2.00e-02 2.50e+03 4.19e+01 bond pdb=" OG1 TPO T 249 " pdb=" P TPO T 249 " ideal model delta sigma weight residual 1.717 1.602 0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" OG1 TPO T 77 " pdb=" P TPO T 77 " ideal model delta sigma weight residual 1.717 1.603 0.114 2.00e-02 2.50e+03 3.23e+01 ... (remaining 40591 not shown) Histogram of bond angle deviations from ideal: 95.51 - 103.80: 611 103.80 - 112.08: 18685 112.08 - 120.37: 19528 120.37 - 128.65: 15735 128.65 - 136.93: 379 Bond angle restraints: 54938 Sorted by residual: angle pdb=" N ASN A 282 " pdb=" CA ASN A 282 " pdb=" C ASN A 282 " ideal model delta sigma weight residual 109.81 123.75 -13.94 2.21e+00 2.05e-01 3.98e+01 angle pdb=" C PRO T 544 " pdb=" N ARG T 545 " pdb=" CA ARG T 545 " ideal model delta sigma weight residual 121.54 132.74 -11.20 1.91e+00 2.74e-01 3.44e+01 angle pdb=" N VAL A1790 " pdb=" CA VAL A1790 " pdb=" C VAL A1790 " ideal model delta sigma weight residual 111.44 103.77 7.67 1.34e+00 5.57e-01 3.28e+01 angle pdb=" N GLY F 695 " pdb=" CA GLY F 695 " pdb=" C GLY F 695 " ideal model delta sigma weight residual 112.51 120.91 -8.40 1.53e+00 4.27e-01 3.01e+01 angle pdb=" C GLY B 534 " pdb=" N GLN B 535 " pdb=" CA GLN B 535 " ideal model delta sigma weight residual 121.54 131.87 -10.33 1.91e+00 2.74e-01 2.92e+01 ... (remaining 54933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.64: 23555 30.64 - 61.29: 704 61.29 - 91.93: 85 91.93 - 122.58: 15 122.58 - 153.22: 2 Dihedral angle restraints: 24361 sinusoidal: 10301 harmonic: 14060 Sorted by residual: dihedral pdb=" CA ASP A1252 " pdb=" C ASP A1252 " pdb=" N ARG A1253 " pdb=" CA ARG A1253 " ideal model delta harmonic sigma weight residual -180.00 -150.31 -29.69 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" C ASN A 282 " pdb=" N ASN A 282 " pdb=" CA ASN A 282 " pdb=" CB ASN A 282 " ideal model delta harmonic sigma weight residual -122.60 -136.45 13.85 0 2.50e+00 1.60e-01 3.07e+01 dihedral pdb=" CA TYR A 417 " pdb=" C TYR A 417 " pdb=" N GLY A 418 " pdb=" CA GLY A 418 " ideal model delta harmonic sigma weight residual 180.00 153.33 26.67 0 5.00e+00 4.00e-02 2.85e+01 ... (remaining 24358 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.925: 5788 0.925 - 1.849: 0 1.849 - 2.774: 0 2.774 - 3.698: 0 3.698 - 4.623: 4 Chirality restraints: 5792 Sorted by residual: chirality pdb=" C5 IHP A2005 " pdb=" C4 IHP A2005 " pdb=" C6 IHP A2005 " pdb=" O15 IHP A2005 " both_signs ideal model delta sigma weight residual False -2.42 2.21 -4.62 2.00e-01 2.50e+01 5.34e+02 chirality pdb=" C2 IHP A2005 " pdb=" C1 IHP A2005 " pdb=" C3 IHP A2005 " pdb=" O12 IHP A2005 " both_signs ideal model delta sigma weight residual False -2.52 2.10 -4.62 2.00e-01 2.50e+01 5.33e+02 chirality pdb=" C3 IHP A2005 " pdb=" C2 IHP A2005 " pdb=" C4 IHP A2005 " pdb=" O13 IHP A2005 " both_signs ideal model delta sigma weight residual False -2.34 2.09 -4.42 2.00e-01 2.50e+01 4.89e+02 ... (remaining 5789 not shown) Planarity restraints: 7040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 LMG A2004 " -0.119 2.00e-02 2.50e+03 6.88e-02 4.73e+01 pdb=" C29 LMG A2004 " 0.036 2.00e-02 2.50e+03 pdb=" O10 LMG A2004 " 0.046 2.00e-02 2.50e+03 pdb=" O8 LMG A2004 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 LMG A2001 " 0.113 2.00e-02 2.50e+03 6.56e-02 4.30e+01 pdb=" C29 LMG A2001 " -0.034 2.00e-02 2.50e+03 pdb=" O10 LMG A2001 " -0.044 2.00e-02 2.50e+03 pdb=" O8 LMG A2001 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 550 " 0.012 2.00e-02 2.50e+03 3.47e-02 3.01e+01 pdb=" CG TRP F 550 " -0.082 2.00e-02 2.50e+03 pdb=" CD1 TRP F 550 " 0.064 2.00e-02 2.50e+03 pdb=" CD2 TRP F 550 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP F 550 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP F 550 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP F 550 " 0.029 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 550 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 550 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP F 550 " -0.001 2.00e-02 2.50e+03 ... (remaining 7037 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 309 2.63 - 3.19: 31544 3.19 - 3.76: 59688 3.76 - 4.33: 84092 4.33 - 4.90: 138141 Nonbonded interactions: 313774 Sorted by model distance: nonbonded pdb=" O3P TPO T 712 " pdb="MG MG T1001 " model vdw 2.057 2.170 nonbonded pdb=" O THR A1228 " pdb=" OD1 ASP A1229 " model vdw 2.127 3.040 nonbonded pdb=" O PHE H 149 " pdb=" NE2 GLN H 153 " model vdw 2.195 2.520 nonbonded pdb=" ND1 HIS T 374 " pdb=" O TYR T 416 " model vdw 2.209 2.520 nonbonded pdb=" O2P TPO T 712 " pdb="MG MG T1001 " model vdw 2.214 2.170 ... (remaining 313769 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 13.530 Check model and map are aligned: 0.510 Set scattering table: 0.290 Process input model: 97.060 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.130 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:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 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 : 0.007 0.139 40596 Z= 0.486 Angle : 1.084 13.941 54938 Z= 0.570 Chirality : 0.133 4.623 5792 Planarity : 0.009 0.109 7040 Dihedral : 15.162 153.220 15320 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.53 % Favored : 94.30 % Rotamer: Outliers : 0.19 % Allowed : 0.46 % Favored : 99.35 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.11), residues: 4699 helix: -0.38 (0.10), residues: 2013 sheet: 0.46 (0.20), residues: 629 loop : -1.59 (0.12), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.003 TRP F 550 HIS 0.027 0.002 HIS C 378 PHE 0.044 0.003 PHE A 44 TYR 0.049 0.003 TYR A1721 ARG 0.031 0.003 ARG A 136 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 4137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 466 time to evaluate : 4.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1402 GLN cc_start: 0.7619 (mm110) cc_final: 0.7353 (mp10) REVERT: A 1891 ARG cc_start: 0.6681 (OUTLIER) cc_final: 0.6444 (tpt170) REVERT: B 257 MET cc_start: 0.8076 (ttt) cc_final: 0.7594 (ttt) REVERT: C 276 LEU cc_start: 0.8761 (tt) cc_final: 0.8337 (tp) REVERT: G 378 ARG cc_start: 0.7179 (mmp80) cc_final: 0.6797 (mmp-170) REVERT: H 100 ARG cc_start: 0.6882 (mmm-85) cc_final: 0.6590 (tpt90) REVERT: O 143 LYS cc_start: 0.7470 (tptt) cc_final: 0.7126 (tptp) REVERT: T 378 MET cc_start: 0.8320 (ttm) cc_final: 0.8101 (ttm) outliers start: 8 outliers final: 3 residues processed: 472 average time/residue: 1.7207 time to fit residues: 966.3821 Evaluate side-chains 369 residues out of total 4137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 365 time to evaluate : 4.