Starting phenix.real_space_refine on Mon Mar 18 16:45:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qx3_4661/03_2024/6qx3_4661.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qx3_4661/03_2024/6qx3_4661.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qx3_4661/03_2024/6qx3_4661.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qx3_4661/03_2024/6qx3_4661.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qx3_4661/03_2024/6qx3_4661.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qx3_4661/03_2024/6qx3_4661.pdb" } resolution = 3.79 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 14 5.49 5 S 79 5.16 5 C 6857 2.51 5 N 1884 2.21 5 O 2107 1.98 5 H 10646 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "O ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 82": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B GLU 97": "OE1" <-> "OE2" Residue "B ARG 126": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 175": "OD1" <-> "OD2" Residue "B GLU 177": "OE1" <-> "OE2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "B GLU 371": "OE1" <-> "OE2" Residue "B ASP 377": "OD1" <-> "OD2" Residue "B GLU 390": "OE1" <-> "OE2" Residue "B TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "B TYR 483": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 563": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 206": "OE1" <-> "OE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A ARG 266": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 286": "OD1" <-> "OD2" Residue "A TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 349": "OE1" <-> "OE2" Residue "A GLU 351": "OE1" <-> "OE2" Residue "A ASP 382": "OD1" <-> "OD2" Residue "A ASP 386": "OD1" <-> "OD2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A ASP 426": "OD1" <-> "OD2" Residue "A GLU 427": "OE1" <-> "OE2" Residue "A ASP 478": "OD1" <-> "OD2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 583": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 593": "OE1" <-> "OE2" Residue "A GLU 629": "OE1" <-> "OE2" Residue "C GLU 123": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21587 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 329 Classifications: {'RNA': 10} Modifications used: {'3*END': 1, 'rna2p_pur': 4, 'rna3p_pur': 4, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 6} Chain: "G" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 122 Classifications: {'RNA': 4} Modifications used: {'3*END': 1, 'rna2p_pyr': 4} Link IDs: {'rna2p': 3} Chain: "O" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1799 Classifications: {'peptide': 121} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 115} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 9750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 9750 Classifications: {'peptide': 615} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 586} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 8157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 8157 Classifications: {'peptide': 515} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 487} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1430 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 6, 'TRANS': 79} Time building chain proxies: 9.89, per 1000 atoms: 0.46 Number of scatterers: 21587 At special positions: 0 Unit cell: (103.68, 102.6, 120.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 79 16.00 P 14 15.00 O 2107 8.00 N 1884 7.00 C 6857 6.00 H 10646 1.00 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: 16.71 Conformation dependent library (CDL) restraints added in 2.6 seconds 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2504 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 10 sheets defined 41.4% alpha, 9.3% beta 0 base pairs and 5 stacking pairs defined. Time for finding SS restraints: 9.29 Creating SS restraints... Processing helix chain 'O' and resid 28 through 32 removed outlier: 4.004A pdb=" N TYR O 32 " --> pdb=" O PHE O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 65 removed outlier: 4.219A pdb=" N LYS O 65 " --> pdb=" O ASP O 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 62 through 65' Processing helix chain 'O' and resid 87 through 91 removed outlier: 3.501A pdb=" N ASP O 90 " --> pdb=" O LYS O 87 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER O 91 " --> pdb=" O PRO O 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 87 through 91' Processing helix chain 'B' and resid 4 through 11 removed outlier: 3.540A pdb=" N LEU B 7 " --> pdb=" O ASN B 4 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE B 9 " --> pdb=" O THR B 6 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS B 11 " --> pdb=" O LEU B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 21 Processing helix chain 'B' and resid 38 through 49 removed outlier: 3.575A pdb=" N VAL B 43 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN B 44 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS B 47 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR B 49 " --> pdb=" O ARG B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 99 removed outlier: 3.698A pdb=" N LEU B 89 " --> pdb=" O THR B 85 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B 