Starting phenix.real_space_refine on Thu Apr 11 03:03:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vgz_8672/04_2024/5vgz_8672_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vgz_8672/04_2024/5vgz_8672.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vgz_8672/04_2024/5vgz_8672.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vgz_8672/04_2024/5vgz_8672.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vgz_8672/04_2024/5vgz_8672_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vgz_8672/04_2024/5vgz_8672_neut.pdb" } resolution = 4.5 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 36736 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 184 5.16 5 C 23324 2.51 5 N 6298 2.21 5 O 6934 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 97": "NH1" <-> "NH2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "C ARG 113": "NH1" <-> "NH2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 121": "NH1" <-> "NH2" Residue "E ARG 30": "NH1" <-> "NH2" Residue "E ARG 78": "NH1" <-> "NH2" Residue "E ARG 84": "NH1" <-> "NH2" Residue "E ARG 85": "NH1" <-> "NH2" Residue "E ARG 97": "NH1" <-> "NH2" Residue "E ARG 113": "NH1" <-> "NH2" Residue "F ARG 61": "NH1" <-> "NH2" Residue "U ARG 55": "NH1" <-> "NH2" Residue "U ARG 57": "NH1" <-> "NH2" Residue "U ARG 194": "NH1" <-> "NH2" Residue "U TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 344": "NH1" <-> "NH2" Residue "U ARG 361": "NH1" <-> "NH2" Residue "U ARG 546": "NH1" <-> "NH2" Residue "U ARG 559": "NH1" <-> "NH2" Residue "U ARG 600": "NH1" <-> "NH2" Residue "U ARG 601": "NH1" <-> "NH2" Residue "U ARG 684": "NH1" <-> "NH2" Residue "U ARG 751": "NH1" <-> "NH2" Residue "V TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 200": "NH1" <-> "NH2" Residue "V ARG 236": "NH1" <-> "NH2" Residue "V TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 306": "NH1" <-> "NH2" Residue "V ARG 314": "NH1" <-> "NH2" Residue "V ARG 345": "NH1" <-> "NH2" Residue "V ARG 355": "NH1" <-> "NH2" Residue "V TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 470": "NH1" <-> "NH2" Residue "V PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 479": "NH1" <-> "NH2" Residue "W ARG 12": "NH1" <-> "NH2" Residue "W ARG 94": "NH1" <-> "NH2" Residue "W ARG 129": "NH1" <-> "NH2" Residue "W ARG 142": "NH1" <-> "NH2" Residue "W ARG 182": "NH1" <-> "NH2" Residue "W ARG 191": "NH1" <-> "NH2" Residue "W GLU 220": "OE1" <-> "OE2" Residue "W ARG 329": "NH1" <-> "NH2" Residue "X ARG 363": "NH1" <-> "NH2" Residue "Y ARG 177": "NH1" <-> "NH2" Residue "Y ARG 342": "NH1" <-> "NH2" Residue "Z ARG 25": "NH1" <-> "NH2" Residue "a ARG 352": "NH1" <-> "NH2" Residue "d TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 25": "NH1" <-> "NH2" Residue "d ARG 65": "NH1" <-> "NH2" Residue "d ARG 251": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 36741 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 654 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 8, 'TRANS': 74} Chain: "B" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 556 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "C" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 954 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "D" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 870 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "E" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 853 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain: "F" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 799 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain breaks: 1 Chain: "U" Number of atoms: 6568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 845, 6568 Classifications: {'peptide': 845} Link IDs: {'PTRANS': 32, 'TRANS': 812} Chain breaks: 3 Chain: "V" Number of atoms: 3919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3919 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 23, 'TRANS': 464} Chain: "W" Number of atoms: 3703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3703 Classifications: {'peptide': 456} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 447} Chain breaks: 1 Chain: "X" Number of atoms: 3048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3048 Classifications: {'peptide': 385} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 374} Chain breaks: 1 Chain: "Y" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3115 Classifications: {'peptide': 378} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 370} Chain: "Z" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2281 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain: "a" Number of atoms: 3003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3003 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 361} Chain: "b" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1458 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 9, 'TRANS': 181} Chain: "c" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2260 Classifications: {'peptide': 287} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 276} Chain: "d" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2116 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 245} Chain: "e" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 583 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N ALA X 359 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA X 359 " occ=0.50 residue: pdb=" N GLN X 380 " occ=0.50 ... (7 atoms not shown) pdb=" NE2 GLN X 380 " occ=0.50 residue: pdb=" N GLY Z 30 " occ=0.38 ... (2 atoms not shown) pdb=" O GLY Z 30 " occ=0.38 residue: pdb=" N ILE b 90 " occ=0.46 ... (6 atoms not shown) pdb=" CD1 ILE b 90 " occ=0.46 residue: pdb=" N SER b 115 " occ=0.70 ... (4 atoms not shown) pdb=" OG SER b 115 " occ=0.70 residue: pdb=" N ILE b 140 " occ=0.39 ... (6 atoms not shown) pdb=" CD1 ILE b 140 " occ=0.39 residue: pdb=" N VAL b 173 " occ=0.89 ... (5 atoms not shown) pdb=" CG2 VAL b 173 " occ=0.89 residue: pdb=" N GLY b 191 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY b 191 " occ=0.50 residue: pdb=" N ILE d 63 " occ=0.78 ... (6 atoms not shown) pdb=" CD1 ILE d 63 " occ=0.78 residue: pdb=" N SER d 70 " occ=0.95 ... (4 atoms not shown) pdb=" OG SER d 70 " occ=0.95 residue: pdb=" N MET d 95 " occ=0.66 ... (6 atoms not shown) pdb=" CE MET d 95 " occ=0.66 residue: pdb=" N MET d 144 " occ=0.52 ... (6 atoms not shown) pdb=" CE MET d 144 " occ=0.52 Time building chain proxies: 14.37, per 1000 atoms: 0.39 Number of scatterers: 36741 At special positions: 0 Unit cell: (212.66, 191.1, 188.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 184 16.00 O 6934 8.00 N 6298 7.00 C 23324 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.84 Conformation dependent library (CDL) restraints added in 5.2 seconds 9114 Ramachandran restraints generated. 4557 Oldfield, 0 Emsley, 4557 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8762 Finding SS restraints... Secondary structure from input PDB file: 224 helices and 16 sheets defined 61.7% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.86 Creating SS restraints... Processing helix chain 'A' and resid 74 through 82 removed outlier: 3.885A pdb=" N TRP A 78 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP A 79 " --> pdb=" O PRO A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 89 removed outlier: 4.038A pdb=" N GLN A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 134 Processing helix chain 'B' and resid 98 through 102 removed outlier: 3.967A pdb=" N ASP B 101 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 68 removed outlier: 4.078A pdb=" N GLN C 64 " --> pdb=" O ARG C 60 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 56 removed outlier: 4.254A pdb=" N LYS D 45 " --> pdb=" O TYR D 41 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU D 50 " --> pdb=" O LYS D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 81 removed outlier: 3.697A pdb=" N TYR D 60 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS D 69 " --> pdb=" O GLN D 65 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS D 70 " --> pdb=" O LYS D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 removed outlier: 3.694A pdb=" N LEU D 123 " --> pdb=" O ASP D 120 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS D 125 " --> pdb=" O GLU D 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 28 removed outlier: 3.982A pdb=" N LEU E 16 " --> pdb=" O TYR E 12 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU E 17 " --> pdb=" O ARG E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 35 removed outlier: 4.029A pdb=" N GLU E 35 " --> pdb=" O GLU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 50 removed outlier: 3.860A pdb=" N GLN E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU E 44 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 57 Processing helix chain 'F' and resid 58 through 77 removed outlier: 3.583A pdb=" N VAL F 62 " --> pdb=" O GLU F 58 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LYS F 74 " --> pdb=" O LYS F 70 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N GLU F 75 " --> pdb=" O ASP F 71 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASN F 76 " --> pdb=" O LYS F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 84 removed outlier: 4.134A pdb=" N LYS F 81 " --> pdb=" O SER F 77 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL F 82 " --> pdb=" O GLU F 78 " (cutoff:3.500A) Processing helix chain 'U' and resid 6 through 13 Processing helix chain 'U' and resid 19 through 31 removed outlier: 3.699A pdb=" N ALA U 23 " --> pdb=" O LEU U 19 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA U 29 " --> pdb=" O HIS U 25 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL U 30 " --> pdb=" O LYS U 26 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 51 removed outlier: 3.553A pdb=" N ASP U 51 " --> pdb=" O VAL U 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 72 removed outlier: 3.529A pdb=" N ALA U 60 " --> pdb=" O SER U 56 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL U 63 " --> pdb=" O PHE U 59 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N TYR U 69 " --> pdb=" O SER U 65 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N HIS U 70 " --> pdb=" O LYS U 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 82 removed outlier: 3.520A pdb=" N SER U 77 " --> pdb=" O ALA U 73 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR U 80 " --> pdb=" O GLU U 76 " (cutoff:3.500A) Processing helix chain 'U' and resid 94 through 115 Processing helix chain 'U' and resid 127 through 142 removed outlier: 3.637A pdb=" N GLU U 131 " --> pdb=" O ASP U 127 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET U 137 " --> pdb=" O ILE U 133 " (cutoff:3.500A) Processing helix chain 'U' and resid 143 through 147 removed outlier: 6.792A pdb=" N LYS U 146 " --> pdb=" O ASP U 143 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TYR U 147 " --> pdb=" O ASP U 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 143 through 147' Processing helix chain 'U' and resid 148 through 157 removed outlier: 3.655A pdb=" N GLY U 152 " --> pdb=" O LYS U 148 " (cutoff:3.500A) Processing helix chain 'U' and resid 172 through 185 Processing helix chain 'U' and resid 193 through 202 Processing helix chain 'U' and resid 212 through 221 removed outlier: 3.782A pdb=" N VAL U 216 " --> pdb=" O ASP U 212 " (cutoff:3.500A) Processing helix chain 'U' and resid 225 through 228 Processing helix chain 'U' and resid 229 through 240 removed outlier: 3.857A pdb=" N GLU U 234 " --> pdb=" O SER U 230 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU U 236 " --> pdb=" O ILE U 232 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL U 237 " --> pdb=" O LEU U 233 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS U 238 " --> pdb=" O GLU U 234 " (cutoff:3.500A) Processing helix chain 'U' and resid 241 through 255 removed outlier: 4.095A pdb=" N ALA U 245 " --> pdb=" O ASN U 241 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR U 246 " --> pdb=" O LEU U 242 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLN U 247 " --> pdb=" O LEU U 243 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE U 248 " --> pdb=" O MET U 244 " (cutoff:3.500A) Processing helix chain 'U' and resid 258 through 271 removed outlier: 3.968A pdb=" N GLN U 266 " --> pdb=" O SER U 262 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL U 271 " --> pdb=" O ASN U 267 " (cutoff:3.500A) Processing helix chain 'U' and resid 318 through 329 removed outlier: 3.730A pdb=" N LEU U 323 " --> pdb=" O LYS U 319 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU U 329 " --> pdb=" O MET U 325 " (cutoff:3.500A) Processing helix chain 'U' and resid 331 through 345 removed outlier: 3.826A pdb=" N ILE U 335 " --> pdb=" O GLY U 331 " (cutoff:3.500A) Processing helix chain 'U' and resid 349 through 360 removed outlier: 3.531A pdb=" N LEU U 353 " --> pdb=" O ASP U 349 " (cutoff:3.500A) Processing helix chain 'U' and resid 364 through 377 removed outlier: 3.995A pdb=" N ALA U 368 " --> pdb=" O VAL U 364 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL U 370 " --> pdb=" O HIS U 366 " (cutoff:3.500A) Processing helix chain 'U' and resid 399 through 412 removed outlier: 3.584A pdb=" N HIS U 412 " --> pdb=" O LEU U 408 " (cutoff:3.500A) Processing helix chain 'U' and resid 417 through 425 Processing helix chain 'U' and resid 436 through 450 Processing helix chain 'U' and resid 457 through 466 removed outlier: 3.789A pdb=" N ASN U 463 " --> pdb=" O ASP U 459 " (cutoff:3.500A) Processing helix chain 'U' and resid 474 through 485 Processing helix chain 'U' and resid 490 through 502 Processing helix chain 'U' and resid 505 through 520 removed outlier: 3.787A pdb=" N LEU U 518 " --> pdb=" O LEU U 514 " (cutoff:3.500A) Processing