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1891 ARG Chi-restraints excluded: chain A residue 1987 LEU Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain W residue 256 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 402 optimal weight: 0.7980 chunk 361 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 243 optimal weight: 2.9990 chunk 193 optimal weight: 6.9990 chunk 373 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 chunk 227 optimal weight: 0.9990 chunk 278 optimal weight: 5.9990 chunk 433 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN A 431 HIS A 688 GLN A 822 HIS A 838 ASN A1180 GLN ** A1609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1702 GLN B 703 HIS C 453 GLN F 621 ASN ** F 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 733 HIS F 867 ASN ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 264 ASN K 84 ASN T 771 HIS W 256 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 40596 Z= 0.286 Angle : 0.682 15.575 54938 Z= 0.349 Chirality : 0.045 0.208 5792 Planarity : 0.006 0.075 7040 Dihedral : 9.693 119.054 5718 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.60 % Favored : 95.38 % Rotamer: Outliers : 1.35 % Allowed : 6.91 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: -0.26 (0.12), residues: 4699 helix: 0.78 (0.11), residues: 2019 sheet: 0.61 (0.20), residues: 632 loop : -1.41 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 388 HIS 0.009 0.002 HIS A1444 PHE 0.028 0.002 PHE H 87 TYR 0.019 0.002 TYR A 417 ARG 0.007 0.001 ARG T 545 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 4137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 390 time to evaluate : 4.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 750 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8066 (mmtm) REVERT: A 864 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6923 (pp20) REVERT: A 1402 GLN cc_start: 0.7621 (mm110) cc_final: 0.7307 (mp10) REVERT: A 1476 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7464 (tm-30) REVERT: A 1891 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.6559 (tpt170) REVERT: B 257 MET cc_start: 0.8038 (ttt) cc_final: 0.7552 (ttt) REVERT: B 378 MET cc_start: 0.7228 (tpt) cc_final: 0.6917 (tpt) REVERT: C 276 LEU cc_start: 0.8770 (tt) cc_final: 0.8482 (tp) REVERT: G 357 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7232 (mp0) REVERT: O 143 LYS cc_start: 0.7512 (tptt) cc_final: 0.7137 (tptp) REVERT: O 146 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.5999 (mpt180) REVERT: O 219 ASP cc_start: 0.5993 (m-30) cc_final: 0.5475 (p0) REVERT: T 267 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7984 (mt-10) outliers start: 56 outliers final: 22 residues processed: 418 average time/residue: 1.7245 time to fit residues: 861.2294 Evaluate side-chains 383 residues out of total 4137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 354 time to evaluate : 4.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 750 LYS Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1476 GLN Chi-restraints excluded: chain A residue 1672 VAL Chi-restraints excluded: chain A residue 1891 ARG Chi-restraints excluded: chain A residue 1925 MET Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain F residue 677 LEU Chi-restraints excluded: chain G residue 357 GLU Chi-restraints excluded: chain I residue 68 ASP Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 146 ARG Chi-restraints excluded: chain O residue 251 LYS Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain Q residue 215 SER Chi-restraints excluded: chain T residue 267 GLU Chi-restraints excluded: chain T residue 649 ASP Chi-restraints excluded: chain W residue 101 MET Chi-restraints excluded: chain W residue 242 LEU Chi-restraints excluded: chain W residue 253 GLN Chi-restraints excluded: chain W residue 256 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 240 optimal weight: 0.7980 chunk 134 optimal weight: 0.4980 chunk 360 optimal weight: 0.8980 chunk 294 optimal weight: 9.9990 chunk 119 optimal weight: 0.8980 chunk 433 optimal weight: 3.9990 chunk 468 optimal weight: 0.2980 chunk 386 optimal weight: 2.9990 chunk 430 optimal weight: 0.9980 chunk 147 optimal weight: 0.6980 chunk 348 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1609 ASN A1644 GLN C 453 GLN D 71 HIS F 621 ASN ** F 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 40596 Z= 0.147 Angle : 0.551 9.833 54938 Z= 0.283 Chirality : 0.041 0.248 5792 Planarity : 0.004 0.069 7040 Dihedral : 8.598 124.964 5714 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.55 % Favored : 95.42 % Rotamer: Outliers : 1.14 % Allowed : 9.62 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.12), residues: 4699 helix: 1.42 (0.12), residues: 2009 sheet: 0.72 (0.20), residues: 638 loop : -1.24 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 388 HIS 0.004 0.001 HIS A1807 PHE 0.028 0.001 PHE H 87 TYR 0.020 0.001 TYR A 86 ARG 0.006 0.000 ARG A 662 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 4137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 383 time to evaluate : 4.