96 " --> pdb=" O MET B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 114 removed outlier: 3.866A pdb=" N LEU B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 removed outlier: 3.954A pdb=" N THR B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN B 124 " --> pdb=" O ASP B 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 119 through 124' Processing helix chain 'B' and resid 140 through 153 removed outlier: 3.965A pdb=" N ALA B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN B 153 " --> pdb=" O VAL B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 161 removed outlier: 3.516A pdb=" N GLU B 159 " --> pdb=" O THR B 156 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER B 160 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.518A pdb=" N PHE B 166 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP B 169 " --> pdb=" O ASP B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 222 removed outlier: 4.332A pdb=" N ILE B 219 " --> pdb=" O ARG B 215 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 263 removed outlier: 4.345A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR B 253 " --> pdb=" O ARG B 249 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 289 removed outlier: 3.804A pdb=" N LYS B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA B 280 " --> pdb=" O ASN B 276 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA B 283 " --> pdb=" O LYS B 279 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.884A pdb=" N ASN B 312 " --> pdb=" O LYS B 308 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN B 313 " --> pdb=" O TRP B 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 308 through 313' Processing helix chain 'B' and resid 314 through 326 removed outlier: 3.909A pdb=" N PHE B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 345 removed outlier: 3.959A pdb=" N LEU B 337 " --> pdb=" O PHE B 333 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER B 338 " --> pdb=" O ARG B 334 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 370 through 375 Processing helix chain 'B' and resid 382 through 393 removed outlier: 3.941A pdb=" N LYS B 391 " --> pdb=" O LYS B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 426 removed outlier: 3.967A pdb=" N VAL B 418 " --> pdb=" O MET B 414 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B 419 " --> pdb=" O LEU B 415 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY B 420 " --> pdb=" O SER B 416 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE B 423 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 424 " --> pdb=" O GLY B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 470 removed outlier: 3.614A pdb=" N PHE B 466 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG B 468 " --> pdb=" O ASP B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 536 removed outlier: 3.650A pdb=" N SER B 524 " --> pdb=" O SER B 520 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B 527 " --> pdb=" O MET B 523 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR B 528 " --> pdb=" O SER B 524 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE B 530 " --> pdb=" O GLY B 526 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LYS B 531 " --> pdb=" O VAL B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 560 removed outlier: 3.554A pdb=" N ILE B 552 " --> pdb=" O LEU B 548 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR B 558 " --> pdb=" O ASP B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 583 removed outlier: 3.921A pdb=" N LEU B 576 " --> pdb=" O ARG B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 594 removed outlier: 4.062A pdb=" N GLY B 594 " --> pdb=" O VAL B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 617 through 625 removed outlier: 3.901A pdb=" N CYS B 625 " --> pdb=" O GLN B 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 226 through 235 removed outlier: 3.581A pdb=" N ALA A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR A 232 " --> pdb=" O ASN A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 removed outlier: 3.738A pdb=" N SER A 247 " --> pdb=" O GLU A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 312 removed outlier: 3.553A pdb=" N CYS A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.775A pdb=" N LEU A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER A 337 " --> pdb=" O ASN A 333 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 removed outlier: 4.234A pdb=" N ALA A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 385 Processing helix chain 'A' and resid 407 through 412 Processing helix chain 'A' and resid 433 through 451 removed outlier: 3.538A pdb=" N TYR A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 439 " --> pdb=" O ILE A 435 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 460 removed outlier: 3.982A pdb=" N TYR A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 476 removed outlier: 4.204A pdb=" N TYR A 464 " --> pdb=" O MET A 460 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 465 " --> pdb=" O LYS A 461 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASN A 466 " --> pdb=" O GLY A 462 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N