helix chain 'U' and resid 525 through 537 removed outlier: 3.573A pdb=" N ILE U 529 " --> pdb=" O ASN U 525 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU U 530 " --> pdb=" O ALA U 526 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN U 537 " --> pdb=" O VAL U 533 " (cutoff:3.500A) Processing helix chain 'U' and resid 542 through 555 removed outlier: 3.935A pdb=" N VAL U 555 " --> pdb=" O GLY U 551 " (cutoff:3.500A) Processing helix chain 'U' and resid 563 through 572 removed outlier: 3.765A pdb=" N ARG U 572 " --> pdb=" O GLU U 568 " (cutoff:3.500A) Processing helix chain 'U' and resid 575 through 591 removed outlier: 3.785A pdb=" N MET U 583 " --> pdb=" O ARG U 579 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N MET U 588 " --> pdb=" O TYR U 584 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA U 589 " --> pdb=" O THR U 585 " (cutoff:3.500A) Processing helix chain 'U' and resid 597 through 609 removed outlier: 3.848A pdb=" N ARG U 601 " --> pdb=" O LYS U 597 " (cutoff:3.500A) Processing helix chain 'U' and resid 611 through 617 removed outlier: 3.817A pdb=" N ARG U 615 " --> pdb=" O ASN U 611 " (cutoff:3.500A) Processing helix chain 'U' and resid 618 through 626 removed outlier: 4.116A pdb=" N LEU U 622 " --> pdb=" O ALA U 618 " (cutoff:3.500A) Processing helix chain 'U' and resid 627 through 629 No H-bonds generated for 'chain 'U' and resid 627 through 629' Processing helix chain 'U' and resid 631 through 637 removed outlier: 4.310A pdb=" N SER U 635 " --> pdb=" O GLU U 631 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL U 636 " --> pdb=" O GLN U 632 " (cutoff:3.500A) Processing helix chain 'U' and resid 637 through 642 removed outlier: 4.468A pdb=" N GLU U 642 " --> pdb=" O SER U 638 " (cutoff:3.500A) Processing helix chain 'U' and resid 645 through 660 removed outlier: 3.816A pdb=" N ARG U 649 " --> pdb=" O ASN U 645 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N CYS U 660 " --> pdb=" O LEU U 656 " (cutoff:3.500A) Processing helix chain 'U' and resid 665 through 670 removed outlier: 4.141A pdb=" N ILE U 669 " --> pdb=" O ASN U 665 " (cutoff:3.500A) Processing helix chain 'U' and resid 671 through 676 Processing helix chain 'U' and resid 680 through 693 Processing helix chain 'U' and resid 705 through 714 Processing helix chain 'U' and resid 717 through 721 removed outlier: 4.167A pdb=" N LYS U 720 " --> pdb=" O ILE U 717 " (cutoff:3.500A) Processing helix chain 'U' and resid 723 through 738 removed outlier: 3.645A pdb=" N PHE U 728 " --> pdb=" O VAL U 724 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE U 736 " --> pdb=" O LEU U 732 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU U 737 " --> pdb=" O ALA U 733 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP U 738 " --> pdb=" O GLN U 734 " (cutoff:3.500A) Processing helix chain 'U' and resid 739 through 742 Processing helix chain 'U' and resid 756 through 768 Processing helix chain 'U' and resid 772 through 781 removed outlier: 3.770A pdb=" N SER U 780 " --> pdb=" O HIS U 777 " (cutoff:3.500A) Processing helix chain 'U' and resid 807 through 812 removed outlier: 3.562A pdb=" N PHE U 811 " --> pdb=" O PRO U 808 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA U 812 " --> pdb=" O SER U 809 " (cutoff:3.500A) Processing helix chain 'U' and resid 885 through 890 removed outlier: 3.796A pdb=" N LYS U 890 " --> pdb=" O ALA U 887 " (cutoff:3.500A) Processing helix chain 'V' and resid 19 through 24 Processing helix chain 'V' and resid 31 through 52 removed outlier: 3.939A pdb=" N VAL V 35 " --> pdb=" O ALA V 31 " (cutoff:3.500A) Processing helix chain 'V' and resid 62 through 73 Processing helix chain 'V' and resid 86 through 90 removed outlier: 3.804A pdb=" N LYS V 89 " --> pdb=" O VAL V 86 " (cutoff:3.500A) Processing helix chain 'V' and resid 104 through 118 removed outlier: 4.126A pdb=" N VAL V 112 " --> pdb=" O LEU V 108 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS V 115 " --> pdb=" O TYR V 111 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN V 118 " --> pdb=" O TYR V 114 " (cutoff:3.500A) Processing helix chain 'V' and resid 131 through 134 Processing helix chain 'V' and resid 135 through 141 removed outlier: 3.994A pdb=" N ASP V 140 " --> pdb=" O GLU V 136 " (cutoff:3.500A) Processing helix chain 'V' and resid 147 through 164 Proline residue: V 158 - end of helix Proline residue: V 161 - end of helix Processing helix chain 'V' and resid 170 through 186 removed outlier: 4.029A pdb=" N PHE V 174 " --> pdb=" O LEU V 170 " (cutoff:3.500A) Processing helix chain 'V' and resid 197 through 214 removed outlier: 4.346A pdb=" N LEU V 205 " --> pdb=" O ARG V 201 " (cutoff:3.500A) Processing helix chain 'V' and resid 214 through 222 removed outlier: 3.707A pdb=" N LEU V 221 " --> pdb=" O VAL V 217 " (cutoff:3.500A) Processing helix chain 'V' and resid 226 through 236 removed outlier: 3.883A pdb=" N HIS V 232 " --> pdb=" O ARG V 228 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA V 233 " --> pdb=" O SER V 229 " (cutoff:3.500A) Processing helix chain 'V' and resid 244 through 261 removed outlier: 3.539A pdb=" N LEU V 253 " --> pdb=" O THR V 249 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU V 254 " --> pdb=" O LEU V 250 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS V 260 " --> pdb=" O ARG V 256 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TYR V 261 " --> pdb=" O ASN V 257 " (cutoff:3.500A) Processing helix chain 'V' and resid 267 through 272 Processing helix chain 'V' and resid 283 through 296 Processing helix chain 'V' and resid 303 through 315 removed outlier: 3.713A pdb=" N ARG V 307 " --> pdb=" O SER V 303 " (cutoff:3.500A) Processing helix chain 'V' and resid 324 through 337 removed outlier: 4.305A pdb=" N VAL V 328 " --> pdb=" O PHE V 324 " (cutoff:3.500A) Processing helix chain 'V' and resid 338 through 340 No H-bonds generated for 'chain 'V' and resid 338 through 340' Processing helix chain 'V' and resid 352 through 358 Processing helix chain 'V' and resid 360 through 370 removed outlier: 4.715A pdb=" N ARG V 368 " --> pdb=" O THR V 364 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR V 369 " --> pdb=" O GLN V 365 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY V 370 " --> pdb=" O ALA V 366 " (cutoff:3.500A) Processing helix chain 'V' and resid 371 through 382 removed outlier: 3.570A pdb=" N GLN V 377 " --> pdb=" O ALA V 373 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP V 380 " --> pdb=" O ASN V 376 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE V 382 " --> pdb=" O VAL V 378 " (cutoff:3.500A) Processing helix chain 'V' and resid 392 through 399 Processing helix chain 'V' and resid 401 through 412 Processing helix chain 'V' and resid 420 through 426 Processing helix chain 'V' and resid 430 through 443 removed outlier: 3.777A pdb=" N ALA V 434 " --> pdb=" O SER V 430 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU V 435 " --> pdb=" O PRO V 431 " (cutoff:3.500A) Processing helix chain 'V' and resid 471 through 493 removed outlier: 4.254A pdb=" N GLN V 478 " --> pdb=" O LEU V 474 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG V 479 " --> pdb=" O ALA V 475 " (cutoff:3.500A) Processing helix chain 'V' and resid 495 through 503 Processing helix chain 'W' and resid 2 through 16 removed outlier: 3.509A pdb=" N GLU W 7 " --> pdb=" O ASP W 3 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG W 8 " --> pdb=" O GLY W 4 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL W 14 " --> pdb=" O ASP W 10 " (cutoff:3.500A) Processing helix chain 'W' and resid 20 through 37 removed outlier: 3.791A pdb=" N VAL W 24 " --> pdb=" O TYR W 20 " (cutoff:3.500A) Proline residue: W 29 - end of helix removed outlier: 3.566A pdb=" N LYS W 33 " --> pdb=" O PRO W 29 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU W 34 " --> pdb=" O GLU W 30 " (cutoff:3.500A) Processing helix chain 'W' and resid 44 through 49 Processing helix chain 'W' and resid 50 through 63 Processing helix chain 'W' and resid 69 through 79 removed outlier: 3.640A pdb=" N GLU W 76 " --> pdb=" O LYS W 72 " (cutoff:3.500A) Processing helix chain 'W' and resid 82 through 87 removed outlier: 4.213A pdb=" N ASN W 86 " --> pdb=" O LEU W 82 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE W 87 " --> pdb=" O LEU W 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 82 through 87' Processing helix chain 'W' and resid 96 through 111 Processing helix chain 'W' and resid 116 through 135 removed outlier: 4.360A pdb=" N ILE W 120 " --> pdb=" O THR W 116 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS W 121 " --> pdb=" O ASP W 117 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU W 122 " --> pdb=" O LEU W 118 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG W 129 " --> pdb=" O ILE W 125 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR W 132 " --> pdb=" O LEU W 128 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS W 135 " --> pdb=" O VAL W 131 " (cutoff:3.500A) Processing helix chain 'W' and resid 140 through 157 removed outlier: 4.265A pdb=" N THR W 146 " --> pdb=" O ARG W 142 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE W 152 " --> pdb=" O THR W 148 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN W 155 " --> pdb=" O THR W 151 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY W 157 " --> pdb=" O LYS W 153 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 160 No H-bonds generated for 'chain 'W' and resid 158 through 160' Processing helix chain 'W' and resid 161 through 172 removed outlier: 3.728A pdb=" N GLN W 170 " --> pdb=" O LEU W 166 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL W 171 " --> pdb=" O GLN W 167 " (cutoff:3.500A) Processing helix chain 'W' and resid 179 through 186 removed outlier: 3.884A pdb=" N VAL W 183 " --> pdb=" O LYS W 179 " (cutoff:3.500A) Processing helix chain 'W' and resid 187 through 189 No H-bonds generated for 'chain 'W' and resid 187 through 189' Processing helix chain 'W' and resid 192 through 197 Processing helix chain 'W' and resid 198 through 205 Processing helix chain 'W' and resid 207 through 210 No H-bonds generated for 'chain 'W' and resid 207 through 210' Processing helix chain 'W' and resid 222 through 238 removed outlier: 3.529A pdb=" N TYR W 226 " --> pdb=" O LEU W 222 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE W 231 " --> pdb=" O TYR W 227 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN W 232 " --> pdb=" O ASN W 228 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LEU W 233 " --> pdb=" O LEU W 229 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP W 234 " --> pdb=" O MET W 230 " (cutoff:3.500A) Processing helix chain 'W' and resid 240 through 244 removed outlier: 3.560A pdb=" N ILE W 243 " --> pdb=" O TYR W 240 " (cutoff:3.500A) Processing helix chain 'W' and resid 252 through 257 Processing helix chain 'W' and resid 268 through 276 removed outlier: 4.117A pdb=" N LEU W 272 " --> pdb=" O LYS W 268 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR W 273 " --> pdb=" O SER W 269 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N VAL W 274 " --> pdb=" O VAL W 270 " (cutoff:3.500A) Processing helix chain 'W' and resid 281 through 291 removed outlier: 3.702A pdb=" N VAL W 287 " --> pdb=" O GLN W 283 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N HIS W 288 " --> pdb=" O SER W 284 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG W 289 " --> pdb=" O ASP W 285 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE W 290 " --> pdb=" O LEU W 286 " (cutoff:3.500A) Processing helix chain 'W' and resid 293 through 298 removed outlier: 3.969A pdb=" N GLU W 297 " --> pdb=" O ASP W 293 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU W 298 " --> pdb=" O LYS W 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 293 through 298' Processing helix chain 'W' and resid 301 through 308 Processing helix chain 'W' and resid 317 through 330 removed outlier: 3.983A pdb=" N GLU W 322 " --> pdb=" O SER W 318 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP W 323 " --> pdb=" O THR W 319 " (cutoff:3.500A) Processing helix chain 'W' and resid 336 through 341 Processing helix chain 'W' and resid 345 through 367 removed outlier: 4.250A pdb=" N ILE W 363 " --> pdb=" O VAL W 359 " (cutoff:3.500A) Processing helix chain 'W' and resid 374 through 382 removed outlier: 3.523A pdb=" N GLN W 380 " --> pdb=" O LYS W 376 " (cutoff:3.500A) Processing helix chain 'W' and resid 385 through 398 removed outlier: 3.674A pdb=" N VAL W 398 " --> pdb=" O SER W 394 " (cutoff:3.500A) Processing helix chain 'W' and resid 424 through 452 removed outlier: 4.087A pdb=" N HIS W 444 " --> pdb=" O ASN W 440 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU W 445 " --> pdb=" O LYS W 441 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE W 446 " --> pdb=" O THR W 442 " (cutoff:3.500A) Processing helix chain 'W' and resid 453 through 456 removed outlier: 3.504A pdb=" N GLN W 456 " --> pdb=" O HIS W 453 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 453 through 456' Processing helix chain 'X' and resid 39 through 60 Processing helix chain 'X' and resid 63 through 73 removed outlier: 3.813A pdb=" N LEU X 70 " --> pdb=" O LEU X 66 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS X 71 " --> pdb=" O GLY X 67 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 80 removed outlier: 3.538A pdb=" N ILE X 80 " --> pdb=" O LEU X 77 " (cutoff:3.500A) Processing helix chain 'X' and resid 81 through 98 Processing helix chain 'X' and resid 102 through 120 removed outlier: 3.550A pdb=" N GLU X 106 " --> pdb=" O ALA X 102 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL X 107 " --> pdb=" O THR X 103 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU X 108 " --> pdb=" O GLY X 104 " (cutoff:3.500A) Processing helix chain 'X' and resid 122 through 141 removed outlier: 3.927A pdb=" N SER X 135 " --> pdb=" O ALA X 131 " (cutoff:3.500A) Processing helix chain 'X' and resid 142 through 156 removed outlier: 3.510A pdb=" N LEU X 147 " --> pdb=" O TYR X 143 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU X 156 " --> pdb=" O GLN X 152 " (cutoff:3.500A) Processing helix chain 'X' and resid 162 through 180 removed outlier: 3.757A pdb=" N LEU X 166 " --> pdb=" O ASP X 162 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL X 167 " --> pdb=" O LYS X 163 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU X 168 " --> pdb=" O ALA X 164 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL X 169 " --> pdb=" O LEU X 165 " (cutoff:3.500A) Processing helix chain 'X' and resid 182 through 197 Processing helix chain 'X' and resid 203 through 222 removed outlier: 3.973A pdb=" N THR X 209 " --> pdb=" O LYS X 205 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU X 210 " --> pdb=" O LEU X 206 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASP X 211 " --> pdb=" O GLN X 207 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE X 216 " --> pdb=" O MET X 212 " (cutoff:3.500A) Processing helix chain 'X' and resid 224 through 239 Processing helix chain 'X' and resid 243 through 261 Processing helix chain 'X' and resid 263 through 271 removed outlier: 3.512A pdb=" N VAL X 267 " --> pdb=" O THR X 263 " (cutoff:3.500A) Processing helix chain 'X' and resid 273 through 278 removed outlier: 3.974A pdb=" N ARG X 278 " --> pdb=" O LYS X 274 " (cutoff:3.500A) Processing helix chain 'X' and resid 281 through 296 removed outlier: 4.157A pdb=" N ALA X 286 " --> pdb=" O ARG X 282 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU X 287 " --> pdb=" O GLN X 283 " (cutoff:3.500A) Processing helix chain 'X' and resid 299 through 309 removed outlier: 3.601A pdb=" N TYR X 309 " --> pdb=" O ALA X 305 " (cutoff:3.500A) Processing helix chain 'X' and resid 319 through 339 Processing helix chain 'X' and resid 346 through 352 Processing helix chain 'X' and resid 357 through 371 removed outlier: 4.085A pdb=" N VAL X 361 " --> pdb=" O SER X 357 " (cutoff:3.500A) Processing helix chain 'X' and resid 393 through 422 removed outlier: 3.869A pdb=" N TYR X 397 " --> pdb=" O VAL X 393 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU X 398 " --> pdb=" O ASP X 394 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER X 408 " --> pdb=" O ILE X 404 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS X 409 " --> pdb=" O GLN X 405 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR X 422 " --> pdb=" O ALA X 418 " (cutoff:3.500A) Processing helix chain 'Y' and resid 15 through 20 Processing helix chain 'Y' and resid 22 through 28 Processing helix chain 'Y' and resid 34 through 43 Processing helix chain 'Y' and resid 44 through 46 No H-bonds generated for 'chain 'Y' and resid 44 through 46' Processing helix chain 'Y' and resid 49 through 56 removed outlier: 3.511A pdb=" N TYR Y 53 " --> pdb=" O ASN Y 49 " (cutoff:3.500A) Processing helix chain 'Y' and resid 57 through 60 Processing helix chain 'Y' and resid 65 through 92 removed outlier: 4.256A pdb=" N LEU Y 69 " --> pdb=" O ILE Y 65 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU Y 70 " --> pdb=" O ASP Y 66 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASN Y 71 " --> pdb=" O VAL Y 67 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS Y 72 " --> pdb=" O ASP Y 68 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS Y 75 " --> pdb=" O ASN Y 71 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU Y 78 " --> pdb=" O LYS Y 74 " (cutoff:3.500A) Processing helix chain 'Y' and resid 97 through 115 Processing helix chain 'Y' and resid 116 through 130 removed outlier: 3.527A pdb=" N ALA Y 120 " --> pdb=" O ASP Y 116 " (cutoff:3.500A) Processing helix chain 'Y' and resid 133 through 152 removed outlier: 4.040A pdb=" N ILE Y 147 " --> pdb=" O TYR Y 143 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE Y 150 " --> pdb=" O ARG Y 146 " (cutoff:3.500A) Processing helix chain 'Y' and resid 154 through 164 removed outlier: 4.151A pdb=" N ASN Y 160 " --> pdb=" O LEU Y 156 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR Y 161 " --> pdb=" O ILE Y 157 " (cutoff:3.500A) Processing helix chain 'Y' and resid 175 through 191 Processing helix chain 'Y' and resid 199 through 204 removed outlier: 3.937A pdb=" N ASP Y 203 " --> pdb=" O LEU Y 200 " (cutoff:3.500A) Processing helix chain 'Y' and resid 215 through 231 removed outlier: 4.391A pdb=" N TYR Y 225 " --> pdb=" O THR Y 221 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL Y 226 " --> pdb=" O TYR Y 222 " (cutoff:3.500A) Processing helix chain 'Y' and resid 232 through 239 Processing helix chain 'Y' and resid 244 through 250 Processing helix chain 'Y' and resid 253 through 265 removed outlier: 3.996A pdb=" N ARG Y 257 " --> pdb=" O LEU Y 253 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU Y 263 " --> pdb=" O TYR Y 259 " (cutoff:3.500A) Processing helix chain 'Y' and resid 267 through 283 removed outlier: 3.776A pdb=" N GLN Y 273 " --> pdb=" O SER Y 269 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA Y 276 " --> pdb=" O PHE Y 272 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N VAL Y 277 " --> pdb=" O GLN Y 273 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL Y 278 " --> pdb=" O SER Y 274 " (cutoff:3.500A) Processing helix chain 'Y' and resid 291 through 310 removed outlier: 3.705A pdb=" N VAL Y 296 " --> pdb=" O TYR Y 292 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER Y 310 " --> pdb=" O GLN Y 306 " (cutoff:3.500A) Processing helix chain 'Y' and resid 316 through 324 Processing helix chain 'Y' and resid 326 through 340 removed outlier: 3.832A pdb=" N ILE Y 330 " --> pdb=" O GLY Y 326 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN Y 332 " --> pdb=" O GLU Y 328 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA Y 339 " --> pdb=" O SER Y 335 " (cutoff:3.500A) Processing helix chain 'Y' and resid 363 through 368 Processing helix chain 'Y' and resid 369 through 387 removed outlier: 3.582A pdb=" N ILE Y 387 " --> pdb=" O LEU Y 383 " (cutoff:3.500A) Processing helix chain 'Z' and resid 12 through 23 removed outlier: 4.237A pdb=" N LEU Z 16 " --> pdb=" O HIS Z 12 " (cutoff:3.500A) Processing helix chain 'Z' and resid 71 through 86 removed outlier: 3.658A pdb=" N LEU Z 75 " --> pdb=" O ASP Z 71 " (cutoff:3.500A) Processing helix chain 'Z' and resid 104 through 115 removed outlier: 3.506A pdb=" N LEU Z 111 " --> pdb=" O ALA Z 107 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N MET Z 112 " --> pdb=" O ILE Z 108 " (cutoff:3.500A) Processing helix chain 'Z' and resid 166 through 177 removed outlier: 3.607A pdb=" N VAL Z 170 " --> pdb=" O GLU Z 166 " (cutoff:3.500A) Processing helix chain 'Z' and resid 186 through 217 removed outlier: 3.838A pdb=" N THR Z 192 " --> pdb=" O SER Z 188 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N GLY Z 197 " --> pdb=" O ASN Z 193 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU Z 198 " --> pdb=" O GLN Z 194 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER Z 203 " --> pdb=" O LYS Z 199 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG Z 209 " --> pdb=" O LEU Z 205 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N SER Z 210 " --> pdb=" O LEU Z 206 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA Z 216 " --> pdb=" O LEU Z 212 " (cutoff:3.500A) Processing helix chain 'Z' and resid 225 through 235 removed outlier: 3.798A pdb=" N GLN Z 229 " --> pdb=" O GLN Z 225 " (cutoff:3.500A) Processing helix chain 'Z' and resid 245 through 288 removed outlier: 4.005A pdb=" N LEU Z 272 " --> pdb=" O SER Z 268 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N HIS Z 273 " --> pdb=" O VAL Z 269 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN Z 274 " --> pdb=" O VAL Z 270 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LYS Z 279 " --> pdb=" O LEU Z 275 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASN Z 282 " --> pdb=" O ASN Z 278 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP Z 284 " --> pdb=" O ILE Z 280 " (cutoff:3.500A) Processing helix chain 'a' and resid 4 through 6 No H-bonds generated for 'chain 'a' and resid 4 through 6' Processing helix chain 'a' and resid 7 through 13 Processing helix chain 'a' and resid 18 through 32 removed outlier: 3.854A pdb=" N ARG a 24 " --> pdb=" O ALA a 20 " (cutoff:3.500A) Processing helix chain 'a' and resid 33 through 47 Processing helix chain 'a' and resid 54 through 67 removed outlier: 3.648A pdb=" N LEU a 59 " --> pdb=" O GLY a 55 " (cutoff:3.500A) Processing helix chain 'a' and resid 73 through 88 Processing helix chain 'a' and resid 89 through 104 removed outlier: 3.521A pdb=" N LEU a 94 " --> pdb=" O PRO a 90 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR a 95 " --> pdb=" O ASN a 91 " (cutoff:3.500A) Processing helix chain 'a' and resid 110 through 123 Processing helix chain 'a' and resid 128 through 142 removed outlier: 4.184A pdb=" N LEU a 142 " --> pdb=" O VAL a 138 " (cutoff:3.500A) Processing helix chain 'a' and resid 149 through 165 removed outlier: 3.588A pdb=" N THR a 165 " --> pdb=" O LYS a 161 " (cutoff:3.500A) Processing helix chain 'a' and resid 169 through 183 removed outlier: 3.636A pdb=" N ARG a 178 " --> pdb=" O LYS a 174 " (cutoff:3.500A) Processing helix chain 'a' and resid 189 through 207 removed outlier: 4.715A pdb=" N GLU a 195 " --> pdb=" O SER a 191 " (cutoff:3.500A) Processing helix chain 'a' and resid 213 through 219 Processing helix chain 'a' and resid 219 through 225 removed outlier: 4.204A pdb=" N GLU a 223 " --> pdb=" O HIS a 219 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 243 removed outlier: 3.606A pdb=" N THR a 236 " --> pdb=" O TRP a 232 " (cutoff:3.500A) Processing helix chain 'a' and resid 248 through 253 Processing helix chain 'a' and resid 260 through 282 removed outlier: 3.954A pdb=" N ASN a 264 " --> pdb=" O ASP a 260 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA a 266 " --> pdb=" O ALA a 262 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLN a 267 " --> pdb=" O ALA a 263 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU a 274 " --> pdb=" O ARG a 270 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU a 275 " --> pdb=" O LYS a 271 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS a 276 " --> pdb=" O ILE a 272 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU a 277 " --> pdb=" O GLN a 273 " (cutoff:3.500A) Processing helix chain 'a' and resid 292 through 301 removed outlier: 3.952A pdb=" N ILE a 296 " --> pdb=" O THR a 292 " (cutoff:3.500A) Processing helix chain 'a' and resid 306 through 318 removed outlier: 3.580A pdb=" N GLY a 318 " --> pdb=" O ALA a 314 " (cutoff:3.500A) Processing helix chain 'a' and resid 342 through 375 removed outlier: 4.416A pdb=" N GLN a 370 " --> pdb=" O LEU a 366 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP a 373 " --> pdb=" O HIS a 369 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 17 removed outlier: 3.794A pdb=" N MET b 16 " --> pdb=" O SER b 13 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG b 17 " --> pdb=" O GLU b 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 13 through 17' Processing helix chain 'b' and resid 24 through 44 removed outlier: 3.868A pdb=" N ALA b 28 " --> pdb=" O THR b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 68 through 75 removed outlier: 3.887A pdb=" N SER b 73 " --> pdb=" O GLY b 69 " (cutoff:3.500A) Processing helix chain 'b' and resid 86 through 95 removed outlier: 3.941A pdb=" N ALA b 93 " --> pdb=" O GLY b 89 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU b 95 " --> pdb=" O ARG b 91 " (cutoff:3.500A) Processing helix chain 'b' and resid 96 through 100 removed outlier: 3.523A pdb=" N HIS b 99 " --> pdb=" O ALA b 96 " (cutoff:3.500A) Processing helix chain 'b' and resid 120 through 135 Processing helix chain 'b' and resid 151 through 161 removed outlier: 4.415A pdb=" N ALA b 155 " --> pdb=" O GLU b 151 " (cutoff:3.500A) Processing helix chain 'b' and resid 180 through 185 Processing helix chain 'c' and resid 34 through 47 Processing helix chain 'c' and resid 88 through 101 Processing helix chain 'c' and resid 123 through 134 Processing helix chain 'c' and resid 164 through 169 removed outlier: 3.780A pdb=" N MET c 168 " --> pdb=" O ALA c 165 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL c 169 " --> pdb=" O ASN c 166 " (cutoff:3.500A) Processing helix chain 'c' and resid 180 through 185 Processing helix chain 'c' and resid 210 through 224 Processing helix chain 'c' and resid 233 through 244 removed outlier: 3.603A pdb=" N HIS c 237 " --> pdb=" O ASP c 233 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU c 242 " --> pdb=" O CYS c 238 " (cutoff:3.500A) Processing helix chain 'c' and resid 244 through 264 removed outlier: 3.556A pdb=" N MET c 248 " --> pdb=" O VAL c 244 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU c 262 " --> pdb=" O ALA c 258 " (cutoff:3.500A) Processing helix chain 'c' and resid 265 through 270 removed outlier: 3.808A pdb=" N GLN c 269 " --> pdb=" O MET c 265 " (cutoff:3.500A) Processing helix chain 'c' and resid 284 through 295 Processing helix chain 'c' and resid 295 through 310 removed outlier: 3.697A pdb=" N ALA c 302 " --> pdb=" O GLN c 298 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET c 303 " --> pdb=" O CYS c 299 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 30 removed outlier: 3.760A pdb=" N GLU d 21 " --> pdb=" O SER d 17 " (cutoff:3.500A) Processing helix chain 'd' and resid 44 through 65 Processing helix