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 PHE cc_start: 0.7284 (t80) cc_final: 0.7059 (t80) REVERT: A 1402 GLN cc_start: 0.7521 (mm110) cc_final: 0.7165 (mp10) REVERT: A 1891 ARG cc_start: 0.6948 (OUTLIER) cc_final: 0.6537 (tpt170) REVERT: B 213 ASP cc_start: 0.7368 (OUTLIER) cc_final: 0.6789 (m-30) REVERT: B 378 MET cc_start: 0.7257 (tpt) cc_final: 0.6921 (tpt) REVERT: C 276 LEU cc_start: 0.8773 (tt) cc_final: 0.8547 (tp) REVERT: D 75 LYS cc_start: 0.7718 (mtmm) cc_final: 0.7331 (mmmm) REVERT: F 677 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7810 (pp) REVERT: G 360 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7254 (mt-10) REVERT: I 87 ILE cc_start: 0.8306 (mp) cc_final: 0.8099 (mt) REVERT: O 143 LYS cc_start: 0.7433 (tptt) cc_final: 0.7016 (tptp) REVERT: O 146 ARG cc_start: 0.6843 (OUTLIER) cc_final: 0.5978 (mpt180) REVERT: O 175 THR cc_start: 0.8424 (m) cc_final: 0.8123 (m) REVERT: O 219 ASP cc_start: 0.5966 (m-30) cc_final: 0.5496 (p0) REVERT: T 267 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7869 (mt-10) REVERT: T 719 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7551 (mtm) REVERT: T 848 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7641 (mm) REVERT: W 169 ASN cc_start: 0.8419 (t0) cc_final: 0.8207 (t0) outliers start: 47 outliers final: 17 residues processed: 404 average time/residue: 1.7455 time to fit residues: 840.7901 Evaluate side-chains 383 residues out of total 4137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 358 time to evaluate : 4.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 640 LYS Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1387 ASN Chi-restraints excluded: chain A residue 1672 VAL Chi-restraints excluded: chain A residue 1891 ARG Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain F residue 677 LEU Chi-restraints excluded: chain G residue 357 GLU Chi-restraints excluded: chain G residue 360 GLU Chi-restraints excluded: chain I residue 68 ASP Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 146 ARG Chi-restraints excluded: chain Q residue 215 SER Chi-restraints excluded: chain T residue 267 GLU Chi-restraints excluded: chain T residue 362 GLU Chi-restraints excluded: chain T residue 649 ASP Chi-restraints excluded: chain T residue 719 MET Chi-restraints excluded: chain T residue 848 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 428 optimal weight: 6.9990 chunk 326 optimal weight: 6.9990 chunk 225 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 291 optimal weight: 10.0000 chunk 435 optimal weight: 4.9990 chunk 461 optimal weight: 5.9990 chunk 227 optimal weight: 1.9990 chunk 412 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 484 ASN A1644 GLN A1702 GLN B 139 ASN B 703 HIS C 453 GLN ** F 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 40596 Z= 0.452 Angle : 0.740 10.258 54938 Z= 0.382 Chirality : 0.049 0.284 5792 Planarity : 0.006 0.076 7040 Dihedral : 8.776 118.175 5711 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.49 % Favored : 94.47 % Rotamer: Outliers : 2.30 % Allowed : 10.86 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 (0.12), residues: 4699 helix: 1.15 (0.12), residues: 2024 sheet: 0.69 (0.20), residues: 634 loop : -1.32 (0.13), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP G 388 HIS 0.017 0.002 HIS A1075 PHE 0.035 0.003 PHE M 28 TYR 0.023 0.003 TYR A 304 ARG 0.009 0.001 ARG A1808 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 4137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 373 time to evaluate : 5.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7374 (mm-30) REVERT: A 1402 GLN cc_start: 0.7625 (mm110) cc_final: 0.7256 (mp10) REVERT: A 1476 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7472 (tm-30) REVERT: A 1891 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6738 (tpt170) REVERT: B 141 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8191 (tptp) REVERT: B 146 ASP cc_start: 0.4808 (OUTLIER) cc_final: 0.4524 (m-30) REVERT: B 213 ASP cc_start: 0.7437 (OUTLIER) cc_final: 0.6762 (m-30) REVERT: K 65 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.6985 (mtm180) REVERT: K 75 LYS cc_start: 0.8563 (ptmm) cc_final: 0.8096 (ptmm) REVERT: O 143 LYS cc_start: 0.7583 (tptt) cc_final: 0.7287 (tptp) REVERT: O 146 ARG cc_start: 0.6892 (OUTLIER) cc_final: 0.6021 (mpt180) REVERT: O 301 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7477 (tptp) REVERT: T 267 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8089 (mt-10) REVERT: T 719 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.7951 (mtm) outliers start: 95 outliers final: 42 residues processed: 435 average time/residue: 1.7070 time to fit residues: 889.0586 Evaluate side-chains 412 residues out of total 4137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 359 time to evaluate : 4.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 640 LYS Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 1075 HIS Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1387 ASN Chi-restraints excluded: chain A residue 1476 GLN Chi-restraints excluded: chain A residue 1591 VAL Chi-restraints excluded: chain A residue 1606 VAL Chi-restraints excluded: chain A residue 1672 VAL Chi-restraints excluded: chain A residue 1891 ARG Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 660 VAL Chi-restraints excluded: chain F residue 677 LEU Chi-restraints excluded: chain F residue 844 MET Chi-restraints excluded: chain F residue 897 ASN Chi-restraints excluded: chain G residue 357 GLU Chi-restraints excluded: chain I residue 68 ASP Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 1278 MET Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 146 ARG Chi-restraints excluded: chain O residue 178 LEU Chi-restraints excluded: chain O residue 251 LYS Chi-restraints excluded: chain O residue 301 LYS Chi-restraints excluded: chain O residue 318 THR Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain Q residue 201 THR Chi-restraints excluded: chain Q residue 215 SER Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 267 GLU Chi-restraints excluded: chain T residue 362 GLU Chi-restraints excluded: chain T residue 649 ASP Chi-restraints excluded: chain T residue 719 MET Chi-restraints excluded: chain W residue 101 MET Chi-restraints excluded: chain W residue 242 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 383 optimal weight: 0.9990 chunk 261 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 343 optimal weight: 0.9990 chunk 190 optimal weight: 6.9990 chunk 393 optimal weight: 9.9990 chunk 318 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 235 optimal weight: 20.0000 chunk 413 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1673 ASN C 453 GLN ** F 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 256 GLN W 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 40596 Z= 0.234 Angle : 0.601 12.488 54938 Z= 0.311 Chirality : 0.043 0.213 5792 Planarity : 0.005 0.071 7040 Dihedral : 8.383 108.366 5711 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.51 % Favored : 95.45 % Rotamer: Outliers : 2.06 % Allowed : 12.28 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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 (0.12), residues: 4699 helix: 1.48 (0.12), residues: 2009 sheet: 0.69 (0.20), residues: 634 loop : -1.23 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 278 HIS 0.006 0.001 HIS A1747 PHE 0.029 0.002 PHE A 872 TYR 0.021 0.002 TYR N1287 ARG 0.007 0.000 ARG A 662 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 4137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 370 time to evaluate : 4.