CYS A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 475 " --> pdb=" O ASN A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 600 removed outlier: 4.120A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE A 592 " --> pdb=" O SER A 588 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU A 599 " --> pdb=" O MET A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 612 removed outlier: 3.516A pdb=" N PHE A 611 " --> pdb=" O MET A 607 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE A 612 " --> pdb=" O THR A 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 607 through 612' Processing helix chain 'A' and resid 632 through 650 removed outlier: 4.487A pdb=" N LEU A 641 " --> pdb=" O CYS A 637 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 662 removed outlier: 3.803A pdb=" N GLU A 656 " --> pdb=" O SER A 652 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 674 removed outlier: 3.535A pdb=" N LEU A 672 " --> pdb=" O VAL A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 692 removed outlier: 3.648A pdb=" N ALA A 689 " --> pdb=" O GLY A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 711 removed outlier: 4.352A pdb=" N SER A 705 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN A 708 " --> pdb=" O ALA A 704 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 709 " --> pdb=" O SER A 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 53 removed outlier: 4.235A pdb=" N ARG C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET C 51 " --> pdb=" O MET C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 67 removed outlier: 4.166A pdb=" N GLU C 65 " --> pdb=" O LYS C 61 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N MET C 66 " --> pdb=" O ARG C 62 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 67' Processing helix chain 'C' and resid 93 through 102 removed outlier: 3.676A pdb=" N THR C 97 " --> pdb=" O PRO C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 removed outlier: 3.620A pdb=" N TYR C 115 " --> pdb=" O TYR C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 126 removed outlier: 3.715A pdb=" N LYS C 121 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL C 122 " --> pdb=" O TYR C 118 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU C 123 " --> pdb=" O PHE C 119 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS C 126 " --> pdb=" O VAL C 122 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'O' and resid 3 through 7 removed outlier: 3.861A pdb=" N GLN O 3 " --> pdb=" O SER O 25 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER O 25 " --> pdb=" O GLN O 3 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU O 23 " --> pdb=" O GLN O 5 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER O 21 " --> pdb=" O SER O 7 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU O 81 " --> pdb=" O LEU O 20 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS O 22 " --> pdb=" O LEU O 79 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU O 79 " --> pdb=" O CYS O 22 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP O 73 " --> pdb=" O THR O 78 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER O 71 " --> pdb=" O TYR O 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'O' and resid 58 through 60 removed outlier: 3.986A pdb=" N THR O 59 " --> pdb=" O MET O 50 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET O 50 " --> pdb=" O THR O 59 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N MET O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N MET O 34 " --> pdb=" O MET O 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 56 through 57 removed outlier: 3.580A pdb=" N THR B 56 " --> pdb=" O GLN B 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 128 through 130 removed outlier: 3.677A pdb=" N ASP B 130 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG B 135 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 225 through 227 removed outlier: 3.520A pdb=" N ILE B 241 " --> pdb=" O MET B 227 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 437 through 442 removed outlier: 3.520A pdb=" N TRP B 437 " --> pdb=" O ASN B 452 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP B 439 " --> pdb=" O ILE B 450 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE B 447 " --> pdb=" O GLY B 304 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY B 304 " --> pdb=" O PHE B 447 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 449 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR B 483 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 348 through 350 removed outlier: 3.741A pdb=" N ALA B 401 " --> pdb=" O ALA B 349 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 356 through 359 removed outlier: 3.555A pdb=" N LEU B 364 " --> pdb=" O SER B 359 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN B 367 " --> pdb=" O VAL A 379 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 317 through 324 removed outlier: 6.081A pdb=" N ILE A 545 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N LEU A 543 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N ILE A 322 " --> pdb=" O CYS A 541 " (cutoff:3.500A) removed outlier: 