chain 'd' and resid 67 through 83 removed outlier: 4.129A pdb=" N CYS d 80 " --> pdb=" O ALA d 76 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR d 81 " --> pdb=" O GLN d 77 " (cutoff:3.500A) Processing helix chain 'd' and resid 94 through 109 Processing helix chain 'd' and resid 111 through 119 Processing helix chain 'd' and resid 130 through 146 removed outlier: 3.611A pdb=" N LYS d 134 " --> pdb=" O ASN d 130 " (cutoff:3.500A) Proline residue: d 136 - end of helix Processing helix chain 'd' and resid 148 through 154 Processing helix chain 'd' and resid 163 through 183 removed outlier: 4.795A pdb=" N ASP d 176 " --> pdb=" O ASP d 172 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N GLU d 177 " --> pdb=" O THR d 173 " (cutoff:3.500A) Processing helix chain 'd' and resid 191 through 198 removed outlier: 4.114A pdb=" N ARG d 196 " --> pdb=" O THR d 192 " (cutoff:3.500A) Processing helix chain 'd' and resid 203 through 213 removed outlier: 3.730A pdb=" N ALA d 210 " --> pdb=" O MET d 206 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS d 211 " --> pdb=" O THR d 207 " (cutoff:3.500A) Processing helix chain 'd' and resid 235 through 254 Processing helix chain 'e' and resid 4 through 17 removed outlier: 3.779A pdb=" N VAL e 8 " --> pdb=" O LYS e 4 " (cutoff:3.500A) Processing helix chain 'e' and resid 21 through 35 removed outlier: 3.775A pdb=" N LEU e 30 " --> pdb=" O ASP e 26 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASP e 33 " --> pdb=" O GLY e 29 " (cutoff:3.500A) Processing helix chain 'e' and resid 40 through 55 removed outlier: 3.551A pdb=" N ASP e 44 " --> pdb=" O GLU e 40 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASN e 54 " --> pdb=" O ASP e 50 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLN e 55 " --> pdb=" O ASP e 51 " (cutoff:3.500A) Processing helix chain 'e' and resid 59 through 70 removed outlier: 4.242A pdb=" N GLY e 64 " --> pdb=" O LEU e 60 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N TYR e 65 " --> pdb=" O GLU e 61 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLU e 68 " --> pdb=" O GLY e 64 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR e 69 " --> pdb=" O TYR e 65 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 101 through 105 removed outlier: 3.520A pdb=" N ILE A 101 " --> pdb=" O ASN A 114 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE A 112 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASP A 105 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LYS A 110 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 123 " --> pdb=" O TYR A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 122 through 124 removed outlier: 7.140A pdb=" N ILE B 122 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 71 through 72 removed outlier: 7.855A pdb=" N THR D 100 " --> pdb=" O ALA D 95 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ALA D 95 " --> pdb=" O THR D 100 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ILE D 102 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU D 93 " --> pdb=" O ILE D 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 87 through 88 removed outlier: 7.500A pdb=" N ARG C 113 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ILE C 126 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ALA C 115 " --> pdb=" O HIS C 124 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 87 through 88 removed outlier: 3.825A pdb=" N LEU D 87 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ARG E 109 " --> pdb=" O ALA E 99 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ASP E 101 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE E 107 " --> pdb=" O ASP E 101 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 87 through 88 removed outlier: 3.825A pdb=" N LEU D 87 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN E 55 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR F 132 " --> pdb=" O ILE F 124 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE F 124 " --> pdb=" O TYR F 132 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU F 134 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 129 through 131 removed outlier: 4.453A pdb=" N SER D 129 " --> pdb=" O LEU D 143 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP D 141 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'U' and resid 744 through 746 Processing sheet with id=AA9, first strand: chain 'U' and resid 789 through 790 removed outlier: 5.184A pdb=" N ILE U 789 " --> pdb=" O ILE U 912 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'U' and resid 803 through 804 Processing sheet with id=AB2, first strand: chain 'X' and resid 378 through 379 removed outlier: 8.000A pdb=" N LEU X 378 " --> pdb=" O ARG Y 312 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU Y 314 " --> pdb=" O LEU X 378 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Z' and resid 48 through 50 removed outlier: 7.196A pdb=" N LYS Z 8 " --> pdb=" O LEU Z 48 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N VAL Z 50 " --> pdb=" O LYS Z 8 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL Z 10 " --> pdb=" O VAL Z 50 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N SER Z 152 " --> pdb=" O GLU Z 143 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU Z 143 " --> pdb=" O SER Z 152 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA Z 137 " --> pdb=" O VAL Z 158 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG Z 90 " --> pdb=" O GLY Z 41 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL Z 92 " --> pdb=" O LEU Z 39 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LEU Z 39 " --> pdb=" O VAL Z 92 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N TRP Z 94 " --> pdb=" O GLY Z 37 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLY Z 37 " --> pdb=" O TRP Z 94 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE Z 54 " --> pdb=" O VAL Z 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Z' and resid 59 through 60 removed outlier: 3.819A pdb=" N ASP Z 59 " --> pdb=" O PHE Z 69 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'b' and resid 62 through 65 removed outlier: 4.036A pdb=" N LEU b 64 " --> pdb=" O VAL b 49 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N VAL b 49 " --> pdb=" O LEU b 64 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N GLY b 50 " --> pdb=" O GLU b 4 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR b 6 " --> pdb=" O GLY b 50 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ILE b 52 " --> pdb=" O THR b 6 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N VAL b 8 " --> pdb=" O ILE b 52 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N SER b 5 " --> pdb=" O ARG b 108 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ILE b 110 " --> pdb=" O SER b 5 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N MET b 7 " --> pdb=" O ILE b 110 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N PHE b 112 " --> pdb=" O MET b 7 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N CYS b 9 " --> pdb=" O PHE b 112 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA b 111 " --> pdb=" O ASP b 139 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL b 171 " --> pdb=" O VAL b 138 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE b 140 " --> pdb=" O VAL b 171 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'c' and resid 200 through 203 removed outlier: 4.334A pdb=" N ALA c 159 " --> pdb=" O ILE c 203 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASP c 158 " --> pdb=" O VAL c 144 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL c 144 " --> pdb=" O ASP c 158 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA c 142 " --> pdb=" O PHE c 160 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL c 143 " --> pdb=" O TRP c 111 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N MET c 57 " --> pdb=" O VAL c 109 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N TRP c 111 " --> pdb=" O GLY c 55 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY c 55 " --> pdb=" O TRP c 111 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N MET c 54 " --> pdb=" O MET c 75 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLU c 60 " --> pdb=" O VAL c 69 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N VAL c 69 " --> pdb=" O GLU c 60 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL c 67 " --> pdb=" O GLN c 30 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N VAL c 31 " --> pdb=" O ASN c 206 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'd' and resid 189 through 190 removed outlier: 3.543A pdb=" N ILE d 189 " --> pdb=" O TYR d 222 " (cutoff:3.500A) 1765 hydrogen bonds defined for protein. 5178 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: 9.68 Time building geometry restraints manager: 11.98 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: 10195 1.33 - 1.45: 6090 1.45 - 1.57: 20770 1.57 - 1.69: 0 1.69 - 1.81: 310 Bond restraints: 37365 Sorted by residual: bond pdb=" N GLU W 220 " pdb=" CA GLU W 220 " ideal model delta sigma weight residual 1.458 1.416 0.042 1.00e-02 1.00e+04 1.76e+01 bond pdb=" C GLN A 91 " pdb=" N PRO A 92 " ideal model delta sigma weight residual 1.328 1.372 -0.044 1.26e-02 6.30e+03 1.22e+01 bond pdb=" CA GLU W 220 " pdb=" C GLU W 220 " ideal model delta sigma weight residual 1.526 1.569 -0.043 1.31e-02 5.83e+03 1.08e+01 bond pdb=" CA SER V 188 " pdb=" C SER V 188 " ideal model delta sigma weight residual 1.522 1.567 -0.045 1.40e-02 5.10e+03 1.05e+01 bond pdb=" C PRO X 391 " pdb=" N PRO X 392 " ideal model delta sigma weight residual 1.334 1.394 -0.060 2.34e-02 1.83e+03 6.60e+00 ... (remaining 37360 not shown) Histogram of bond angle deviations from ideal: 97.50 - 105.74: 721 105.74 - 113.98: 21842 113.98 - 122.22: 21611 122.22 - 130.46: 6096 130.46 - 138.70: 193 Bond angle restraints: 50463 Sorted by residual: angle pdb=" C LEU a 188 " pdb=" N PRO a 189 " pdb=" CA PRO a 189 " ideal model delta sigma weight residual 119.84 134.19 -14.35 1.25e+00 6.40e-01 1.32e+02 angle pdb=" N VAL a 190 " pdb=" CA VAL a 190 " pdb=" C VAL a 190 " ideal model delta sigma weight residual 110.53 101.28 9.25 9.40e-01 1.13e+00 9.68e+01 angle pdb=" C LEU Z 220 " pdb=" N PRO Z 221 " pdb=" CA PRO Z 221 " ideal model delta sigma weight residual 119.84 131.12 -11.28 1.25e+00 6.40e-01 8.14e+01 angle pdb=" C GLN V 279 " pdb=" N ALA V 280 " pdb=" CA ALA V 280 " ideal model delta sigma weight residual 122.44 113.43 9.01 1.19e+00 7.06e-01 5.73e+01 angle pdb=" N SER V 188 " pdb=" CA SER V 188 " pdb=" C SER V 188 " ideal model delta sigma weight residual 112.90 102.99 9.91 1.31e+00 5.83e-01 5.72e+01 ... (remaining 50458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 21715 17.66 - 35.32: 1077 35.32 - 52.98: 150 52.98 - 70.64: 16 70.64 - 88.30: 24 Dihedral angle restraints: 22982 sinusoidal: 9477 harmonic: 13505 Sorted by residual: dihedral pdb=" CA TYR V 261 " pdb=" C TYR V 261 " pdb=" N SER V 262 " pdb=" CA SER V 262 " ideal model delta harmonic sigma weight residual 180.00 151.91 28.09 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA ASP a 328 " pdb=" C ASP a 328 " pdb=" N LYS a 329 " pdb=" CA LYS a 329 " ideal model delta harmonic sigma weight residual -180.00 -154.63 -25.37 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA ALA Y 289 " pdb=" C ALA Y 289 " pdb=" N PRO Y 290 " pdb=" CA PRO Y 290 " ideal model delta harmonic sigma weight residual -180.00 -155.11 -24.89 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 22979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 4747 0.075 - 0.149: 891 0.149 - 0.224: 111 0.224 - 0.298: 16 0.298 - 0.373: 2 Chirality restraints: 5767 Sorted by residual: chirality pdb=" CA TYR U 147 " pdb=" N TYR U 147 " pdb=" C TYR U 147 " pdb=" CB TYR U 147 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CB ILE V 342 " pdb=" CA ILE V 342 " pdb=" CG1 ILE V 342 " pdb=" CG2 ILE V 342 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA VAL a 190 " pdb=" N VAL a 190 " pdb=" C VAL a 190 " pdb=" CB VAL a 190 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 5764 not shown) Planarity restraints: 6471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET V 192 " -0.022 2.00e-02 2.50e+03 4.65e-02 2.17e+01 pdb=" C MET V 192 " 0.080 2.00e-02 2.50e+03 pdb=" O MET V 192 " -0.031 2.00e-02 2.50e+03 pdb=" N GLN V 193 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU e 21 " 0.022 2.00e-02 2.50e+03 4.57e-02 2.08e+01 pdb=" C GLU e 21 " -0.079 2.00e-02 2.50e+03 pdb=" O GLU e 21 " 0.031 2.00e-02 2.50e+03 pdb=" N PHE e 22 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR W 219 " 0.019 2.00e-02 2.50e+03 4.39e-02 1.93e+01 pdb=" C THR W 219 " -0.076 2.00e-02 2.50e+03 pdb=" O THR W 219 " 0.031 2.00e-02 2.50e+03 pdb=" N GLU W 220 " 0.026 2.00e-02 2.50e+03 ... (remaining 6468 not shown) Histogram of nonbonded interaction distances: 0.87 - 1.68: 8 1.68 - 2.48: 260 2.48 - 3.29: 42868 3.29 - 4.09: 89767 4.09 - 4.90: 160498 Warning: very small nonbonded interaction distances. Nonbonded interactions: 293401 Sorted by model distance: nonbonded pdb=" NH2 ARG W 417 " pdb=" O PRO W 418 " model vdw 0.875 2.520 nonbonded pdb=" NH1 ARG W 417 " pdb=" OD2 ASP W 420 " model vdw 1.037 2.520 nonbonded pdb=" CD LYS U 146 " pdb=" NE2 GLN U 149 " model vdw 1.164 3.520 nonbonded pdb=" CZ ARG W 417 " pdb=" O PRO W 418 " model vdw 1.453 3.270 nonbonded pdb=" O GLU V 268 " pdb=" OG SER V 272 " model vdw 1.576 2.440 ... (remaining 293396 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.360 Construct map_model_manager: 0.030 Extract box with map and model: 5.090 Check model and map are aligned: 0.430 Set scattering table: 0.280 Process input model: 72.160 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 37365 Z= 0.340 Angle : 1.129 14.846 50463 Z= 0.624 Chirality : 0.059 0.373 5767 Planarity : 0.007 0.085 6471 Dihedral : 11.281 88.304 14220 Min Nonbonded Distance : 0.875 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.48 % Favored : 92.08 % Rotamer: Outliers : 0.81 % Allowed : 3.40 % Favored : 95.79 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.68 (0.10), residues: 4557 helix: -3.42 (0.07), residues: 2429 sheet: -1.75 (0.33), residues: 194 loop : -2.63 (0.13), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP d 61 HIS 0.022 0.003 HIS U 338 PHE 0.034 0.003 PHE c 160 TYR 0.031 0.003 TYR U 590 ARG 0.020 0.001 ARG W 408 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9114 Ramachandran restraints generated. 