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7377 (mm-30) REVERT: A 1351 LYS cc_start: 0.8239 (ptpt) cc_final: 0.7933 (pttt) REVERT: A 1402 GLN cc_start: 0.7586 (mm110) cc_final: 0.7239 (mp10) REVERT: A 1473 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7127 (mp0) REVERT: A 1476 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7441 (tm-30) REVERT: A 1891 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6622 (tpm170) REVERT: B 213 ASP cc_start: 0.7363 (OUTLIER) cc_final: 0.6638 (m-30) REVERT: B 378 MET cc_start: 0.7182 (tpt) cc_final: 0.6881 (tpt) REVERT: H 159 MET cc_start: -0.0298 (OUTLIER) cc_final: -0.0530 (mmt) REVERT: O 143 LYS cc_start: 0.7525 (tptt) cc_final: 0.7211 (tptp) REVERT: O 146 ARG cc_start: 0.6804 (OUTLIER) cc_final: 0.6013 (mpt180) REVERT: O 219 ASP cc_start: 0.5948 (m-30) cc_final: 0.5520 (p0) REVERT: T 267 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7991 (mt-10) REVERT: T 671 LEU cc_start: 0.8105 (mp) cc_final: 0.7862 (mp) REVERT: T 719 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7715 (mtm) REVERT: T 798 GLN cc_start: 0.7671 (mm-40) cc_final: 0.7348 (mm-40) outliers start: 85 outliers final: 44 residues processed: 425 average time/residue: 1.7037 time to fit residues: 867.3999 Evaluate side-chains 411 residues out of total 4137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 358 time to evaluate : 4.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 640 LYS Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1387 ASN Chi-restraints excluded: chain A residue 1473 GLU Chi-restraints excluded: chain A residue 1476 GLN Chi-restraints excluded: chain A residue 1672 VAL Chi-restraints excluded: chain A residue 1891 ARG Chi-restraints excluded: chain A residue 1925 MET Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain F residue 660 VAL Chi-restraints excluded: chain F residue 677 LEU Chi-restraints excluded: chain F residue 844 MET Chi-restraints excluded: chain F residue 897 ASN Chi-restraints excluded: chain G residue 357 GLU Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 159 MET Chi-restraints excluded: chain I residue 68 ASP Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 1278 MET Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 146 ARG Chi-restraints excluded: chain O residue 178 LEU Chi-restraints excluded: chain O residue 251 LYS Chi-restraints excluded: chain O residue 318 THR Chi-restraints excluded: chain O residue 320 GLN Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain Q residue 201 THR Chi-restraints excluded: chain Q residue 215 SER Chi-restraints excluded: chain T residue 267 GLU Chi-restraints excluded: chain T residue 362 GLU Chi-restraints excluded: chain T residue 649 ASP Chi-restraints excluded: chain T residue 719 MET Chi-restraints excluded: chain T residue 784 LEU Chi-restraints excluded: chain W residue 101 MET Chi-restraints excluded: chain W residue 108 MET Chi-restraints excluded: chain W residue 195 VAL Chi-restraints excluded: chain W residue 242 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 155 optimal weight: 1.9990 chunk 415 optimal weight: 8.9990 chunk 91 optimal weight: 0.8980 chunk 270 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 461 optimal weight: 5.9990 chunk 383 optimal weight: 6.9990 chunk 213 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 242 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1674 ASN B 247 ASN B 368 HIS C 453 GLN F 621 ASN ** F 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 ASN ** W 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.123 40596 Z= 0.472 Angle : 0.741 11.877 54938 Z= 0.383 Chirality : 0.050 0.283 5792 Planarity : 0.006 0.077 7040 Dihedral : 8.529 108.293 5711 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.58 % Favored : 94.36 % Rotamer: Outliers : 2.95 % Allowed : 12.89 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.08 (0.12), residues: 4699 helix: 1.21 (0.12), residues: 2021 sheet: 0.67 (0.20), residues: 633 loop : -1.35 (0.13), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 351 HIS 0.014 0.002 HIS A1075 PHE 0.034 0.003 PHE M 28 TYR 0.023 0.003 TYR A 304 ARG 0.010 0.001 ARG T 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 4137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 362 time to evaluate : 4.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6577 (tp30) REVERT: A 48 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7396 (mm-30) REVERT: A 744 ARG cc_start: 0.6510 (OUTLIER) cc_final: 0.6002 (ttm110) REVERT: A 1402 GLN cc_start: 0.7619 (mm110) cc_final: 0.7196 (mp10) REVERT: A 1473 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: A 1476 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7457 (tm-30) REVERT: A 1891 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.6744 (tpm170) REVERT: B 146 ASP cc_start: 0.4858 (OUTLIER) cc_final: 0.4575 (m-30) REVERT: B 213 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.6677 (m-30) REVERT: B 290 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.6494 (mm-30) REVERT: B 378 MET cc_start: 0.7241 (tpt) cc_final: 0.6865 (tpt) REVERT: F 752 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7702 (tpp) REVERT: H 159 MET cc_start: 0.0009 (OUTLIER) cc_final: -0.0234 (mmt) REVERT: K 65 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.6985 (mtm180) REVERT: N 1283 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7810 (tm) REVERT: O 146 ARG cc_start: 0.6866 (OUTLIER) cc_final: 0.6076 (tpt170) REVERT: O 219 ASP cc_start: 0.5949 (m-30) cc_final: 0.5493 (p0) REVERT: O 301 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7395 (tptp) REVERT: Q 217 LYS cc_start: 0.6907 (OUTLIER) cc_final: 0.6355 (mmtt) REVERT: T 267 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8100 (mt-10) REVERT: T 408 LYS cc_start: 0.7082 (OUTLIER) cc_final: 0.6298 (tptt) REVERT: T 671 LEU cc_start: 0.8106 (mp) cc_final: 0.7899 (mp) REVERT: T 719 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.7969 (mtm) outliers start: 122 outliers final: 58 residues processed: 437 average time/residue: 1.6908 time to fit residues: 887.4009 Evaluate side-chains 431 residues out of total 4137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 354 time to evaluate : 4.