11.117A pdb=" N CYS A 541 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 563 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A 524 " --> pdb=" O TYR A 564 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE A 525 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N THR A 498 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N CYS A 489 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LEU A 500 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N SER A 487 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY A 502 " --> pdb=" O MET A 485 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 57 through 58 removed outlier: 3.870A pdb=" N ILE C 57 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL C 91 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N MET C 90 " --> pdb=" O SER C 79 " (cutoff:3.500A) 305 hydrogen bonds defined for protein. 849 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 5 stacking parallelities Total time for adding SS restraints: 7.50 Time building geometry restraints manager: 17.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10625 1.03 - 1.23: 39 1.23 - 1.42: 4686 1.42 - 1.62: 6363 1.62 - 1.81: 137 Bond restraints: 21850 Sorted by residual: bond pdb=" C ASN A 331 " pdb=" N PRO A 332 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.08e-02 8.57e+03 3.16e+00 bond pdb=" CB VAL A 636 " pdb=" CG2 VAL A 636 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.93e+00 bond pdb=" CB PRO B 29 " pdb=" CG PRO B 29 " ideal model delta sigma weight residual 1.492 1.425 0.067 5.00e-02 4.00e+02 1.81e+00 bond pdb=" C ILE B 667 " pdb=" N PRO B 668 " ideal model delta sigma weight residual 1.330 1.347 -0.017 1.25e-02 6.40e+03 1.79e+00 bond pdb=" CB LYS B 471 " pdb=" CG LYS B 471 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.61e+00 ... (remaining 21845 not shown) Histogram of bond angle deviations from ideal: 98.54 - 105.66: 339 105.66 - 112.77: 24994 112.77 - 119.88: 6242 119.88 - 126.99: 7667 126.99 - 134.10: 187 Bond angle restraints: 39429 Sorted by residual: angle pdb=" C1' C G 11 " pdb=" N1 C G 11 " pdb=" C2 C G 11 " ideal model delta sigma weight residual 118.80 128.85 -10.05 3.00e+00 1.11e-01 1.12e+01 angle pdb=" C PRO B 28 " pdb=" N PRO B 29 " pdb=" CA PRO B 29 " ideal model delta sigma weight residual 119.84 115.83 4.01 1.25e+00 6.40e-01 1.03e+01 angle pdb=" N GLY B 564 " pdb=" CA GLY B 564 " pdb=" C GLY B 564 " ideal model delta sigma weight residual 112.50 116.15 -3.65 1.16e+00 7.43e-01 9.89e+00 angle pdb=" N GLU A 613 " pdb=" CA GLU A 613 " pdb=" C GLU A 613 " ideal model delta sigma weight residual 110.91 107.30 3.61 1.17e+00 7.31e-01 9.50e+00 angle pdb=" CA PRO B 28 " pdb=" C PRO B 28 " pdb=" N PRO B 29 " ideal model delta sigma weight residual 117.93 121.60 -3.67 1.20e+00 6.94e-01 9.35e+00 ... (remaining 39424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.10: 9683 26.10 - 52.21: 520 52.21 - 78.31: 96 78.31 - 104.42: 11 104.42 - 130.52: 1 Dihedral angle restraints: 10311 sinusoidal: 5763 harmonic: 4548 Sorted by residual: dihedral pdb=" O4' C G 11 " pdb=" C1' C G 11 " pdb=" N1 C G 11 " pdb=" C2 C G 11 " ideal model delta sinusoidal sigma weight residual 232.00 101.48 130.52 1 1.70e+01 3.46e-03 5.48e+01 dihedral pdb=" O4' U G 9 " pdb=" C1' U G 9 " pdb=" N1 U G 9 " pdb=" C2 U G 9 " ideal model delta sinusoidal sigma weight residual -128.00 -49.85 -78.15 1 1.70e+01 3.46e-03 2.64e+01 dihedral pdb=" CA GLN B 442 " pdb=" C GLN B 442 " pdb=" N SER B 443 " pdb=" CA SER B 443 " ideal model delta harmonic sigma weight residual 180.00 156.09 23.91 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 10308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 927 0.032 - 0.063: 526 0.063 - 0.095: 148 0.095 - 0.127: 55 0.127 - 0.158: 10 Chirality restraints: 1666 Sorted by residual: chirality pdb=" C1' C G 11 " pdb=" O4' C G 11 " pdb=" C2' C G 11 " pdb=" N1 C G 11 " both_signs ideal model delta sigma weight residual False 2.45 2.29 0.16 2.00e-01 2.50e+01 6.26e-01 chirality pdb=" CA ILE B 606 " pdb=" N ILE B 606 " pdb=" C ILE B 606 " pdb=" CB ILE B 606 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA ILE B 475 " pdb=" N ILE B 475 " pdb=" C ILE B 475 " pdb=" CB ILE B 475 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 1663 not shown) Planarity restraints: 3190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 28 " 0.044 5.00e-02 4.00e+02 6.49e-02 6.75e+00 pdb=" N PRO B 29 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 29 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 29 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 23 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.21e+00 pdb=" C PRO B 23 " -0.035 2.00e-02 2.50e+03 pdb=" O PRO B 23 " 0.013 2.00e-02 2.50e+03 pdb=" N TYR B 24 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 219 " -0.029 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO A 220 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " -0.024 5.00e-02 4.00e+02 ... (remaining 3187 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 3598 2.27 - 2.85: 47581 2.85 - 3.44: 50761 3.44 - 4.02: 69994 4.02 - 4.60: 109075 Nonbonded interactions: 281009 Sorted by model