4557 Oldfield, 0 Emsley, 4557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9114 Ramachandran restraints generated. 4557 Oldfield, 0 Emsley, 4557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 826 time to evaluate : 3.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASN cc_start: 0.7989 (t0) cc_final: 0.7724 (m-40) REVERT: B 152 LEU cc_start: 0.8473 (mp) cc_final: 0.8127 (mm) REVERT: C 57 ARG cc_start: 0.9263 (tpp-160) cc_final: 0.9041 (ttm110) REVERT: C 60 ARG cc_start: 0.9106 (ttt-90) cc_final: 0.8693 (ptp-110) REVERT: C 61 GLU cc_start: 0.9207 (tt0) cc_final: 0.8980 (tm-30) REVERT: C 103 ILE cc_start: 0.7662 (mm) cc_final: 0.7426 (mt) REVERT: U 86 ASP cc_start: 0.7784 (t0) cc_final: 0.7469 (t0) REVERT: U 146 LYS cc_start: 0.2636 (OUTLIER) cc_final: 0.2311 (mtmt) REVERT: U 556 MET cc_start: 0.8688 (tpp) cc_final: 0.8342 (mmm) REVERT: U 691 SER cc_start: 0.9222 (t) cc_final: 0.8803 (p) REVERT: U 695 MET cc_start: 0.8327 (ptp) cc_final: 0.8079 (ptt) REVERT: U 710 ARG cc_start: 0.9544 (mmt-90) cc_final: 0.9341 (mmt180) REVERT: U 718 ASN cc_start: 0.8842 (t0) cc_final: 0.8530 (t0) REVERT: V 175 MET cc_start: 0.9212 (tpt) cc_final: 0.8574 (mtt) REVERT: V 176 MET cc_start: 0.9493 (tpt) cc_final: 0.9271 (tpt) REVERT: V 192 MET cc_start: 0.6778 (ptp) cc_final: 0.5651 (tpp) REVERT: V 211 TYR cc_start: 0.8030 (m-10) cc_final: 0.7681 (m-80) REVERT: V 289 LEU cc_start: 0.8981 (tt) cc_final: 0.8760 (tp) REVERT: V 429 ASP cc_start: 0.7423 (p0) cc_final: 0.6939 (p0) REVERT: V 482 PHE cc_start: 0.8371 (m-10) cc_final: 0.7979 (m-10) REVERT: V 494 MET cc_start: 0.7711 (ptm) cc_final: 0.6940 (ppp) REVERT: W 26 GLN cc_start: 0.8599 (mt0) cc_final: 0.8383 (tp40) REVERT: W 109 CYS cc_start: 0.8893 (t) cc_final: 0.8556 (m) REVERT: X 182 ASN cc_start: 0.8492 (t0) cc_final: 0.8177 (m-40) REVERT: X 402 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8119 (mm-30) REVERT: Y 277 VAL cc_start: 0.9426 (t) cc_final: 0.9191 (p) REVERT: Y 299 MET cc_start: 0.9103 (ttt) cc_final: 0.8443 (tmm) REVERT: Y 376 LEU cc_start: 0.9479 (tt) cc_final: 0.9262 (pp) REVERT: Z 28 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.6069 (tptp) REVERT: Z 43 TRP cc_start: 0.6171 (t-100) cc_final: 0.4731 (t60) REVERT: Z 138 TYR cc_start: 0.6536 (m-10) cc_final: 0.5968 (m-80) REVERT: Z 161 GLU cc_start: 0.8219 (pt0) cc_final: 0.7720 (pm20) REVERT: Z 168 GLU cc_start: 0.7321 (tt0) cc_final: 0.6748 (mp0) REVERT: Z 265 LEU cc_start: 0.9369 (mp) cc_final: 0.9114 (mm) REVERT: a 60 TYR cc_start: 0.8975 (m-10) cc_final: 0.8688 (m-10) REVERT: a 166 ILE cc_start: 0.8508 (mm) cc_final: 0.8256 (pt) REVERT: a 305 ASN cc_start: 0.8888 (m-40) cc_final: 0.8651 (m-40) REVERT: b 120 ASN cc_start: 0.8778 (p0) cc_final: 0.8450 (p0) REVERT: c 32 TYR cc_start: 0.8425 (m-10) cc_final: 0.8084 (m-10) REVERT: c 57 MET cc_start: 0.8859 (mtm) cc_final: 0.8656 (mtm) REVERT: c 128 ASN cc_start: 0.9075 (m-40) cc_final: 0.8468 (t0) REVERT: c 218 LEU cc_start: 0.9192 (tt) cc_final: 0.8912 (tp) REVERT: c 221 HIS cc_start: 0.8218 (t-170) cc_final: 0.7737 (t70) REVERT: c 236 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8260 (mt-10) REVERT: c 262 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8766 (tm-30) REVERT: d 11 ARG cc_start: 0.8723 (ttm-80) cc_final: 0.8456 (tpm170) REVERT: d 19 CYS cc_start: 0.8535 (m) cc_final: 0.8202 (m) REVERT: d 35 PHE cc_start: 0.6865 (m-80) cc_final: 0.6303 (m-80) REVERT: d 110 ASN cc_start: 0.8536 (t0) cc_final: 0.7844 (t0) REVERT: d 230 GLN cc_start: 0.6648 (mm110) cc_final: 0.5979 (tm-30) REVERT: e 5 LYS cc_start: 0.6535 (mttt) cc_final: 0.6040 (tttm) REVERT: e 14 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8120 (tt0) REVERT: e 22 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.6846 (t80) outliers start: 33 outliers final: 11 residues processed: 854 average time/residue: 0.4622 time to fit residues: 603.2314 Evaluate side-chains 424 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 410 time to evaluate : 3.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 381 optimal weight: 8.9990 chunk 342 optimal weight: 6.9990 chunk 190 optimal weight: 20.0000 chunk 117 optimal weight: 20.0000 chunk 231 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 354 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 215 optimal weight: 20.0000 chunk 263 optimal weight: 20.0000 chunk 410 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 HIS ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN D 98 GLN F 116 GLN ** U 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 247 GLN ** U 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 340 GLN U 373 ASN ** U 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 743 ASN ** U 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 901 GLN V 109 ASN ** V 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 452 ASN ** V 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 62 GLN X 218 HIS X 333 GLN X 349 HIS ** Y 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 367 GLN Z 102 HIS Z 189 GLN Z 194 GLN ** Z 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 35 HIS a 144 ASN ** a 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 244 ASN a 288 HIS ** a 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 372 HIS b 27 GLN b 29 GLN b 76 HIS b 99 HIS b 149 ASN c 219 ASN c 232 GLN c 241 ASN c 254 ASN ** c 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 60 GLN ** d 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 37365 Z= 0.259 Angle : 0.785 13.348 50463 Z= 0.408 Chirality : 0.044 0.196 5767 Planarity : 0.006 0.073 6471 Dihedral : 6.641 89.799 4974 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 22.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.16 % Favored : 91.81 % Rotamer: Outliers : 0.05 % Allowed : 3.62 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.63 % 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: -3.38 (0.11), residues: 4557 helix: -2.04 (0.09), residues: 2475 sheet: -1.90 (0.33), residues: 197 loop : -2.41 (0.14), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP c 225 HIS 0.009 0.002 HIS U 107 PHE 0.034 0.002 PHE W 392 TYR 0.030 0.002 TYR C 23 ARG 0.032 0.001 ARG b 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9114 Ramachandran restraints generated. 4557 Oldfield, 0 Emsley, 4557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9114 Ramachandran restraints generated. 4557 Oldfield, 0 Emsley, 4557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 514 time to evaluate : 3.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.8565 (mp0) cc_final: 0.7745 (mp0) REVERT: A 145 ASN cc_start: 0.8041 (t0) cc_final: 0.7784 (m-40) REVERT: B 132 TYR cc_start: 0.7388 (p90) cc_final: 0.7075 (p90) REVERT: C 60 ARG cc_start: 0.9131 (ttt-90) cc_final: 0.8702 (mmp80) REVERT: E 45 ASN cc_start: 0.8950 (t0) cc_final: 0.8726 (t0) REVERT: E 108 MET cc_start: 0.8014 (mmm) cc_final: 0.7788 (mmm) REVERT: U 86 ASP cc_start: 0.7870 (t0) cc_final: 0.7568 (t0) REVERT: U 188 MET cc_start: 0.6587 (tpt) cc_final: 0.6316 (tpt) REVERT: U 250 PHE cc_start: 0.9114 (m-80) cc_final: 0.8652 (m-10) REVERT: U 333 MET cc_start: 0.9327 (mmp) cc_final: 0.8962 (mtm) REVERT: U 411 ILE cc_start: 0.8950 (mm) cc_final: 0.8717 (mm) REVERT: U 510 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8185 (tm-30) REVERT: U 556 MET cc_start: 0.8610 (tpp) cc_final: 0.8190 (mmp) REVERT: U 654 MET cc_start: 0.8767 (mpp) cc_final: 0.8370 (mpp) REVERT: U 691 SER cc_start: 0.9387 (t) cc_final: 0.8952 (p) REVERT: U 695 MET cc_start: 0.8414 (ptp) cc_final: 0.8156 (ptt) REVERT: U 710 ARG cc_start: 0.9552 (mmt-90) cc_final: 0.9247 (mmt180) REVERT: U 718 ASN cc_start: 0.8803 (t0) cc_final: 0.8536 (t0) REVERT: U 725 MET cc_start: 0.8806 (ppp) cc_final: 0.8473 (ppp) REVERT: V 147 PHE cc_start: 0.6573 (m-80) cc_final: 0.6070 (m-80) REVERT: V 175 MET cc_start: 0.9208 (tpt) cc_final: 0.8706 (mtt) REVERT: V 211 TYR cc_start: 0.8438 (m-10) cc_final: 0.8035 (m-80) REVERT: V 219 GLU cc_start: 0.9267 (mt-10) cc_final: 0.8548 (pp20) REVERT: V 494 MET cc_start: 0.8017 (ptm) cc_final: 0.7335 (ttp) REVERT: W 26 GLN cc_start: 0.8608 (mt0) cc_final: 0.8247 (tp-100) REVERT: W 109 CYS cc_start: 0.8880 (t) cc_final: 0.8678 (m) REVERT: W 326 MET cc_start: 0.6971 (ptt) cc_final: 0.6447 (ppp) REVERT: Y 376 LEU cc_start: 0.9532 (tt) cc_final: 0.9248 (pp) REVERT: Z 82 PHE cc_start: 0.8940 (m-80) cc_final: 0.8652 (m-80) REVERT: Z 114 ARG cc_start: 0.8981 (mtm-85) cc_final: 0.8443 (mtm-85) REVERT: Z 276 ILE cc_start: 0.8396 (mt) cc_final: 0.8191 (mm) REVERT: a 60 TYR cc_start: 0.9049 (m-10) cc_final: 0.8781 (m-10) REVERT: a 280 MET cc_start: 0.8329 (ptp) cc_final: 0.8026 (ptm) REVERT: a 305 ASN cc_start: 0.8972 (m-40) cc_final: 0.8688 (m110) REVERT: a 312 MET cc_start: 0.8835 (mmp) cc_final: 0.8488 (mmm) REVERT: c 54 MET cc_start: 0.6581 (ptm) cc_final: 0.5943 (pmm) REVERT: c 122 LEU cc_start: 0.9267 (mt) cc_final: 0.8986 (mt) REVERT: c 128 ASN cc_start: 0.9108 (m-40) cc_final: 0.8688 (t0) REVERT: c 299 CYS cc_start: 0.8782 (m) cc_final: 0.8555 (t) REVERT: d 11 ARG cc_start: 0.8667 (ttm-80) cc_final: 0.8249 (tpm170) REVERT: d 230 GLN cc_start: 0.6717 (mm110) cc_final: 0.6068 (tm-30) outliers start: 2 outliers final: 0 residues processed: 516 average time/residue: 0.4314 time to fit residues: 346.2921 Evaluate side-chains 362 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 362 time to evaluate : 3.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 228 optimal weight: 8.9990 chunk 127 optimal weight: 2.9990 chunk 341 optimal weight: 6.9990 chunk 279 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 411 optimal weight: 3.9990 chunk 444 optimal weight: 5.9990 chunk 366 optimal weight: 6.9990 chunk 407 optimal weight: 10.0000 chunk 140 optimal weight: 40.0000 chunk 329 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 HIS U 355 ASN ** U 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 540 GLN ** U 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 168 GLN ** V 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 296 ASN ** Y 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 194 GLN ** Z 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 29 GLN ** b 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 219 ASN c 232 GLN ** c 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 295 ASN ** d 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37365 Z= 0.203 Angle : 0.719 13.476 50463 Z= 0.369 Chirality : 0.044 0.185 5767 Planarity : 0.005 0.069 6471 Dihedral : 6.199 80.057 4974 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.99 % Favored : 91.99 % Rotamer: Outliers : 0.17 % Allowed : 4.44 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.63 % 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: -2.70 (0.11), residues: 4557 helix: -1.37 (0.09), residues: 2488 sheet: -1.83 (0.31), residues: 207 loop : -2.24 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP c 225 HIS 0.008 0.001 HIS Z 22 PHE 0.030 0.002 PHE W 392 TYR 0.043 0.002 TYR d 148 ARG 0.015 0.001 ARG c 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9114 Ramachandran restraints generated. 4557 Oldfield, 0 Emsley, 4557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9114 Ramachandran restraints generated. 4557 Oldfield, 0 Emsley, 4557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 488 time to evaluate : 3.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASN cc_start: 0.8145 (t0) cc_final: 0.7816 (m-40) REVERT: B 132 TYR cc_start: 0.7410 (p90) cc_final: 0.7146 (p90) REVERT: E 69 PHE cc_start: 0.6387 (p90) cc_final: 0.6063 (p90) REVERT: E 108 MET cc_start: 0.8010 (mmm) cc_final: 0.7648 (mmp) REVERT: U 34 PHE cc_start: 0.8115 (m-80) cc_final: 0.7862 (m-10) REVERT: U 86 ASP cc_start: 0.7845 (t0) cc_final: 0.7537 (t0) REVERT: U 250 PHE cc_start: 0.9104 (m-80) cc_final: 0.8589 (m-80) REVERT: U 327 LYS cc_start: 0.9312 (mmpt) cc_final: 0.8970 (pttt) REVERT: U 333 MET cc_start: 0.9363 (mmp) cc_final: 0.8940 (mtm) REVERT: U 411 ILE cc_start: 0.8900 (mm) cc_final: 0.8671 (mm) REVERT: U 510 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8193 (tm-30) REVERT: U 556 MET cc_start: 0.8560 (tpp) cc_final: 0.8187 (mmp) REVERT: U 654 MET cc_start: 0.8729 (mpp) cc_final: 0.8368 (mpp) REVERT: U 691 SER cc_start: 0.9367 (t) cc_final: 0.8869 (p) REVERT: U 695 MET cc_start: 0.8369 (ptp) cc_final: 0.8001 (ptt) REVERT: U 710 ARG cc_start: 0.9555 (mmt-90) cc_final: 0.9250 (mmt180) REVERT: U 718 ASN cc_start: 0.8730 (t0) cc_final: 0.8477 (t0) REVERT: V 175 MET cc_start: 0.9185 (tpt) cc_final: 0.8688 (mtt) REVERT: V 211 TYR cc_start: 0.8468 (m-10) cc_final: 0.8022 (m-80) REVERT: V 494 MET cc_start: 0.8096 (ptm) cc_final: 0.7438 (ttp) REVERT: W 26 GLN cc_start: 0.8654 (mt0) cc_final: 0.8271 (tm-30) REVERT: W 280 ASP cc_start: 0.8805 (p0) cc_final: 0.8498 (p0) REVERT: X 108 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8430 (tp30) REVERT: X 254 MET cc_start: 0.5070 (mmm) cc_final: 0.4649 (mmm) REVERT: Y 228 MET cc_start: 0.8897 (ttt) cc_final: 0.8474 (ptm) REVERT: Y 376 LEU cc_start: 0.9513 (tt) cc_final: 0.9238 (pp) REVERT: Z 78 MET cc_start: 0.8901 (mmt) cc_final: 0.7397 (mmt) REVERT: Z 82 PHE cc_start: 0.8942 (m-80) cc_final: 0.8498 (m-80) REVERT: a 60 TYR cc_start: 0.9037 (m-10) cc_final: 0.8767 (m-10) REVERT: a 161 LYS cc_start: 0.8915 (mmmt) cc_final: 0.8658 (tttt) REVERT: a 166 ILE cc_start: 0.8462 (mm) cc_final: 0.8237 (pt) REVERT: a 218 MET cc_start: 0.8345 (ptp) cc_final: 0.8139 (ptt) REVERT: a 280 MET cc_start: 0.8327 (ptp) cc_final: 0.8002 (ptm) REVERT: a 305 ASN cc_start: 0.9038 (m-40) cc_final: 0.8632 (p0) REVERT: a 312 MET cc_start: 0.8676 (mmp) cc_final: 0.8385 (mmm) REVERT: c 41 MET cc_start: 0.9151 (mmp) cc_final: 0.8808 (mmm) REVERT: c 54 MET cc_start: 0.6435 (ptm) cc_final: 0.6007 (pmm) REVERT: c 122 LEU cc_start: 0.9271 (mt) cc_final: 0.9065 (mt) REVERT: c 128 ASN cc_start: 0.9124 (m-40) cc_final: 0.8663 (t0) REVERT: d 11 ARG cc_start: 0.8694 (ttm-80) cc_final: 0.8334 (tpt170) REVERT: d 230 GLN cc_start: 0.6636 (mm110) cc_final: 0.5914 (tm-30) REVERT: d 257 VAL cc_start: 0.4761 (t) cc_final: 0.4429 (t) outliers start: 7 outliers final: 0 residues processed: 495 average time/residue: 0.4229 time to fit residues: 328.9892 Evaluate side-chains 355 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 355 time to evaluate : 3.