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 610 LYS Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 640 LYS Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain A residue 1075 HIS Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1387 ASN Chi-restraints excluded: chain A residue 1473 GLU Chi-restraints excluded: chain A residue 1476 GLN Chi-restraints excluded: chain A residue 1606 VAL Chi-restraints excluded: chain A residue 1672 VAL Chi-restraints excluded: chain A residue 1891 ARG Chi-restraints excluded: chain A residue 1925 MET Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 660 VAL Chi-restraints excluded: chain F residue 677 LEU Chi-restraints excluded: chain F residue 752 MET Chi-restraints excluded: chain F residue 844 MET Chi-restraints excluded: chain F residue 897 ASN Chi-restraints excluded: chain F residue 915 VAL Chi-restraints excluded: chain G residue 357 GLU Chi-restraints excluded: chain G residue 383 ASP Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 159 MET Chi-restraints excluded: chain I residue 68 ASP Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 1278 MET Chi-restraints excluded: chain N residue 1283 LEU Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 146 ARG Chi-restraints excluded: chain O residue 178 LEU Chi-restraints excluded: chain O residue 251 LYS Chi-restraints excluded: chain O residue 301 LYS Chi-restraints excluded: chain O residue 318 THR Chi-restraints excluded: chain O residue 320 GLN Chi-restraints excluded: chain Q residue 121 ARG Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain Q residue 201 THR Chi-restraints excluded: chain Q residue 215 SER Chi-restraints excluded: chain Q residue 217 LYS Chi-restraints excluded: chain T residue 267 GLU Chi-restraints excluded: chain T residue 362 GLU Chi-restraints excluded: chain T residue 408 LYS Chi-restraints excluded: chain T residue 649 ASP Chi-restraints excluded: chain T residue 719 MET Chi-restraints excluded: chain T residue 784 LEU Chi-restraints excluded: chain T residue 848 LEU Chi-restraints excluded: chain W residue 101 MET Chi-restraints excluded: chain W residue 195 VAL Chi-restraints excluded: chain W residue 242 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 444 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 262 optimal weight: 2.9990 chunk 337 optimal weight: 9.9990 chunk 261 optimal weight: 0.8980 chunk 388 optimal weight: 0.8980 chunk 257 optimal weight: 0.9980 chunk 459 optimal weight: 4.9990 chunk 287 optimal weight: 3.9990 chunk 280 optimal weight: 2.9990 chunk 212 optimal weight: 6.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1609 ASN C 453 GLN ** F 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 40596 Z= 0.259 Angle : 0.626 15.545 54938 Z= 0.323 Chirality : 0.044 0.239 5792 Planarity : 0.005 0.074 7040 Dihedral : 8.244 105.320 5711 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.62 % Favored : 95.32 % Rotamer: Outliers : 2.68 % Allowed : 13.81 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.12), residues: 4699 helix: 1.46 (0.12), residues: 2014 sheet: 0.67 (0.20), residues: 637 loop : -1.26 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 278 HIS 0.008 0.001 HIS A1075 PHE 0.031 0.002 PHE A 872 TYR 0.019 0.002 TYR A 304 ARG 0.011 0.000 ARG A 662 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 4137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 360 time to evaluate : 4.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7331 (mm-30) REVERT: A 1402 GLN cc_start: 0.7641 (mm110) cc_final: 0.7223 (mp10) REVERT: A 1473 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7132 (mp0) REVERT: A 1476 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7438 (tm-30) REVERT: A 1891 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.6769 (tpm170) REVERT: B 213 ASP cc_start: 0.7360 (OUTLIER) cc_final: 0.6651 (m-30) REVERT: B 290 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.6381 (mm-30) REVERT: B 378 MET cc_start: 0.7268 (tpt) cc_final: 0.6786 (tpt) REVERT: F 752 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7732 (tpp) REVERT: H 159 MET cc_start: 0.0042 (OUTLIER) cc_final: -0.0207 (mmt) REVERT: I 332 ARG cc_start: 0.6340 (OUTLIER) cc_final: 0.5735 (ptp-110) REVERT: K 65 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.6974 (mtm180) REVERT: N 1283 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7738 (tm) REVERT: O 143 LYS cc_start: 0.7500 (tptp) cc_final: 0.7160 (tptp) REVERT: O 146 ARG cc_start: 0.6806 (OUTLIER) cc_final: 0.6020 (mpt180) REVERT: O 219 ASP cc_start: 0.5991 (m-30) cc_final: 0.5522 (p0) REVERT: T 267 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8002 (mt-10) REVERT: T 408 LYS cc_start: 0.7094 (OUTLIER) cc_final: 0.6244 (tptt) REVERT: T 671 LEU cc_start: 0.7978 (mp) cc_final: 0.7729 (mp) REVERT: T 719 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.7729 (mtm) REVERT: T 798 GLN cc_start: 0.7793 (mm-40) cc_final: 0.7418 (mm-40) outliers start: 111 outliers final: 64 residues processed: 428 average time/residue: 1.6525 time to fit residues: 854.4802 Evaluate side-chains 433 residues out of total 4137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 354 time to evaluate : 4.