distance: nonbonded pdb=" OD1 ASP O 90 " pdb=" HH TYR O 94 " model vdw 1.690 1.850 nonbonded pdb=" HE ARG A 566 " pdb=" O THR A 567 " model vdw 1.707 1.850 nonbonded pdb=" HZ1 LYS B 347 " pdb=" O GLY B 406 " model vdw 1.726 1.850 nonbonded pdb=" HZ1 LYS B 168 " pdb=" O GLU A 203 " model vdw 1.726 1.850 nonbonded pdb=" OD1 ASN B 455 " pdb=" H GLY B 458 " model vdw 1.726 1.850 ... (remaining 281004 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.350 Extract box with map and model: 2.880 Check model and map are aligned: 0.350 Set scattering table: 0.220 Process input model: 75.970 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 11204 Z= 0.425 Angle : 0.772 10.055 15209 Z= 0.411 Chirality : 0.043 0.158 1666 Planarity : 0.004 0.065 1914 Dihedral : 15.059 130.521 4299 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.16 (0.18), residues: 1325 helix: -4.00 (0.13), residues: 459 sheet: -3.57 (0.37), residues: 130 loop : -3.05 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 580 HIS 0.006 0.002 HIS A 297 PHE 0.021 0.002 PHE A 520 TYR 0.015 0.002 TYR B 24 ARG 0.008 0.000 ARG A 663 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 87 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Evaluate side-chains 251 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.917 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: B 65 GLN cc_start: 0.7644 (pt0) cc_final: 0.7233 (pp30) REVERT: B 220 ARG cc_start: 0.8231 (mtm180) cc_final: 0.7869 (ttm-80) REVERT: B 290 MET cc_start: 0.7411 (tpt) cc_final: 0.7066 (ppp) REVERT: B 342 ILE cc_start: 0.8763 (mm) cc_final: 0.8461 (mt) REVERT: B 357 PHE cc_start: 0.7430 (m-80) cc_final: 0.6979 (m-80) REVERT: B 358 GLU cc_start: 0.8110 (pp20) cc_final: 0.7653 (pp20) REVERT: B 476 ASN cc_start: 0.8096 (m-40) cc_final: 0.7888 (m-40) REVERT: B 531 LYS cc_start: 0.7794 (ttpt) cc_final: 0.6926 (tptt) REVERT: A 716 ARG cc_start: 0.7518 (mtt-85) cc_final: 0.7263 (mtt90) REVERT: C 53 MET cc_start: 0.7525 (tpp) cc_final: 0.7317 (tpp) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.6413 time to fit residues: 213.5091 Evaluate side-chains 179 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 77 optimal weight: 0.0570 chunk 120 optimal weight: 1.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 621 GLN ** B 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 ASN A 591 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11204 Z= 0.164 Angle : 0.554 6.717 15209 Z= 0.292 Chirality : 0.037 0.141 1666 Planarity : 0.004 0.054 1914 Dihedral : 10.492 127.949 1654 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.86 % Allowed : 8.65 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.20), residues: 1325 helix: -2.40 (0.19), residues: 489 sheet: -3.02 (0.36), residues: 146 loop : -2.79 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 580 HIS 0.004 0.001 HIS B 456 PHE 0.012 0.001 PHE B 318 TYR 0.019 0.001 TYR B 24 ARG 0.005 0.000 ARG B 249 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 87 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Evaluate side-chains 203 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 193 time to evaluate : 1.824 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: B 65 GLN cc_start: 0.7490 (pt0) cc_final: 0.6993 (pp30) REVERT: B 148 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7847 (tm-30) REVERT: B 150 PHE cc_start: 0.7585 (m-80) cc_final: 0.7352 (m-80) REVERT: B 342 ILE cc_start: 0.8953 (mm) cc_final: 0.8742 (mt) REVERT: B 356 MET cc_start: 0.7331 (mmt) cc_final: 0.6318 (mmm) REVERT: B 554 ASP cc_start: 0.8446 (m-30) cc_final: 0.7425 (t0) REVERT: A 501 TYR cc_start: 0.8267 (m-80) cc_final: 0.7869 (m-80) REVERT: A 716 ARG cc_start: 0.7748 (mtt-85) cc_final: 0.7506 (mtt90) REVERT: C 111 TYR cc_start: 0.6441 (m-80) cc_final: 0.6083 (t80) outliers start: 10 outliers final: 7 residues processed: 198 average time/residue: 0.5935 time to fit residues: 162.4168 Evaluate side-chains 172 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 164 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 TYR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 519 ASN Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain C residue 97 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 GLN B 313 GLN ** B 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS C 42 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11204 Z= 0.288 Angle : 0.590 7.206 15209 Z= 0.310 Chirality : 0.040 0.169 1666 Planarity : 0.004 0.051 1914 Dihedral : 10.538 122.668 1654 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 2.14 % Allowed : 10.63 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.21), residues: 1325 helix: -1.72 (0.21), residues: 499 sheet: -2.76 (0.38), residues: 136 loop : -2.85 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 580 HIS 0.003 0.001 HIS A 326 PHE 0.013 0.002 PHE B 381 TYR 0.019 0.001 TYR B 24 ARG 0.003 0.000 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 87 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Evaluate side-chains 203 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 178 time to evaluate : 1.623 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: B 65 GLN cc_start: 0.7743 (pt0) cc_final: 0.7094 (pp30) REVERT: B 124 GLN cc_start: 0.8300 (pp30) cc_final: 0.8038 (pt0) REVERT: B 284 ASN cc_start: 0.8366 (OUTLIER) cc_final: 0.8015 (t0) REVERT: B 554 ASP cc_start: 0.8507 (m-30) cc_final: 0.7714 (t0) REVERT: A 661 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7129 (mm-30) REVERT: C 90 MET cc_start: 0.7575 (mmt) cc_final: 0.7020 (mmp) REVERT: C 111 TYR cc_start: 0.6576 (m-80) cc_final: 0.6156 (t80) outliers start: 25 outliers final: 15 residues processed: 190 average time/residue: 0.5886 time to fit residues: 154.2847 Evaluate side-chains 186 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 170 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 519 ASN Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 630 ASP Chi-restraints excluded: chain C residue 42 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 63 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 84 ASN B 310 ASN B 413 ASN ** B 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11204 Z= 0.186 Angle : 0.528 6.970 15209 Z= 0.275 Chirality : 0.037 0.136 1666 Planarity : 0.004 0.046 1914 Dihedral : 10.364 120.623 1654 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 1.63 % Allowed : 12.25 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.22), residues: 1325 helix: -1.16 (0.22), residues: 498 sheet: -2.46 (0.39), residues: 148 loop : -2.72 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 580 HIS 0.004 0.001 HIS A 297 PHE 0.010 0.001 PHE A 612 TYR 0.019 0.001 TYR B 24 ARG 0.002 0.000 ARG B 249 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 87 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 173 time to evaluate : 1.836 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: B 65 GLN cc_start: 0.7650 (pt0) cc_final: 0.7116 (pp30) REVERT: B 284 ASN cc_start: 0.8379 (OUTLIER) cc_final: 0.8093 (t0) REVERT: B 554 ASP cc_start: 0.8480 (m-30) cc_final: 0.7783 (t0) REVERT: A 300 GLU cc_start: 0.6526 (pt0) cc_final: 0.6291 (pt0) REVERT: A 496 ARG cc_start: 0.7727 (mpp80) cc_final: 0.7480 (mtm180) REVERT: A 661 GLU cc_start: 0.7604 (mm-30) cc_final: 0.6982 (mm-30) REVERT: C 90 MET cc_start: 0.7599 (mmt) cc_final: 0.7009 (mmp) REVERT: C 111 TYR cc_start: 0.6393 (m-80) cc_final: 0.6019 (t80) outliers start: 19 outliers final: 16 residues processed: 184 average time/residue: 0.5779 time to fit residues: 145.3092 Evaluate side-chains 183 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 166 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain B residue 24 TYR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 519 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 630 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 88 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11204 Z= 0.228 Angle : 0.540 6.942 15209 Z= 0.282 Chirality : 0.038 0.138 1666 Planarity : 0.004 0.046 1914 Dihedral : 10.338 117.165 1654 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 2.66 % Allowed : 12.77 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.22), residues: 1325 helix: -0.92 (0.23), residues: 511 sheet: -2.36 (0.39), residues: 148 loop : -2.81 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 580 HIS 0.004 0.001 HIS A 297 PHE 0.011 0.001 PHE B 574 TYR 0.017 0.001 TYR B 24 ARG 0.002 0.000 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 87 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Evaluate side-chains 202 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 171 time to evaluate : 1.922 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: B 65 GLN cc_start: 0.7698 (pt0) cc_final: 0.7106 (pp30) REVERT: B 554 ASP cc_start: 0.8421 (m-30) cc_final: 0.7821 (t0) REVERT: A 300 GLU cc_start: 0.6483 (pt0) cc_final: 0.6276 (pt0) REVERT: A 496 ARG cc_start: 0.7787 (mpp80) cc_final: 0.7527 (mtm180) REVERT: A 661 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7038 (mm-30) REVERT: C 90 MET cc_start: 0.7613 (mmt) cc_final: 0.7118 (mmp) REVERT: C 111 TYR cc_start: 0.6427 (m-80) cc_final: 0.6049 (t80) outliers start: 31 outliers final: 26 residues processed: 189 average time/residue: 0.5789 time to fit residues: 152.5453 Evaluate side-chains 191 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 165 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 24 TYR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 519 ASN Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 630 ASP Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 50 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 GLN B 225 ASN B 452 ASN ** B 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 11204 Z= 0.293 Angle : 0.567 6.889 15209 Z= 0.298 Chirality : 0.039 0.142 1666 Planarity : 0.004 0.045 1914 Dihedral : 10.410 114.957 1654 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % Rotamer: Outliers : 2.57 % Allowed : 13.54 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.22), residues: 1325 helix: -0.89 (0.23), residues: 513 sheet: -2.35 (0.39), residues: 158 loop : -2.82 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 580 HIS 0.004 0.001 HIS A 297 PHE 0.020 0.001 PHE B 333 TYR 0.018 0.001 TYR B 24 ARG 0.002 0.000 