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 406 optimal weight: 8.9990 chunk 309 optimal weight: 6.9990 chunk 213 optimal weight: 9.9990 chunk 45 optimal weight: 0.1980 chunk 196 optimal weight: 0.0980 chunk 276 optimal weight: 0.9980 chunk 412 optimal weight: 20.0000 chunk 436 optimal weight: 5.9990 chunk 215 optimal weight: 0.0980 chunk 391 optimal weight: 9.9990 chunk 117 optimal weight: 20.0000 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 207 ASN ** U 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 450 HIS ** U 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 387 GLN ** V 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 380 GLN W 430 GLN X 296 ASN ** Y 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 367 GLN Z 24 ASN ** Z 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 29 GLN ** b 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 142 ASN ** c 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 37365 Z= 0.166 Angle : 0.674 11.042 50463 Z= 0.343 Chirality : 0.043 0.279 5767 Planarity : 0.005 0.083 6471 Dihedral : 5.850 75.494 4974 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.20 % Favored : 92.78 % Rotamer: Outliers : 0.07 % Allowed : 3.23 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.63 % 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: -2.24 (0.12), residues: 4557 helix: -0.92 (0.10), residues: 2533 sheet: -1.71 (0.32), residues: 210 loop : -2.17 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 78 HIS 0.009 0.001 HIS Z 22 PHE 0.021 0.001 PHE a 67 TYR 0.034 0.002 TYR Z 211 ARG 0.013 0.000 ARG c 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9114 Ramachandran restraints generated. 4557 Oldfield, 0 Emsley, 4557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9114 Ramachandran restraints generated. 4557 Oldfield, 0 Emsley, 4557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 499 time to evaluate : 3.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7514 (m-30) cc_final: 0.7017 (t0) REVERT: B 132 TYR cc_start: 0.7339 (p90) cc_final: 0.7086 (p90) REVERT: F 61 ARG cc_start: 0.7953 (tpt170) cc_final: 0.7750 (tpt170) REVERT: U 1 MET cc_start: 0.2355 (tpt) cc_final: 0.0355 (ttm) REVERT: U 34 PHE cc_start: 0.8113 (m-80) cc_final: 0.7610 (m-80) REVERT: U 86 ASP cc_start: 0.7844 (t0) cc_final: 0.7546 (t0) REVERT: U 327 LYS cc_start: 0.9341 (mmpt) cc_final: 0.9004 (pttt) REVERT: U 333 MET cc_start: 0.9383 (mmp) cc_final: 0.8917 (mtm) REVERT: U 411 ILE cc_start: 0.8856 (mm) cc_final: 0.8618 (mm) REVERT: U 510 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8113 (tm-30) REVERT: U 612 ASP cc_start: 0.8726 (m-30) cc_final: 0.8326 (m-30) REVERT: U 654 MET cc_start: 0.8785 (mpp) cc_final: 0.8374 (mpp) REVERT: U 691 SER cc_start: 0.9405 (t) cc_final: 0.9096 (p) REVERT: U 695 MET cc_start: 0.8102 (ptp) cc_final: 0.7849 (ptt) REVERT: U 710 ARG cc_start: 0.9525 (mmt-90) cc_final: 0.9214 (mmt180) REVERT: U 718 ASN cc_start: 0.8748 (t0) cc_final: 0.8463 (t0) REVERT: V 175 MET cc_start: 0.9139 (tpt) cc_final: 0.8687 (mtt) REVERT: V 211 TYR cc_start: 0.8477 (m-10) cc_final: 0.8005 (m-80) REVERT: V 255 LEU cc_start: 0.9219 (tt) cc_final: 0.9013 (tt) REVERT: V 494 MET cc_start: 0.8104 (ptm) cc_final: 0.7447 (ttp) REVERT: W 26 GLN cc_start: 0.8684 (mt0) cc_final: 0.8319 (tm-30) REVERT: W 278 PRO cc_start: 0.8180 (Cg_exo) cc_final: 0.7626 (Cg_endo) REVERT: W 280 ASP cc_start: 0.8758 (p0) cc_final: 0.8386 (p0) REVERT: W 282 GLU cc_start: 0.8861 (mp0) cc_final: 0.8608 (mp0) REVERT: X 116 TRP cc_start: 0.7156 (t-100) cc_final: 0.6809 (t-100) REVERT: Y 42 MET cc_start: 0.8622 (mmp) cc_final: 0.8176 (mmt) REVERT: Y 228 MET cc_start: 0.8868 (ttt) cc_final: 0.8394 (ptm) REVERT: Y 376 LEU cc_start: 0.9511 (tt) cc_final: 0.9243 (pp) REVERT: Z 73 ASP cc_start: 0.8847 (t0) cc_final: 0.8423 (m-30) REVERT: Z 78 MET cc_start: 0.8784 (mmt) cc_final: 0.7330 (mmt) REVERT: Z 82 PHE cc_start: 0.8890 (m-80) cc_final: 0.8642 (m-80) REVERT: Z 207 ASP cc_start: 0.8142 (m-30) cc_final: 0.7686 (m-30) REVERT: Z 211 TYR cc_start: 0.6330 (m-80) cc_final: 0.5775 (m-80) REVERT: a 60 TYR cc_start: 0.8992 (m-10) cc_final: 0.8724 (m-10) REVERT: a 161 LYS cc_start: 0.8912 (mmmt) cc_final: 0.8659 (tttt) REVERT: a 166 ILE cc_start: 0.8327 (mm) cc_final: 0.8074 (pt) REVERT: a 218 MET cc_start: 0.8293 (ptp) cc_final: 0.7902 (ptt) REVERT: a 280 MET cc_start: 0.8289 (ptp) cc_final: 0.7954 (ptm) REVERT: a 305 ASN cc_start: 0.9075 (m-40) cc_final: 0.8657 (p0) REVERT: a 312 MET cc_start: 0.8577 (mmp) cc_final: 0.8328 (mmm) REVERT: c 41 MET cc_start: 0.9176 (mmp) cc_final: 0.8636 (mmm) REVERT: c 54 MET cc_start: 0.6553 (ptm) cc_final: 0.6254 (pmm) REVERT: c 58 LEU cc_start: 0.9342 (mp) cc_final: 0.8968 (mp) REVERT: c 121 TRP cc_start: 0.8314 (p-90) cc_final: 0.7877 (p-90) REVERT: c 122 LEU cc_start: 0.9219 (mt) cc_final: 0.8969 (mt) REVERT: c 128 ASN cc_start: 0.9060 (m-40) cc_final: 0.8659 (t0) REVERT: c 168 MET cc_start: 0.8048 (mmm) cc_final: 0.7807 (mmt) REVERT: d 11 ARG cc_start: 0.8557 (ttm-80) cc_final: 0.8301 (tpt170) REVERT: d 230 GLN cc_start: 0.6527 (mm110) cc_final: 0.5902 (tm-30) REVERT: d 257 VAL cc_start: 0.4661 (t) cc_final: 0.4305 (t) outliers start: 3 outliers final: 0 residues processed: 502 average time/residue: 0.4245 time to fit residues: 337.7358 Evaluate side-chains 365 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 3.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 363 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 325 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 chunk 372 optimal weight: 3.9990 chunk 302 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 chunk 223 optimal weight: 9.9990 chunk 392 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 340 GLN ** U 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 14 ASN ** Y 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 29 GLN c 237 HIS c 240 HIS ** c 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37365 Z= 0.201 Angle : 0.681 11.010 50463 Z= 0.348 Chirality : 0.043 0.234 5767 Planarity : 0.005 0.092 6471 Dihedral : 5.762 78.625 4974 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 21.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.99 % Favored : 91.99 % Rotamer: Outliers : 0.02 % Allowed : 2.39 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.63 % 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: -2.01 (0.12), residues: 4557 helix: -0.70 (0.10), residues: 2538 sheet: -1.54 (0.33), residues: 214 loop : -2.14 (0.15), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 78 HIS 0.012 0.001 HIS c 240 PHE 0.036 0.002 PHE W 392 TYR 0.033 0.002 TYR d 148 ARG 0.014 0.001 ARG V 470 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9114 Ramachandran restraints generated. 4557 Oldfield, 0 Emsley, 4557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9114 Ramachandran restraints generated. 4557 Oldfield, 0 Emsley, 4557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 452 time to evaluate : 4.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.7587 (m-30) cc_final: 0.7107 (t0) REVERT: B 132 TYR cc_start: 0.7457 (p90) cc_final: 0.7052 (p90) REVERT: C 51 GLU cc_start: 0.9176 (tp30) cc_final: 0.8407 (pp20) REVERT: C 78 ARG cc_start: 0.6903 (ptm160) cc_final: 0.6157 (ptm160) REVERT: F 96 LEU cc_start: 0.6217 (mp) cc_final: 0.4964 (mp) REVERT: U 86 ASP cc_start: 0.7898 (t0) cc_final: 0.7577 (t0) REVERT: U 333 MET cc_start: 0.9396 (mmp) cc_final: 0.8927 (mtm) REVERT: U 510 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8124 (tm-30) REVERT: U 612 ASP cc_start: 0.8792 (m-30) cc_final: 0.8421 (m-30) REVERT: U 654 MET cc_start: 0.8745 (mpp) cc_final: 0.8326 (mpp) REVERT: U 718 ASN cc_start: 0.8764 (t0) cc_final: 0.8516 (t0) REVERT: V 37 MET cc_start: 0.8481 (mtm) cc_final: 0.8253 (mtp) REVERT: V 38 LYS cc_start: 0.9156 (mmpt) cc_final: 0.8757 (mmtm) REVERT: V 175 MET cc_start: 0.9157 (tpt) cc_final: 0.8716 (mtt) REVERT: V 176 MET cc_start: 0.9540 (tpt) cc_final: 0.9255 (tpt) REVERT: V 211 TYR cc_start: 0.8544 (m-10) cc_final: 0.8024 (m-80) REVERT: V 289 LEU cc_start: 0.9344 (mm) cc_final: 0.8632 (tp) REVERT: V 494 MET cc_start: 0.8269 (ptm) cc_final: 0.7664 (ttp) REVERT: W 26 GLN cc_start: 0.8704 (mt0) cc_final: 0.8329 (tm-30) REVERT: W 278 PRO cc_start: 0.8280 (Cg_exo) cc_final: 0.7677 (Cg_endo) REVERT: W 280 ASP cc_start: 0.8824 (p0) cc_final: 0.8378 (p0) REVERT: W 282 GLU cc_start: 0.8866 (mp0) cc_final: 0.8613 (mp0) REVERT: W 326 MET cc_start: 0.6802 (ptt) cc_final: 0.6186 (ppp) REVERT: X 116 TRP cc_start: 0.7189 (t-100) cc_final: 0.6804 (t-100) REVERT: Y 42 MET cc_start: 0.8710 (mmp) cc_final: 0.8269 (mmt) REVERT: Y 228 MET cc_start: 0.8957 (ttt) cc_final: 0.8490 (ptm) REVERT: Y 259 TYR cc_start: 0.7365 (m-80) cc_final: 0.6991 (m-80) REVERT: Y 376 LEU cc_start: 0.9525 (tt) cc_final: 0.9208 (pp) REVERT: Z 73 ASP cc_start: 0.8880 (t0) cc_final: 0.8553 (m-30) REVERT: Z 207 ASP cc_start: 0.8266 (m-30) cc_final: 0.7763 (m-30) REVERT: Z 211 TYR cc_start: 0.6558 (m-80) cc_final: 0.5934 (m-80) REVERT: a 60 TYR cc_start: 0.8988 (m-10) cc_final: 0.8739 (m-10) REVERT: a 166 ILE cc_start: 0.8363 (mm) cc_final: 0.8099 (pt) REVERT: a 218 MET cc_start: 0.8321 (ptp) cc_final: 0.7948 (ptt) REVERT: a 280 MET cc_start: 0.8268 (ptp) cc_final: 0.7906 (ptm) REVERT: a 305 ASN cc_start: 0.9094 (m-40) cc_final: 0.8605 (p0) REVERT: a 312 MET cc_start: 0.8581 (mmp) cc_final: 0.8380 (mmm) REVERT: c 41 MET cc_start: 0.9214 (mmp) cc_final: 0.8661 (mmm) REVERT: c 54 MET cc_start: 0.6744 (ptm) cc_final: 0.6397 (pmm) REVERT: c 58 LEU cc_start: 0.9332 (mp) cc_final: 0.8973 (mp) REVERT: c 128 ASN cc_start: 0.9152 (m-40) cc_final: 0.8766 (t0) REVERT: c 212 LEU cc_start: 0.9387 (tt) cc_final: 0.8982 (pp) REVERT: c 221 HIS cc_start: 0.8164 (t-170) cc_final: 0.7935 (t-170) REVERT: d 11 ARG cc_start: 0.8540 (ttm-80) cc_final: 0.8332 (tpt170) REVERT: d 230 GLN cc_start: 0.6440 (mm110) cc_final: 0.5766 (tm-30) REVERT: d 257 VAL cc_start: 0.4738 (t) cc_final: 0.4356 (t) outliers start: 1 outliers final: 1 residues processed: 453 average time/residue: 0.4163 time to fit residues: 298.5890 Evaluate side-chains 337 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 336 time to evaluate : 3.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 146 optimal weight: 6.9990 chunk 393 optimal weight: 8.9990 chunk 86 optimal weight: 20.0000 chunk 256 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 437 optimal weight: 7.9990 chunk 363 optimal weight: 9.9990 chunk 202 optimal weight: 7.9990 chunk 36 optimal weight: 20.0000 chunk 144 optimal weight: 5.9990 chunk 229 optimal weight: 0.4980 overall best weight: 5.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 296 ASN ** X 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 29 GLN b 142 ASN ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 283 HIS ** d 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 37365 Z= 0.208 Angle : 0.693 10.939 50463 Z= 0.355 Chirality : 0.043 0.185 5767 Planarity : 0.005 0.093 6471 Dihedral : 5.799 83.151 4974 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 22.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.49 % Favored : 91.46 % Rotamer: Outliers : 0.05 % Allowed : 2.54 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.63 % 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: -1.82 (0.12), residues: 4557 helix: -0.55 (0.10), residues: 2552 sheet: -1.49 (0.34), residues: 208 loop : -2.05 (0.15), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 78 HIS 0.011 0.001 HIS c 221 PHE 0.023 0.002 PHE U 341 TYR 0.041 0.002 TYR A 147 ARG 0.019 0.001 ARG c 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9114 Ramachandran restraints generated. 4557 Oldfield, 0 Emsley, 4557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9114 Ramachandran restraints generated. 4557 Oldfield, 0 Emsley, 4557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 444 time to evaluate : 3.