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 640 LYS Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 1075 HIS Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1387 ASN Chi-restraints excluded: chain A residue 1473 GLU Chi-restraints excluded: chain A residue 1476 GLN Chi-restraints excluded: chain A residue 1672 VAL Chi-restraints excluded: chain A residue 1776 THR Chi-restraints excluded: chain A residue 1891 ARG Chi-restraints excluded: chain A residue 1925 MET Chi-restraints excluded: chain A residue 1978 THR Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 544 MET Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain F residue 533 MET Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 660 VAL Chi-restraints excluded: chain F residue 677 LEU Chi-restraints excluded: chain F residue 752 MET Chi-restraints excluded: chain F residue 759 THR Chi-restraints excluded: chain F residue 803 VAL Chi-restraints excluded: chain F residue 844 MET Chi-restraints excluded: chain F residue 897 ASN Chi-restraints excluded: chain G residue 357 GLU Chi-restraints excluded: chain G residue 383 ASP Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 159 MET Chi-restraints excluded: chain I residue 68 ASP Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain I residue 332 ARG Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 1278 MET Chi-restraints excluded: chain N residue 1283 LEU Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 146 ARG Chi-restraints excluded: chain O residue 178 LEU Chi-restraints excluded: chain O residue 179 VAL Chi-restraints excluded: chain O residue 251 LYS Chi-restraints excluded: chain O residue 318 THR Chi-restraints excluded: chain O residue 320 GLN Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain Q residue 201 THR Chi-restraints excluded: chain Q residue 215 SER Chi-restraints excluded: chain T residue 267 GLU Chi-restraints excluded: chain T residue 331 MET Chi-restraints excluded: chain T residue 362 GLU Chi-restraints excluded: chain T residue 394 ASP Chi-restraints excluded: chain T residue 408 LYS Chi-restraints excluded: chain T residue 649 ASP Chi-restraints excluded: chain T residue 719 MET Chi-restraints excluded: chain T residue 784 LEU Chi-restraints excluded: chain T residue 848 LEU Chi-restraints excluded: chain W residue 101 MET Chi-restraints excluded: chain W residue 108 MET Chi-restraints excluded: chain W residue 195 VAL Chi-restraints excluded: chain W residue 242 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 284 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 274 optimal weight: 5.9990 chunk 138 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 89 optimal weight: 0.0670 chunk 292 optimal weight: 3.9990 chunk 313 optimal weight: 10.0000 chunk 227 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 361 optimal weight: 0.9980 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 453 GLN F 621 ASN ** F 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 40596 Z= 0.174 Angle : 0.563 12.669 54938 Z= 0.290 Chirality : 0.041 0.193 5792 Planarity : 0.004 0.066 7040 Dihedral : 7.865 101.716 5711 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.55 % Favored : 95.40 % Rotamer: Outliers : 2.10 % Allowed : 14.75 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 0.57 (0.12), residues: 4699 helix: 1.74 (0.12), residues: 2008 sheet: 0.73 (0.20), residues: 638 loop : -1.17 (0.13), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 278 HIS 0.004 0.001 HIS A1747 PHE 0.033 0.001 PHE A 872 TYR 0.017 0.001 TYR N1287 ARG 0.011 0.000 ARG A 662 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 4137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 361 time to evaluate : 4.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 PHE cc_start: 0.7317 (t80) cc_final: 0.7085 (t80) REVERT: A 1351 LYS cc_start: 0.8277 (ptpt) cc_final: 0.7951 (pttt) REVERT: A 1402 GLN cc_start: 0.7592 (mm110) cc_final: 0.7186 (mp10) REVERT: A 1891 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.6461 (tpm170) REVERT: B 213 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.6611 (m-30) REVERT: B 378 MET cc_start: 0.7397 (tpt) cc_final: 0.6817 (tpt) REVERT: F 677 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7851 (pp) REVERT: F 752 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7713 (tpp) REVERT: F 897 ASN cc_start: 0.8282 (OUTLIER) cc_final: 0.7949 (t0) REVERT: I 87 ILE cc_start: 0.8253 (mp) cc_final: 0.8014 (mt) REVERT: I 332 ARG cc_start: 0.6121 (OUTLIER) cc_final: 0.5571 (ptp-110) REVERT: K 65 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.6960 (mtm180) REVERT: N 1283 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7678 (tm) REVERT: O 146 ARG cc_start: 0.6783 (OUTLIER) cc_final: 0.5994 (mpt180) REVERT: O 219 ASP cc_start: 0.5994 (m-30) cc_final: 0.5545 (p0) REVERT: T 267 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7930 (mt-10) REVERT: T 671 LEU cc_start: 0.8123 (mp) cc_final: 0.7782 (mp) REVERT: T 719 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.7658 (mtm) REVERT: T 798 GLN cc_start: 0.7545 (mm-40) cc_final: 0.7184 (mm-40) REVERT: T 848 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7764 (mm) outliers start: 87 outliers final: 48 residues processed: 413 average time/residue: 1.7378 time to fit residues: 857.2176 Evaluate side-chains 411 residues out of total 4137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 351 time to evaluate : 4.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 1075 HIS Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1387 ASN Chi-restraints excluded: chain A residue 1672 VAL Chi-restraints excluded: chain A residue 1776 THR Chi-restraints excluded: chain A residue 1891 ARG Chi-restraints excluded: chain A residue 1925 MET Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 544 MET Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 660 VAL Chi-restraints excluded: chain F residue 677 LEU Chi-restraints excluded: chain F residue 752 MET Chi-restraints excluded: chain F residue 803 VAL Chi-restraints excluded: chain F residue 844 MET Chi-restraints excluded: chain F residue 897 ASN Chi-restraints excluded: chain G residue 329 LEU Chi-restraints excluded: chain G residue 357 GLU Chi-restraints excluded: chain G residue 383 ASP Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain I residue 332 ARG Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 1283 LEU Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 