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 87 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Evaluate side-chains 201 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 171 time to evaluate : 1.791 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: B 65 GLN cc_start: 0.7761 (pt0) cc_final: 0.7107 (pp30) REVERT: B 554 ASP cc_start: 0.8413 (m-30) cc_final: 0.7813 (t0) REVERT: B 628 LEU cc_start: 0.9105 (mm) cc_final: 0.8570 (tp) REVERT: A 661 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7022 (mm-30) REVERT: C 49 TRP cc_start: 0.5641 (t60) cc_final: 0.5059 (t60) REVERT: C 66 MET cc_start: 0.8225 (mmm) cc_final: 0.7956 (mmm) REVERT: C 90 MET cc_start: 0.7734 (mmt) cc_final: 0.7290 (mmp) REVERT: C 111 TYR cc_start: 0.6467 (m-80) cc_final: 0.6046 (t80) outliers start: 30 outliers final: 27 residues processed: 192 average time/residue: 0.5695 time to fit residues: 150.8870 Evaluate side-chains 192 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 165 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 24 TYR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 566 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 519 ASN Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 630 ASP Chi-restraints excluded: chain A residue 652 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 1.9990 chunk 14 optimal weight: 0.0770 chunk 73 optimal weight: 7.9990 chunk 93 optimal weight: 0.2980 chunk 72 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 chunk 80 optimal weight: 0.0010 chunk 78 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.4544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11204 Z= 0.131 Angle : 0.505 6.697 15209 Z= 0.260 Chirality : 0.037 0.137 1666 Planarity : 0.004 0.043 1914 Dihedral : 10.130 113.124 1654 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 1.80 % Allowed : 14.91 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.23), residues: 1325 helix: -0.33 (0.24), residues: 508 sheet: -2.15 (0.39), residues: 158 loop : -2.59 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 580 HIS 0.004 0.001 HIS A 297 PHE 0.019 0.001 PHE B 333 TYR 0.019 0.001 TYR B 24 ARG 0.002 0.000 ARG B 623 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 87 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Evaluate side-chains 198 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 177 time to evaluate : 1.830 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: B 65 GLN cc_start: 0.7687 (pt0) cc_final: 0.7041 (pp30) REVERT: B 554 ASP cc_start: 0.8321 (m-30) cc_final: 0.7798 (t0) REVERT: B 628 LEU cc_start: 0.9077 (mm) cc_final: 0.8556 (tp) REVERT: A 300 GLU cc_start: 0.6157 (pt0) cc_final: 0.5951 (pt0) REVERT: A 496 ARG cc_start: 0.7717 (mpp80) cc_final: 0.7460 (mtm180) REVERT: A 661 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7087 (mm-30) REVERT: C 90 MET cc_start: 0.7704 (mmt) cc_final: 0.7264 (mmp) REVERT: C 111 TYR cc_start: 0.6426 (m-80) cc_final: 0.6019 (t80) outliers start: 21 outliers final: 17 residues processed: 190 average time/residue: 0.5578 time to fit residues: 146.7606 Evaluate side-chains 187 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 170 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 24 TYR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 519 ASN Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain C residue 50 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 81 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11204 Z= 0.193 Angle : 0.522 6.835 15209 Z= 0.270 Chirality : 0.037 0.133 1666 Planarity : 0.004 0.044 1914 Dihedral : 10.126 110.112 1654 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 1.71 % Allowed : 15.25 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.23), residues: 1325 helix: -0.22 (0.24), residues: 506 sheet: -2.19 (0.38), residues: 168 loop : -2.65 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 580 HIS 0.004 0.001 HIS A 297 PHE 0.018 0.001 PHE B 333 TYR 0.018 0.001 TYR B 24 ARG 0.002 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 87 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 170 time to evaluate : 1.660 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: B 65 GLN cc_start: 0.7745 (pt0) cc_final: 0.7021 (pp30) REVERT: B 108 LEU cc_start: 0.8488 (tt) cc_final: 0.8123 (mt) REVERT: B 554 ASP cc_start: 0.8324 (m-30) cc_final: 0.7797 (t0) REVERT: B 628 LEU cc_start: 0.9091 (mm) cc_final: 0.8568 (tp) REVERT: A 300 GLU cc_start: 0.6217 (pt0) cc_final: 0.6013 (pt0) REVERT: A 496 ARG cc_start: 0.7784 (mpp80) cc_final: 0.7518 (mtm180) REVERT: A 661 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7095 (mm-30) REVERT: C 111 TYR cc_start: 0.6452 (m-80) cc_final: 0.5962 (t80) outliers start: 20 outliers final: 18 residues processed: 183 average time/residue: 0.5882 time to fit residues: 149.0023 Evaluate side-chains 184 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 166 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 24 TYR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 519 ASN Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain C residue 50 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 119 optimal weight: 0.4980 chunk 71 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 93 optimal weight: 0.0470 chunk 36 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 78 optimal weight: 0.1980 chunk 126 optimal weight: 6.