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.8795 (mp0) cc_final: 0.8036 (mp0) REVERT: A 145 ASN cc_start: 0.7503 (m-40) cc_final: 0.6854 (m-40) REVERT: A 146 LYS cc_start: 0.9033 (mptt) cc_final: 0.8792 (mmtt) REVERT: A 150 HIS cc_start: 0.7958 (m-70) cc_final: 0.7639 (m90) REVERT: C 60 ARG cc_start: 0.9174 (tpt90) cc_final: 0.8416 (ttm110) REVERT: C 117 ARG cc_start: 0.8700 (mtm180) cc_final: 0.8415 (ttm110) REVERT: U 1 MET cc_start: 0.2817 (tpt) cc_final: 0.0573 (ttm) REVERT: U 34 PHE cc_start: 0.8238 (m-10) cc_final: 0.7782 (p90) REVERT: U 86 ASP cc_start: 0.7852 (t0) cc_final: 0.7555 (t0) REVERT: U 333 MET cc_start: 0.9427 (mmp) cc_final: 0.8921 (mtm) REVERT: U 510 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8234 (tm-30) REVERT: U 556 MET cc_start: 0.8608 (tpp) cc_final: 0.8187 (mmp) REVERT: U 654 MET cc_start: 0.8659 (mpp) cc_final: 0.8316 (mpp) REVERT: U 718 ASN cc_start: 0.8804 (t0) cc_final: 0.8560 (t0) REVERT: U 725 MET cc_start: 0.8645 (ppp) cc_final: 0.8436 (ppp) REVERT: U 765 VAL cc_start: 0.9541 (p) cc_final: 0.9256 (p) REVERT: V 39 GLU cc_start: 0.8515 (tp30) cc_final: 0.8197 (mt-10) REVERT: V 175 MET cc_start: 0.9131 (tpt) cc_final: 0.8812 (mtt) REVERT: V 176 MET cc_start: 0.9606 (tpt) cc_final: 0.9384 (tpp) REVERT: V 211 TYR cc_start: 0.8554 (m-10) cc_final: 0.8019 (m-80) REVERT: V 289 LEU cc_start: 0.9088 (mm) cc_final: 0.8818 (tp) REVERT: V 296 LYS cc_start: 0.9150 (mtmm) cc_final: 0.8914 (mttt) REVERT: V 494 MET cc_start: 0.8256 (ptm) cc_final: 0.7618 (ttp) REVERT: W 26 GLN cc_start: 0.8725 (mt0) cc_final: 0.8338 (tm-30) REVERT: W 230 MET cc_start: 0.8064 (ptp) cc_final: 0.7706 (ptt) REVERT: W 278 PRO cc_start: 0.8347 (Cg_exo) cc_final: 0.7862 (Cg_endo) REVERT: W 280 ASP cc_start: 0.8941 (p0) cc_final: 0.8479 (p0) REVERT: W 282 GLU cc_start: 0.8861 (mp0) cc_final: 0.8577 (mp0) REVERT: W 309 PHE cc_start: 0.8251 (t80) cc_final: 0.8034 (t80) REVERT: W 326 MET cc_start: 0.6696 (ptt) cc_final: 0.6017 (ppp) REVERT: X 115 GLU cc_start: 0.5647 (OUTLIER) cc_final: 0.5336 (pm20) REVERT: X 116 TRP cc_start: 0.7204 (t-100) cc_final: 0.6758 (t-100) REVERT: X 254 MET cc_start: 0.5213 (mmm) cc_final: 0.4775 (mmm) REVERT: Y 42 MET cc_start: 0.8722 (mmp) cc_final: 0.8286 (mmt) REVERT: Y 228 MET cc_start: 0.8967 (ttt) cc_final: 0.8553 (ptm) REVERT: Y 259 TYR cc_start: 0.7527 (m-80) cc_final: 0.7148 (m-80) REVERT: Y 376 LEU cc_start: 0.9521 (tt) cc_final: 0.9197 (pp) REVERT: Z 73 ASP cc_start: 0.8915 (t0) cc_final: 0.8583 (m-30) REVERT: a 60 TYR cc_start: 0.8958 (m-10) cc_final: 0.8701 (m-10) REVERT: a 166 ILE cc_start: 0.8386 (mm) cc_final: 0.8082 (pt) REVERT: a 218 MET cc_start: 0.8319 (ptp) cc_final: 0.7870 (ptt) REVERT: a 280 MET cc_start: 0.8196 (ptp) cc_final: 0.7842 (ptm) REVERT: a 305 ASN cc_start: 0.9172 (m-40) cc_final: 0.8631 (p0) REVERT: a 312 MET cc_start: 0.8592 (mmp) cc_final: 0.8370 (mmm) REVERT: c 41 MET cc_start: 0.9196 (mmp) cc_final: 0.8679 (mmm) REVERT: c 54 MET cc_start: 0.6712 (ptm) cc_final: 0.6429 (pmm) REVERT: c 58 LEU cc_start: 0.9358 (mp) cc_final: 0.9134 (mp) REVERT: c 122 LEU cc_start: 0.9321 (mt) cc_final: 0.8993 (mt) REVERT: c 128 ASN cc_start: 0.9207 (m-40) cc_final: 0.8881 (t0) REVERT: d 11 ARG cc_start: 0.8620 (ttm-80) cc_final: 0.8397 (tpt170) REVERT: d 255 MET cc_start: 0.7071 (mmm) cc_final: 0.6633 (mmm) REVERT: d 257 VAL cc_start: 0.4636 (t) cc_final: 0.4263 (t) outliers start: 2 outliers final: 0 residues processed: 446 average time/residue: 0.4202 time to fit residues: 295.7407 Evaluate side-chains 331 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 330 time to evaluate : 3.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 421 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 249 optimal weight: 5.9990 chunk 319 optimal weight: 2.9990 chunk 247 optimal weight: 8.9990 chunk 368 optimal weight: 20.0000 chunk 244 optimal weight: 7.9990 chunk 435 optimal weight: 30.0000 chunk 272 optimal weight: 10.0000 chunk 265 optimal weight: 9.9990 chunk 201 optimal weight: 40.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN D 48 GLN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN U 355 ASN U 500 ASN ** U 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 488 ASN ** W 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 296 ASN ** X 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 29 GLN ** b 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 37365 Z= 0.245 Angle : 0.733 11.263 50463 Z= 0.377 Chirality : 0.045 0.282 5767 Planarity : 0.005 0.089 6471 Dihedral : 5.909 88.473 4974 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 25.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.91 % Favored : 91.07 % Rotamer: Outliers : 0.02 % Allowed : 1.97 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.63 % 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: -1.87 (0.12), residues: 4557 helix: -0.57 (0.10), residues: 2553 sheet: -1.47 (0.35), residues: 208 loop : -2.13 (0.15), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP c 121 HIS 0.010 0.002 HIS Z 22 PHE 0.044 0.002 PHE W 392 TYR 0.023 0.002 TYR Y 187 ARG 0.015 0.001 ARG Y 192 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9114 Ramachandran restraints generated. 4557 Oldfield, 0 Emsley, 4557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9114 Ramachandran restraints generated. 4557 Oldfield, 0 Emsley, 4557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 438 time to evaluate : 3.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.5623 (p0) cc_final: 0.5418 (p0) REVERT: A 145 ASN cc_start: 0.7277 (m-40) cc_final: 0.6944 (m-40) REVERT: C 44 ARG cc_start: 0.9243 (tpt90) cc_final: 0.8990 (tpt90) REVERT: C 51 GLU cc_start: 0.9116 (tp30) cc_final: 0.8551 (pp20) REVERT: C 60 ARG cc_start: 0.9185 (tpt90) cc_final: 0.8427 (ttm110) REVERT: U 1 MET cc_start: 0.2723 (tpt) cc_final: 0.0571 (ttm) REVERT: U 3 THR cc_start: 0.7298 (p) cc_final: 0.7018 (p) REVERT: U 86 ASP cc_start: 0.7925 (t0) cc_final: 0.7640 (t0) REVERT: U 333 MET cc_start: 0.9429 (mmp) cc_final: 0.8843 (mtm) REVERT: U 510 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8329 (tm-30) REVERT: U 556 MET cc_start: 0.8504 (tpp) cc_final: 0.8219 (tpp) REVERT: U 654 MET cc_start: 0.8760 (mpp) cc_final: 0.8388 (mpp) REVERT: U 695 MET cc_start: 0.8229 (ptp) cc_final: 0.7895 (ptt) REVERT: U 718 ASN cc_start: 0.8800 (t0) cc_final: 0.8543 (t0) REVERT: U 725 MET cc_start: 0.8700 (ppp) cc_final: 0.8490 (ppp) REVERT: V 37 MET cc_start: 0.8330 (mtm) cc_final: 0.7989 (mtp) REVERT: V 38 LYS cc_start: 0.9117 (mmpt) cc_final: 0.8734 (mmtm) REVERT: V 175 MET cc_start: 0.9150 (tpt) cc_final: 0.8840 (mtt) REVERT: V 211 TYR cc_start: 0.8559 (m-10) cc_final: 0.7830 (m-80) REVERT: V 255 LEU cc_start: 0.9357 (tt) cc_final: 0.9153 (tt) REVERT: V 289 LEU cc_start: 0.9140 (mm) cc_final: 0.8794 (tp) REVERT: V 494 MET cc_start: 0.8396 (ptm) cc_final: 0.7825 (ttp) REVERT: W 13 ILE cc_start: 0.6466 (tp) cc_final: 0.5835 (pt) REVERT: W 26 GLN cc_start: 0.8710 (mt0) cc_final: 0.8328 (tm-30) REVERT: W 278 PRO cc_start: 0.8481 (Cg_exo) cc_final: 0.7975 (Cg_endo) REVERT: W 280 ASP cc_start: 0.8930 (p0) cc_final: 0.8359 (p0) REVERT: W 282 GLU cc_start: 0.8895 (mp0) cc_final: 0.8614 (mp0) REVERT: W 309 PHE cc_start: 0.8306 (t80) cc_final: 0.8092 (t80) REVERT: X 116 TRP cc_start: 0.7320 (t-100) cc_final: 0.6846 (t-100) REVERT: X 160 MET cc_start: 0.4010 (ptt) cc_final: 0.3748 (ptt) REVERT: Y 42 MET cc_start: 0.8725 (mmp) cc_final: 0.8296 (mmt) REVERT: Y 50 MET cc_start: 0.6750 (mmm) cc_final: 0.6308 (mmm) REVERT: Y 73 MET cc_start: 0.7899 (mtp) cc_final: 0.7584 (mtp) REVERT: Y 228 MET cc_start: 0.9018 (ttt) cc_final: 0.8619 (ptm) REVERT: Y 259 TYR cc_start: 0.7605 (m-80) cc_final: 0.7137 (m-80) REVERT: Y 376 LEU cc_start: 0.9515 (tt) cc_final: 0.9232 (pp) REVERT: Z 73 ASP cc_start: 0.8976 (t0) cc_final: 0.8640 (m-30) REVERT: Z 78 MET cc_start: 0.8903 (mmt) cc_final: 0.8257 (mmm) REVERT: Z 276 ILE cc_start: 0.8331 (mt) cc_final: 0.8113 (mm) REVERT: a 60 TYR cc_start: 0.8964 (m-10) cc_final: 0.8726 (m-10) REVERT: a 166 ILE cc_start: 0.8445 (mm) cc_final: 0.8174 (pt) REVERT: a 218 MET cc_start: 0.8303 (ptp) cc_final: 0.7834 (ptt) REVERT: a 280 MET cc_start: 0.8273 (ptp) cc_final: 0.7915 (ptm) REVERT: a 305 ASN cc_start: 0.9220 (m-40) cc_final: 0.8651 (p0) REVERT: a 312 MET cc_start: 0.8709 (mmp) cc_final: 0.8432 (mmm) REVERT: c 41 MET cc_start: 0.9186 (mmp) cc_final: 0.8698 (mmm) REVERT: c 54 MET cc_start: 0.6892 (ptm) cc_final: 0.6658 (pmm) REVERT: c 58 LEU cc_start: 0.9294 (mp) cc_final: 0.9078 (mp) REVERT: d 11 ARG cc_start: 0.8682 (ttm-80) cc_final: 0.8414 (tpt170) REVERT: d 206 MET cc_start: 0.7820 (ptp) cc_final: 0.6992 (ptp) REVERT: d 255 MET cc_start: 0.7029 (mmm) cc_final: 0.6525 (mmm) outliers start: 1 outliers final: 0 residues processed: 439 average time/residue: 0.4218 time to fit residues: 292.6985 Evaluate side-chains 318 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 318 time to evaluate : 3.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 269 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 260 optimal weight: 0.9980 chunk 131 optimal weight: 8.9990 chunk 85 optimal weight: 0.1980 chunk 84 optimal weight: 0.1980 chunk 276 optimal weight: 0.2980 chunk 296 optimal weight: 3.9990 chunk 215 optimal weight: 0.0060 chunk 40 optimal weight: 6.9990 chunk 342 optimal weight: 8.9990 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 171 ASN ** U 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 218 ASN ** X 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 102 HIS ** Z 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 194 GLN ** Z 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 274 ASN ** Z 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 29 GLN b 142 ASN c 130 GLN ** c 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 37365 Z= 0.172 Angle : 0.701 11.822 50463 Z= 0.350 Chirality : 0.044 0.222 5767 Planarity : 0.005 0.069 6471 Dihedral : 5.609 64.716 4974 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.14 % Favored : 91.84 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.63 % 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: -1.68 (0.12), residues: 4557 helix: -0.38 (0.10), residues: 2571 sheet: -1.45 (0.34), residues: 205 loop : -2.09 (0.15), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP c 121 HIS 0.011 0.001 HIS Z 22 PHE 0.023 0.001 PHE U 341 TYR 0.026 0.002 TYR V 212 ARG 0.011 0.001 ARG Z 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9114 Ramachandran restraints generated. 4557 Oldfield, 0 Emsley, 4557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9114 Ramachandran restraints generated. 4557 Oldfield, 0 Emsley, 4557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 458 time to evaluate : 3.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 51 GLU cc_start: 0.9136 (tp30) cc_final: 0.8624 (pp20) REVERT: C 60 ARG cc_start: 0.9156 (tpt90) cc_final: 0.8475 (ttm110) REVERT: U 1 MET cc_start: 0.2500 (tpt) cc_final: 0.0223 (ttm) REVERT: U 74 PHE cc_start: 0.8356 (m-10) cc_final: 0.8121 (m-10) REVERT: U 86 ASP cc_start: 0.7785 (t0) cc_final: 0.7504 (t0) REVERT: U 333 MET cc_start: 0.9396 (mmp) cc_final: 0.8832 (mtm) REVERT: U 376 MET cc_start: 0.7292 (tpt) cc_final: 0.7069 (tpt) REVERT: U 612 ASP cc_start: 0.8778 (m-30) cc_final: 0.8404 (m-30) REVERT: U 654 MET cc_start: 0.8749 (mpp) cc_final: 0.8344 (mpp) REVERT: U 718 ASN cc_start: 0.8850 (t0) cc_final: 0.8623 (t0) REVERT: V 37 MET cc_start: 0.8347 (mtm) cc_final: 0.8096 (mtp) REVERT: V 38 LYS cc_start: 0.9137 (mmpt) cc_final: 0.8757 (mmtm) REVERT: V 139 MET cc_start: 0.7942 (ptt) cc_final: 0.6982 (mmp) REVERT: V 148 ARG cc_start: 0.7016 (pmt170) cc_final: 0.6452 (mtm-85) REVERT: V 175 MET cc_start: 0.9076 (tpt) cc_final: 0.8780 (mtt) REVERT: V 176 MET cc_start: 0.9606 (tpp) cc_final: 0.9365 (tpp) REVERT: V 211 TYR cc_start: 0.8256 (m-10) cc_final: 0.7708 (m-80) REVERT: V 296 LYS cc_start: 0.9114 (mtmm) cc_final: 0.8911 (mttt) REVERT: V 494 MET cc_start: 0.8311 (ptm) cc_final: 0.7709 (ttp) REVERT: W 13 ILE cc_start: 0.6309 (tp) cc_final: 0.5693 (pt) REVERT: W 26 GLN cc_start: 0.8733 (mt0) cc_final: 0.8381 (tm-30) REVERT: W 278 PRO cc_start: 0.8099 (Cg_exo) cc_final: 0.7448 (Cg_endo) REVERT: W 280 ASP cc_start: 0.8808 (p0) cc_final: 0.8385 (p0) REVERT: W 282 GLU cc_start: 0.8746 (mp0) cc_final: 0.8374 (mp0) REVERT: W 309 PHE cc_start: 0.8170 (t80) cc_final: 0.7915 (t80) REVERT: W 326 MET cc_start: 0.6530 (ptt) cc_final: 0.6054 (ppp) REVERT: X 116 TRP cc_start: 0.7184 (t-100) cc_final: 0.6696 (t-100) REVERT: X 254 MET cc_start: 0.4894 (mmm) cc_final: 0.4526 (mmm) REVERT: Y 42 MET cc_start: 0.8660 (mmp) cc_final: 0.8452 (mmm) REVERT: Y 50 MET cc_start: 0.6646 (mmm) cc_final: 0.6260 (mmm) REVERT: Y 73 MET cc_start: 0.7809 (mtp) cc_final: 0.7500 (mtp) REVERT: Y 228 MET cc_start: 0.8961 (ttt) cc_final: 0.8495 (ptm) REVERT: Y 259 TYR cc_start: 0.7448 (m-80) cc_final: 0.6985 (m-80) REVERT: Y 362 LYS cc_start: 0.8471 (mmtt) cc_final: 0.8183 (tmmt) REVERT: Y 376 LEU cc_start: 0.9481 (tt) cc_final: 0.9163 (pp) REVERT: Z 20 VAL cc_start: 0.9586 (t) cc_final: 0.9369 (t) REVERT: Z 73 ASP cc_start: 0.8951 (t0) cc_final: 0.8544 (m-30) REVERT: Z 78 MET cc_start: 0.8675 (mmt) cc_final: 0.8004 (mmm) REVERT: Z 82 PHE cc_start: 0.8744 (m-80) cc_final: 0.8479 (m-80) REVERT: Z 211 TYR cc_start: 0.6813 (m-80) cc_final: 0.6060 (m-80) REVERT: a 60 TYR cc_start: 0.8913 (m-10) cc_final: 0.8670 (m-10) REVERT: a 166 ILE cc_start: 0.8329 (mm) cc_final: 0.8087 (pt) REVERT: a 218 MET cc_start: 0.8291 (ptp) cc_final: 0.7838 (ptt) REVERT: a 280 MET cc_start: 0.8187 (ptp) cc_final: 0.7862 (ptm) REVERT: a 305 ASN cc_start: 0.9219 (m-40) cc_final: 0.8661 (p0) REVERT: a 312 MET cc_start: 0.8664 (mmp) cc_final: 0.8265 (mmm) REVERT: c 41 MET cc_start: 0.9162 (mmp) cc_final: 0.8718 (mmm) REVERT: c 54 MET cc_start: 0.6744 (ptm) cc_final: 0.6453 (pmm) REVERT: c 58 LEU cc_start: 0.9323 (mp) cc_final: 0.8728 (tp) REVERT: c 128 ASN cc_start: 0.9213 (m-40) cc_final: 0.8870 (t0) REVERT: c 212 LEU cc_start: 0.9357 (tp) cc_final: 0.8901 (pp) REVERT: c 233 ASP cc_start: 0.7267 (p0) cc_final: 0.7059 (p0) REVERT: d 2 TYR cc_start: 0.7452 (p90) cc_final: 0.6052 (m-80) REVERT: d 11 ARG cc_start: 0.8583 (ttm-80) cc_final: 0.8376 (tpt170) REVERT: d 56 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7984 (mt-10) REVERT: d 206 MET cc_start: 0.7872 (ptp) cc_final: 0.7135 (ptp) outliers start: 0 outliers final: 0 residues processed: 458 average time/residue: 0.4241 time to fit residues: 307.7286 Evaluate side-chains 336 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 3.