146 ARG Chi-restraints excluded: chain O residue 251 LYS Chi-restraints excluded: chain O residue 318 THR Chi-restraints excluded: chain O residue 320 GLN Chi-restraints excluded: chain Q residue 201 THR Chi-restraints excluded: chain Q residue 215 SER Chi-restraints excluded: chain T residue 267 GLU Chi-restraints excluded: chain T residue 362 GLU Chi-restraints excluded: chain T residue 649 ASP Chi-restraints excluded: chain T residue 719 MET Chi-restraints excluded: chain T residue 784 LEU Chi-restraints excluded: chain T residue 848 LEU Chi-restraints excluded: chain W residue 101 MET Chi-restraints excluded: chain W residue 108 MET Chi-restraints excluded: chain W residue 242 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 418 optimal weight: 0.5980 chunk 440 optimal weight: 1.9990 chunk 401 optimal weight: 6.9990 chunk 428 optimal weight: 5.9990 chunk 257 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 336 optimal weight: 9.9990 chunk 131 optimal weight: 0.9980 chunk 387 optimal weight: 4.9990 chunk 405 optimal weight: 2.9990 chunk 426 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 453 GLN ** F 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 ASN ** W 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 40596 Z= 0.300 Angle : 0.641 11.678 54938 Z= 0.330 Chirality : 0.045 0.241 5792 Planarity : 0.005 0.075 7040 Dihedral : 8.058 104.056 5711 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.21 % Favored : 94.72 % Rotamer: Outliers : 2.01 % Allowed : 15.09 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.45 (0.12), residues: 4699 helix: 1.60 (0.12), residues: 2011 sheet: 0.68 (0.20), residues: 640 loop : -1.20 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 278 HIS 0.010 0.002 HIS A1075 PHE 0.035 0.002 PHE A 872 TYR 0.020 0.002 TYR A 417 ARG 0.013 0.001 ARG A 662 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 4137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 357 time to evaluate : 4.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1351 LYS cc_start: 0.8247 (ptpt) cc_final: 0.7911 (pttt) REVERT: A 1402 GLN cc_start: 0.7660 (mm110) cc_final: 0.7239 (mp10) REVERT: A 1891 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.6466 (tpm170) REVERT: B 146 ASP cc_start: 0.4663 (OUTLIER) cc_final: 0.4344 (m-30) REVERT: B 213 ASP cc_start: 0.7360 (OUTLIER) cc_final: 0.6684 (m-30) REVERT: B 243 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.7229 (t80) REVERT: B 378 MET cc_start: 0.7293 (tpt) cc_final: 0.6845 (tpt) REVERT: F 752 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7779 (tpp) REVERT: I 87 ILE cc_start: 0.8277 (mp) cc_final: 0.8042 (mt) REVERT: I 332 ARG cc_start: 0.6145 (OUTLIER) cc_final: 0.5593 (ptp-110) REVERT: K 65 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7009 (mtm180) REVERT: N 1283 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7748 (tm) REVERT: O 146 ARG cc_start: 0.6809 (OUTLIER) cc_final: 0.6022 (mpt180) REVERT: O 219 ASP cc_start: 0.5950 (m-30) cc_final: 0.5527 (p0) REVERT: T 267 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8047 (mt-10) REVERT: T 671 LEU cc_start: 0.8009 (mp) cc_final: 0.7690 (mp) REVERT: T 719 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.7719 (mtm) REVERT: T 798 GLN cc_start: 0.7601 (mm-40) cc_final: 0.7204 (mm-40) outliers start: 83 outliers final: 62 residues processed: 407 average time/residue: 1.7371 time to fit residues: 847.5004 Evaluate side-chains 428 residues out of total 4137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 355 time to evaluate : 4.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 1075 HIS Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1387 ASN Chi-restraints excluded: chain A residue 1606 VAL Chi-restraints excluded: chain A residue 1638 ASN Chi-restraints excluded: chain A residue 1672 VAL Chi-restraints excluded: chain A residue 1776 THR Chi-restraints excluded: chain A residue 1891 ARG Chi-restraints excluded: chain A residue 1925 MET Chi-restraints excluded: chain A residue 1978 THR Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 243 PHE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 544 MET Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain F residue 559 LEU Chi-restraints excluded: chain F residue 660 VAL Chi-restraints excluded: chain F residue 677 LEU Chi-restraints excluded: chain F residue 752 MET Chi-restraints excluded: chain F residue 759 THR Chi-restraints excluded: chain F residue 803 VAL Chi-restraints excluded: chain F residue 844 MET Chi-restraints excluded: chain F residue 897 ASN Chi-restraints excluded: chain G residue 357 GLU Chi-restraints excluded: chain G residue 383 ASP Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 68 ASP Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain I residue 332 ARG Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 1283 LEU Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 146 ARG Chi-restraints excluded: chain O residue 178 LEU Chi-restraints excluded: chain O residue 179 VAL Chi-restraints excluded: chain O residue 251 LYS Chi-restraints excluded: chain O residue 318 THR Chi-restraints excluded: chain O residue 320 GLN Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain Q residue 201 THR Chi-restraints excluded: chain Q residue 215 SER Chi-restraints excluded: chain T residue 267 GLU Chi-restraints excluded: chain T residue 362 GLU Chi-restraints excluded: chain T residue 649 ASP Chi-restraints excluded: chain T residue 719 MET Chi-restraints excluded: chain T residue 784 LEU Chi-restraints excluded: chain T residue 848 LEU Chi-restraints excluded: chain W residue 101 MET Chi-restraints excluded: chain W residue 108 MET Chi-restraints excluded: chain W residue 242 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 281 optimal weight: 5.9990 chunk 453 optimal weight: 0.7980 chunk 276 optimal weight: 8.9990 chunk 214 optimal weight: 0.9980 chunk 314 optimal weight: 2.9990 chunk 475 optimal weight: 4.9990 chunk 437 optimal weight: 2.9990 chunk 378 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 292 optimal weight: 5.9990 chunk 232 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 453 GLN ** F 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 40596 Z= 0.193 Angle : 0.580 11.424 54938 Z= 0.298 Chirality : 0.042 0.211 5792 Planarity : 0.005 0.069 7040 Dihedral : 7.882 102.732 5711 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.53 % Favored : 95.42 % Rotamer: Outliers : 1.89 % Allowed : 15.23 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 0.57 (0.12), residues: 4699 helix: 1.74 (0.12), residues: 2011 sheet: 0.73 (0.20), residues: 638 loop : -1.16 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 278 HIS 0.005 0.001 HIS A1444 PHE 0.033 0.001 PHE A 872 TYR 0.015 0.001 TYR A 417 ARG 0.014 0.000 ARG A 662 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9398 Ramachandran restraints generated. 