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11204 Z= 0.139 Angle : 0.500 7.291 15209 Z= 0.257 Chirality : 0.037 0.134 1666 Planarity : 0.003 0.042 1914 Dihedral : 9.987 106.668 1654 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 1.63 % Allowed : 15.17 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.23), residues: 1325 helix: 0.07 (0.24), residues: 502 sheet: -2.05 (0.38), residues: 168 loop : -2.54 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 580 HIS 0.004 0.001 HIS A 297 PHE 0.015 0.001 PHE B 333 TYR 0.018 0.001 TYR B 24 ARG 0.002 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 87 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 176 time to evaluate : 1.785 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: B 65 GLN cc_start: 0.7677 (pt0) cc_final: 0.6986 (pp30) REVERT: B 108 LEU cc_start: 0.8453 (tt) cc_final: 0.8109 (mt) REVERT: B 554 ASP cc_start: 0.8324 (m-30) cc_final: 0.7817 (t0) REVERT: B 628 LEU cc_start: 0.9083 (mm) cc_final: 0.8559 (tp) REVERT: A 300 GLU cc_start: 0.5946 (pt0) cc_final: 0.5740 (pt0) REVERT: A 496 ARG cc_start: 0.7742 (mpp80) cc_final: 0.7473 (mtm180) REVERT: A 661 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7143 (mm-30) REVERT: C 111 TYR cc_start: 0.6255 (m-80) cc_final: 0.6008 (t80) outliers start: 19 outliers final: 18 residues processed: 187 average time/residue: 0.5681 time to fit residues: 147.5384 Evaluate side-chains 190 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 172 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 24 TYR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 519 ASN Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain C residue 50 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 chunk 121 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 81 optimal weight: 0.2980 chunk 64 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11204 Z= 0.147 Angle : 0.498 7.906 15209 Z= 0.256 Chirality : 0.037 0.134 1666 Planarity : 0.003 0.043 1914 Dihedral : 9.917 101.489 1654 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 1.63 % Allowed : 15.25 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.23), residues: 1325 helix: 0.25 (0.25), residues: 504 sheet: -1.84 (0.40), residues: 154 loop : -2.53 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 580 HIS 0.004 0.001 HIS A 297 PHE 0.013 0.001 PHE B 333 TYR 0.017 0.001 TYR B 24 ARG 0.002 0.000 ARG A 508 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2650 Ramachandran restraints generated. 1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 87 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue MET 507 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue MET 607 is missing expected H atoms. Skipping. Residue LYS 609 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 175 time to evaluate : 1.746 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: B 65 GLN cc_start: 0.7663 (pt0) cc_final: 0.6959 (pp30) REVERT: B 108 LEU cc_start: 0.8448 (tt) cc_final: 0.8128 (mt) REVERT: B 358 GLU cc_start: 0.8532 (pp20) cc_final: 0.7942 (pp20) REVERT: B 554 ASP cc_start: 0.8319 (m-30) cc_final: 0.7813 (t0) REVERT: B 628 LEU cc_start: 0.9089 (mm) cc_final: 0.8569 (tp) REVERT: A 300 GLU cc_start: 0.5962 (pt0) cc_final: 0.5738 (pt0) REVERT: A 496 ARG cc_start: 0.7740 (mpp80) cc_final: 0.7479 (mtm180) REVERT: A 661 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7135 (mm-30) REVERT: C 111 TYR cc_start: 0.6259 (m-80) cc_final: 0.5933 (t80) outliers start: 19 outliers final: 18 residues processed: 185 average time/residue: 0.5645 time to fit residues: 144.3738 Evaluate side-chains 187 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 169 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 24 TYR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 519 ASN Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain C residue 50 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 92 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.172145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.142380 restraints weight = 44086.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.146913 restraints weight = 22763.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.149973 restraints weight = 15423.523| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11204 Z= 0.161 Angle : 0.508 8.757 15209 Z= 0.261 Chirality : 0.037 0.134 1666 Planarity : 0.004 0.045 1914 Dihedral : 9.901 97.334 1654 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 1.63 % Allowed : 15.25 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.23), residues: 1325 helix: 0.31 (0.25), residues: 503 sheet: -1.83 (0.40), residues: 154 loop : -2.52 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 580 HIS 0.004 0.001 HIS A 297 PHE 0.012 0.001 PHE B 333 TYR 0.017 0.001 TYR B 24 ARG 0.001 0.000 ARG C 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4805.92 seconds wall clock time: 85 minutes 26.46 seconds (5126.46 seconds total)