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 396 optimal weight: 3.9990 chunk 417 optimal weight: 0.2980 chunk 380 optimal weight: 20.0000 chunk 405 optimal weight: 7.9990 chunk 244 optimal weight: 9.9990 chunk 176 optimal weight: 20.0000 chunk 318 optimal weight: 4.9990 chunk 124 optimal weight: 20.0000 chunk 366 optimal weight: 0.7980 chunk 383 optimal weight: 3.9990 chunk 404 optimal weight: 9.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 HIS ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 148 HIS X 296 ASN ** X 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 102 HIS Z 194 GLN ** Z 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 29 GLN ** c 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 37365 Z= 0.175 Angle : 0.683 12.892 50463 Z= 0.343 Chirality : 0.043 0.200 5767 Planarity : 0.005 0.090 6471 Dihedral : 5.509 62.862 4974 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.36 % Favored : 91.62 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.63 % 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: -1.59 (0.12), residues: 4557 helix: -0.30 (0.10), residues: 2581 sheet: -1.40 (0.35), residues: 207 loop : -2.08 (0.15), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP c 121 HIS 0.011 0.001 HIS X 148 PHE 0.030 0.001 PHE d 105 TYR 0.040 0.002 TYR F 88 ARG 0.022 0.001 ARG c 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9114 Ramachandran restraints generated. 4557 Oldfield, 0 Emsley, 4557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9114 Ramachandran restraints generated. 4557 Oldfield, 0 Emsley, 4557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 438 time to evaluate : 4.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.5394 (p0) cc_final: 0.5185 (p0) REVERT: A 145 ASN cc_start: 0.7173 (m-40) cc_final: 0.6969 (m-40) REVERT: C 51 GLU cc_start: 0.9154 (tp30) cc_final: 0.8683 (pp20) REVERT: C 60 ARG cc_start: 0.9148 (tpt90) cc_final: 0.8464 (ttm110) REVERT: E 108 MET cc_start: 0.6575 (mmp) cc_final: 0.5934 (ptm) REVERT: U 1 MET cc_start: 0.2329 (tpt) cc_final: 0.0164 (ttm) REVERT: U 74 PHE cc_start: 0.8379 (m-10) cc_final: 0.8153 (m-10) REVERT: U 86 ASP cc_start: 0.7835 (t0) cc_final: 0.7544 (t0) REVERT: U 252 LEU cc_start: 0.9051 (mt) cc_final: 0.8544 (pp) REVERT: U 333 MET cc_start: 0.9424 (mmp) cc_final: 0.8898 (mtm) REVERT: U 532 MET cc_start: 0.8428 (ptp) cc_final: 0.8194 (ptm) REVERT: U 612 ASP cc_start: 0.8796 (m-30) cc_final: 0.8497 (m-30) REVERT: U 654 MET cc_start: 0.8739 (mpp) cc_final: 0.8359 (mpp) REVERT: U 718 ASN cc_start: 0.8846 (t0) cc_final: 0.8636 (t0) REVERT: V 37 MET cc_start: 0.8262 (mtm) cc_final: 0.7800 (mtm) REVERT: V 38 LYS cc_start: 0.9139 (mmpt) cc_final: 0.8793 (mmtt) REVERT: V 148 ARG cc_start: 0.7035 (pmt170) cc_final: 0.6549 (mtm-85) REVERT: V 175 MET cc_start: 0.9131 (tpt) cc_final: 0.8798 (mtt) REVERT: V 211 TYR cc_start: 0.8243 (m-10) cc_final: 0.7733 (m-80) REVERT: V 296 LYS cc_start: 0.9128 (mtmm) cc_final: 0.8920 (mttt) REVERT: W 13 ILE cc_start: 0.6319 (tp) cc_final: 0.5696 (pt) REVERT: W 26 GLN cc_start: 0.8743 (mt0) cc_final: 0.8368 (tm-30) REVERT: W 200 ILE cc_start: 0.8597 (tp) cc_final: 0.7727 (mt) REVERT: W 278 PRO cc_start: 0.8138 (Cg_exo) cc_final: 0.7478 (Cg_endo) REVERT: W 280 ASP cc_start: 0.8870 (p0) cc_final: 0.8373 (p0) REVERT: W 282 GLU cc_start: 0.8817 (mp0) cc_final: 0.8438 (mp0) REVERT: W 309 PHE cc_start: 0.8223 (t80) cc_final: 0.7988 (t80) REVERT: W 312 MET cc_start: 0.3591 (ppp) cc_final: 0.3331 (ppp) REVERT: W 326 MET cc_start: 0.6680 (ptt) cc_final: 0.6172 (ppp) REVERT: W 339 ASP cc_start: 0.7647 (t70) cc_final: 0.7120 (m-30) REVERT: X 116 TRP cc_start: 0.7223 (t-100) cc_final: 0.7023 (t-100) REVERT: X 148 HIS cc_start: 0.8362 (m90) cc_final: 0.8009 (t70) REVERT: X 254 MET cc_start: 0.4910 (mmm) cc_final: 0.4492 (mmm) REVERT: Y 42 MET cc_start: 0.8673 (mmp) cc_final: 0.8265 (mmt) REVERT: Y 50 MET cc_start: 0.6677 (mmm) cc_final: 0.6342 (mmm) REVERT: Y 73 MET cc_start: 0.7781 (mtp) cc_final: 0.7492 (mtp) REVERT: Y 228 MET cc_start: 0.8991 (ttt) cc_final: 0.8540 (ptm) REVERT: Y 259 TYR cc_start: 0.7480 (m-80) cc_final: 0.7012 (m-80) REVERT: Y 362 LYS cc_start: 0.8475 (mmtt) cc_final: 0.8122 (tmmt) REVERT: Y 376 LEU cc_start: 0.9489 (tt) cc_final: 0.9205 (pp) REVERT: Z 73 ASP cc_start: 0.8979 (t0) cc_final: 0.8622 (m-30) REVERT: Z 78 MET cc_start: 0.8719 (mmt) cc_final: 0.8153 (mmm) REVERT: Z 211 TYR cc_start: 0.6805 (m-80) cc_final: 0.6222 (m-80) REVERT: Z 276 ILE cc_start: 0.8272 (mt) cc_final: 0.8066 (mm) REVERT: a 60 TYR cc_start: 0.8934 (m-10) cc_final: 0.8701 (m-10) REVERT: a 166 ILE cc_start: 0.8331 (mm) cc_final: 0.7946 (tp) REVERT: a 218 MET cc_start: 0.8278 (ptp) cc_final: 0.7850 (ptt) REVERT: a 280 MET cc_start: 0.8123 (ptp) cc_final: 0.7810 (ptm) REVERT: a 305 ASN cc_start: 0.9231 (m-40) cc_final: 0.8671 (p0) REVERT: a 312 MET cc_start: 0.8716 (mmp) cc_final: 0.8315 (mmm) REVERT: c 41 MET cc_start: 0.9157 (mmp) cc_final: 0.8721 (mmm) REVERT: c 54 MET cc_start: 0.6785 (ptm) cc_final: 0.6535 (pmm) REVERT: c 58 LEU cc_start: 0.9338 (mp) cc_final: 0.8743 (tp) REVERT: c 122 LEU cc_start: 0.9216 (mt) cc_final: 0.8981 (mt) REVERT: c 128 ASN cc_start: 0.9237 (m-40) cc_final: 0.8904 (t0) REVERT: c 167 MET cc_start: 0.8123 (tpp) cc_final: 0.7629 (tmm) REVERT: c 212 LEU cc_start: 0.9359 (tp) cc_final: 0.8900 (pp) REVERT: d 11 ARG cc_start: 0.8598 (ttm-80) cc_final: 0.8396 (tpt170) REVERT: d 255 MET cc_start: 0.6904 (mmm) cc_final: 0.6067 (mmm) REVERT: e 1 MET cc_start: 0.5108 (ptm) cc_final: 0.4904 (ptp) outliers start: 0 outliers final: 0 residues processed: 438 average time/residue: 0.4237 time to fit residues: 295.3042 Evaluate side-chains 337 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 3.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 266 optimal weight: 4.9990 chunk 429 optimal weight: 9.9990 chunk 262 optimal weight: 6.9990 chunk 203 optimal weight: 8.9990 chunk 298 optimal weight: 8.9990 chunk 450 optimal weight: 9.9990 chunk 414 optimal weight: 3.9990 chunk 358 optimal weight: 0.1980 chunk 37 optimal weight: 30.0000 chunk 276 optimal weight: 5.9990 chunk 219 optimal weight: 0.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 GLN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 355 ASN ** U 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 296 ASN X 406 ASN ** Y 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 102 HIS Z 194 GLN ** Z 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 29 GLN ** b 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.5359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 37365 Z= 0.179 Angle : 0.687 13.113 50463 Z= 0.346 Chirality : 0.043 0.191 5767 Planarity : 0.005 0.078 6471 Dihedral : 5.467 60.708 4974 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 20.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.71 % Favored : 91.27 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.63 % 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: -1.51 (0.12), residues: 4557 helix: -0.23 (0.10), residues: 2584 sheet: -1.31 (0.34), residues: 217 loop : -2.07 (0.15), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP c 121 HIS 0.010 0.001 HIS Z 22 PHE 0.037 0.002 PHE W 392 TYR 0.047 0.002 TYR V 291 ARG 0.019 0.001 ARG c 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9114 Ramachandran restraints generated. 4557 Oldfield, 0 Emsley, 4557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9114 Ramachandran restraints generated. 4557 Oldfield, 0 Emsley, 4557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 437 time to evaluate : 3.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ASP cc_start: 0.6304 (t0) cc_final: 0.5958 (t0) REVERT: B 107 MET cc_start: 0.5828 (tpt) cc_final: 0.5474 (mmm) REVERT: C 51 GLU cc_start: 0.9133 (tp30) cc_final: 0.8645 (pp20) REVERT: C 60 ARG cc_start: 0.9144 (tpt90) cc_final: 0.8416 (ttm110) REVERT: U 1 MET cc_start: 0.2082 (tpt) cc_final: 0.0041 (ttm) REVERT: U 74 PHE cc_start: 0.8401 (m-10) cc_final: 0.8119 (m-80) REVERT: U 86 ASP cc_start: 0.7848 (t0) cc_final: 0.7552 (t0) REVERT: U 252 LEU cc_start: 0.9093 (mt) cc_final: 0.8587 (pp) REVERT: U 333 MET cc_start: 0.9427 (mmp) cc_final: 0.8898 (mtm) REVERT: U 423 MET cc_start: 0.7089 (tpt) cc_final: 0.6825 (tpt) REVERT: U 532 MET cc_start: 0.8560 (ptp) cc_final: 0.8250 (ptm) REVERT: U 654 MET cc_start: 0.8747 (mpp) cc_final: 0.8359 (mpp) REVERT: U 710 ARG cc_start: 0.9435 (mmt-90) cc_final: 0.9146 (mmp80) REVERT: U 718 ASN cc_start: 0.8876 (t0) cc_final: 0.8636 (t0) REVERT: V 148 ARG cc_start: 0.7065 (pmt170) cc_final: 0.6568 (mtm-85) REVERT: V 175 MET cc_start: 0.9153 (tpt) cc_final: 0.8764 (mtt) REVERT: V 211 TYR cc_start: 0.8244 (m-10) cc_final: 0.7745 (m-80) REVERT: V 296 LYS cc_start: 0.9113 (mtmm) cc_final: 0.8908 (mttt) REVERT: V 309 MET cc_start: 0.7264 (ppp) cc_final: 0.7001 (ppp) REVERT: V 505 LEU cc_start: 0.8366 (mt) cc_final: 0.8134 (mt) REVERT: W 13 ILE cc_start: 0.6319 (tp) cc_final: 0.5702 (pt) REVERT: W 26 GLN cc_start: 0.8777 (mt0) cc_final: 0.8401 (tm-30) REVERT: W 200 ILE cc_start: 0.8627 (tp) cc_final: 0.7755 (mt) REVERT: W 278 PRO cc_start: 0.8161 (Cg_exo) cc_final: 0.7502 (Cg_endo) REVERT: W 280 ASP cc_start: 0.8910 (p0) cc_final: 0.8480 (p0) REVERT: W 282 GLU cc_start: 0.8820 (mp0) cc_final: 0.8461 (mp0) REVERT: W 309 PHE cc_start: 0.8201 (t80) cc_final: 0.7994 (t80) REVERT: W 312 MET cc_start: 0.3611 (ppp) cc_final: 0.3263 (ppp) REVERT: X 116 TRP cc_start: 0.7133 (t-100) cc_final: 0.6930 (t-100) REVERT: X 148 HIS cc_start: 0.8273 (m90) cc_final: 0.8072 (t70) REVERT: X 254 MET cc_start: 0.4994 (mmm) cc_final: 0.4561 (mmm) REVERT: Y 42 MET cc_start: 0.8651 (mmp) cc_final: 0.8239 (mmt) REVERT: Y 50 MET cc_start: 0.6708 (mmm) cc_final: 0.6373 (mmm) REVERT: Y 73 MET cc_start: 0.7788 (mtp) cc_final: 0.7481 (mtp) REVERT: Y 228 MET cc_start: 0.8991 (ttt) cc_final: 0.8531 (ptm) REVERT: Y 259 TYR cc_start: 0.7475 (m-80) cc_final: 0.7008 (m-80) REVERT: Y 362 LYS cc_start: 0.8458 (mmtt) cc_final: 0.8131 (ttpt) REVERT: Y 376 LEU cc_start: 0.9485 (tt) cc_final: 0.9201 (pp) REVERT: Z 73 ASP cc_start: 0.8908 (t0) cc_final: 0.8077 (m-30) REVERT: Z 211 TYR cc_start: 0.6692 (m-80) cc_final: 0.6151 (m-80) REVERT: a 60 TYR cc_start: 0.8903 (m-10) cc_final: 0.8670 (m-10) REVERT: a 135 ILE cc_start: 0.8267 (mm) cc_final: 0.8030 (tt) REVERT: a 166 ILE cc_start: 0.8336 (mm) cc_final: 0.7957 (tp) REVERT: a 218 MET cc_start: 0.8286 (ptp) cc_final: 0.7827 (ptt) REVERT: a 280 MET cc_start: 0.8137 (ptp) cc_final: 0.7829 (ptm) REVERT: a 305 ASN cc_start: 0.9232 (m-40) cc_final: 0.8736 (p0) REVERT: a 312 MET cc_start: 0.8748 (mmp) cc_final: 0.8445 (mmm) REVERT: c 41 MET cc_start: 0.9159 (mmp) cc_final: 0.8763 (mmm) REVERT: c 54 MET cc_start: 0.6809 (ptm) cc_final: 0.6577 (pmm) REVERT: c 57 MET cc_start: 0.9219 (pmm) cc_final: 0.9008 (pmm) REVERT: c 58 LEU cc_start: 0.9336 (mp) cc_final: 0.8751 (tp) REVERT: c 122 LEU cc_start: 0.9244 (mt) cc_final: 0.8959 (mt) REVERT: c 128 ASN cc_start: 0.9251 (m-40) cc_final: 0.8946 (t0) REVERT: c 167 MET cc_start: 0.8172 (tpp) cc_final: 0.7718 (tmm) REVERT: c 212 LEU cc_start: 0.9362 (tp) cc_final: 0.8911 (pp) REVERT: d 211 LYS cc_start: 0.8673 (mppt) cc_final: 0.7897 (pttm) REVERT: d 255 MET cc_start: 0.6948 (mmm) cc_final: 0.6102 (mmm) outliers start: 0 outliers final: 0 residues processed: 437 average time/residue: 0.4177 time to fit residues: 290.4387 Evaluate side-chains 336 residues out of total 4057 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 3.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 284 optimal weight: 20.0000 chunk 381 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 330 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 chunk 99 optimal weight: 40.0000 chunk 359 optimal weight: 20.0000 chunk 150 optimal weight: 0.7980 chunk 368 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 355 ASN U 366 HIS ** U 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 296 ASN X 406 ASN ** Y 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 102 HIS ** Z 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 29 GLN ** b 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.050697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.040472 restraints weight = 469777.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.041209 restraints weight = 367388.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.041800 restraints weight = 303654.163| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3375 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3368 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.5567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 37365 Z= 0.206 Angle : 0.705 12.602 50463 Z= 0.358 Chirality : 0.044 0.208 5767 Planarity : 0.005 0.081 6471 Dihedral : 5.524 56.311 4974 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 23.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.06 % Favored : 90.92 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.63 % 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: -1.49 (0.12), residues: 4557 helix: -0.22 (0.10), residues: 2579 sheet: -1.35 (0.34), residues: 218 loop : -2.02 (0.15), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP c 121 HIS 0.011 0.001 HIS Z 22 PHE 0.025 0.002 PHE d 105 TYR 0.025 0.002 TYR F 88 ARG 0.019 0.001 ARG c 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6672.96 seconds wall clock time: 120 minutes 0.45 seconds (7200.45 seconds total)