4699 Oldfield, 0 Emsley, 4699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 4137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 356 time to evaluate : 4.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1351 LYS cc_start: 0.8223 (ptpt) cc_final: 0.7911 (pttt) REVERT: A 1402 GLN cc_start: 0.7623 (mm110) cc_final: 0.7218 (mp10) REVERT: A 1919 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8104 (ptt180) REVERT: B 146 ASP cc_start: 0.4589 (OUTLIER) cc_final: 0.4252 (m-30) REVERT: B 213 ASP cc_start: 0.7234 (OUTLIER) cc_final: 0.6619 (m-30) REVERT: B 378 MET cc_start: 0.7402 (tpt) cc_final: 0.6814 (tpt) REVERT: F 677 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7855 (pp) REVERT: F 752 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7809 (tpp) REVERT: F 897 ASN cc_start: 0.8256 (OUTLIER) cc_final: 0.7940 (t0) REVERT: H 99 MET cc_start: 0.6238 (mmm) cc_final: 0.6029 (mmm) REVERT: I 87 ILE cc_start: 0.8210 (mp) cc_final: 0.7980 (mt) REVERT: I 332 ARG cc_start: 0.6112 (OUTLIER) cc_final: 0.5566 (ptp-110) REVERT: K 65 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.6981 (mtm180) REVERT: N 1283 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7694 (tm) REVERT: O 146 ARG cc_start: 0.6791 (OUTLIER) cc_final: 0.6006 (mpt180) REVERT: O 219 ASP cc_start: 0.6004 (m-30) cc_final: 0.5554 (p0) REVERT: T 267 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7943 (mt-10) REVERT: T 451 LEU cc_start: 0.8797 (tp) cc_final: 0.8596 (mt) REVERT: T 671 LEU cc_start: 0.8058 (mp) cc_final: 0.7703 (mp) REVERT: T 719 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.7708 (mtm) REVERT: T 798 GLN cc_start: 0.7546 (mm-40) cc_final: 0.7312 (mm-40) outliers start: 78 outliers final: 51 residues processed: 405 average time/residue: 1.6157 time to fit residues: 782.1036 Evaluate side-chains 413 residues out of total 4137 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 350 time to evaluate : 4.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 1075 HIS Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1387 ASN Chi-restraints excluded: chain A residue 1672 VAL Chi-restraints excluded: chain A residue 1776 THR Chi-restraints excluded: chain A residue 1919 ARG Chi-restraints excluded: chain A residue 1925 MET Chi-restraints excluded: chain A residue 1978 THR Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 544 MET Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 274 LYS Chi-restraints excluded: chain F residue 660 VAL Chi-restraints excluded: chain F residue 677 LEU Chi-restraints excluded: chain F residue 752 MET Chi-restraints excluded: chain F residue 759 THR Chi-restraints excluded: chain F residue 803 VAL Chi-restraints excluded: chain F residue 844 MET Chi-restraints excluded: chain F residue 897 ASN Chi-restraints excluded: chain G residue 357 GLU Chi-restraints excluded: chain G residue 383 ASP Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain I residue 332 ARG Chi-restraints excluded: chain K residue 65 ARG Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 78 SER Chi-restraints excluded: chain N residue 1283 LEU Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 146 ARG Chi-restraints excluded: chain O residue 178 LEU Chi-restraints excluded: chain O residue 179 VAL Chi-restraints excluded: chain O residue 251 LYS Chi-restraints excluded: chain O residue 318 THR Chi-restraints excluded: chain O residue 320 GLN Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain Q residue 201 THR Chi-restraints excluded: chain Q residue 215 SER Chi-restraints excluded: chain T residue 267 GLU Chi-restraints excluded: chain T residue 362 GLU Chi-restraints excluded: chain T residue 649 ASP Chi-restraints excluded: chain T residue 719 MET Chi-restraints excluded: chain T residue 784 LEU Chi-restraints excluded: chain T residue 848 LEU Chi-restraints excluded: chain W residue 101 MET Chi-restraints excluded: chain W residue 108 MET Chi-restraints excluded: chain W residue 242 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 300 optimal weight: 0.6980 chunk 403 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 348 optimal weight: 0.5980 chunk 55 optimal weight: 0.4980 chunk 105 optimal weight: 4.9990 chunk 379 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 389 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1158 ASN C 410 GLN C 453 GLN F 621 ASN ** F 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 HIS I 102 GLN K 84 ASN Q 161 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.138016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.104524 restraints weight = 65043.341| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.98 r_work: 0.3203 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 40596 Z= 0.155 Angle : 0.545 11.291 54938 Z= 0.279 Chirality : 0.041 0.237 5792 Planarity : 0.004 0.064 7040 Dihedral : 7.582 100.073 5707 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.49 % Favored : 95.47 % Rotamer: Outliers : 1.64 % Allowed : 15.52 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 0.75 (0.12), residues: 4699 helix: 1.90 (0.12), residues: 2013 sheet: 0.79 (0.20), residues: 639 loop : -1.08 (0.13), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 278 HIS 0.004 0.001 HIS A1747 PHE 0.035 0.001 PHE A 872 TYR 0.014 0.001 TYR B 214 ARG 0.014 0.000 ARG A 662 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14760.71 seconds wall clock time: 261 minutes 13.55 seconds (15673.55 seconds total)