Starting phenix.real_space_refine on Mon Nov 20 22:59:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vbv_21145/11_2023/6vbv_21145_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vbv_21145/11_2023/6vbv_21145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vbv_21145/11_2023/6vbv_21145.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vbv_21145/11_2023/6vbv_21145.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vbv_21145/11_2023/6vbv_21145_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vbv_21145/11_2023/6vbv_21145_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 Ca 2 9.91 5 P 3 5.49 5 S 155 5.16 5 C 20179 2.51 5 N 5414 2.21 5 O 5923 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ASP 22": "OD1" <-> "OD2" Residue "0 GLU 42": "OE1" <-> "OE2" Residue "1 ASP 5": "OD1" <-> "OD2" Residue "1 ASP 9": "OD1" <-> "OD2" Residue "1 PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 38": "OD1" <-> "OD2" Residue "1 ARG 44": "NH1" <-> "NH2" Residue "1 ARG 47": "NH1" <-> "NH2" Residue "1 ASP 64": "OD1" <-> "OD2" Residue "1 ASP 214": "OD1" <-> "OD2" Residue "1 ASP 258": "OD1" <-> "OD2" Residue "1 GLU 260": "OE1" <-> "OE2" Residue "1 PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 277": "NH1" <-> "NH2" Residue "1 ASP 278": "OD1" <-> "OD2" Residue "1 GLU 287": "OE1" <-> "OE2" Residue "1 PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 380": "NH1" <-> "NH2" Residue "1 ASP 385": "OD1" <-> "OD2" Residue "1 ARG 429": "NH1" <-> "NH2" Residue "1 ASP 436": "OD1" <-> "OD2" Residue "1 ARG 440": "NH1" <-> "NH2" Residue "1 GLU 443": "OE1" <-> "OE2" Residue "1 TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 465": "NH1" <-> "NH2" Residue "1 ARG 483": "NH1" <-> "NH2" Residue "1 PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 512": "NH1" <-> "NH2" Residue "1 PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 532": "NH1" <-> "NH2" Residue "1 PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 588": "OE1" <-> "OE2" Residue "2 ARG 23": "NH1" <-> "NH2" Residue "2 ASP 104": "OD1" <-> "OD2" Residue "2 ARG 114": "NH1" <-> "NH2" Residue "2 PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 153": "OD1" <-> "OD2" Residue "2 PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 161": "OD1" <-> "OD2" Residue "2 ASP 170": "OD1" <-> "OD2" Residue "2 ASP 174": "OD1" <-> "OD2" Residue "2 GLU 184": "OE1" <-> "OE2" Residue "2 GLU 193": "OE1" <-> "OE2" Residue "2 PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 274": "OD1" <-> "OD2" Residue "2 ARG 275": "NH1" <-> "NH2" Residue "2 PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 296": "OD1" <-> "OD2" Residue "2 ARG 298": "NH1" <-> "NH2" Residue "2 ASP 311": "OD1" <-> "OD2" Residue "2 ARG 315": "NH1" <-> "NH2" Residue "2 TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 356": "OE1" <-> "OE2" Residue "2 ARG 413": "NH1" <-> "NH2" Residue "2 PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 426": "OE1" <-> "OE2" Residue "2 PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 473": "OE1" <-> "OE2" Residue "2 ARG 476": "NH1" <-> "NH2" Residue "2 ASP 490": "OD1" <-> "OD2" Residue "2 TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 509": "NH1" <-> "NH2" Residue "2 PHE 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 522": "OE1" <-> "OE2" Residue "2 TYR 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 630": "OD1" <-> "OD2" Residue "2 ARG 632": "NH1" <-> "NH2" Residue "2 ARG 635": "NH1" <-> "NH2" Residue "2 TYR 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 661": "NH1" <-> "NH2" Residue "2 ARG 686": "NH1" <-> "NH2" Residue "2 ARG 699": "NH1" <-> "NH2" Residue "4 ASP 47": "OD1" <-> "OD2" Residue "4 GLU 49": "OE1" <-> "OE2" Residue "4 GLU 61": "OE1" <-> "OE2" Residue "4 ARG 109": "NH1" <-> "NH2" Residue "4 TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 196": "OE1" <-> "OE2" Residue "4 PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 389": "NH1" <-> "NH2" Residue "4 TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 399": "OE1" <-> "OE2" Residue "4 GLU 412": "OE1" <-> "OE2" Residue "4 PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 416": "OE1" <-> "OE2" Residue "5 ARG 11": "NH1" <-> "NH2" Residue "5 ASP 12": "OD1" <-> "OD2" Residue "5 ARG 25": "NH1" <-> "NH2" Residue "5 ASP 46": "OD1" <-> "OD2" Residue "5 ARG 56": "NH1" <-> "NH2" Residue "5 ARG 66": "NH1" <-> "NH2" Residue "5 ARG 82": "NH1" <-> "NH2" Residue "5 ARG 89": "NH1" <-> "NH2" Residue "5 TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 119": "NH1" <-> "NH2" Residue "5 TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 138": "NH1" <-> "NH2" Residue "5 ARG 143": "NH1" <-> "NH2" Residue "5 GLU 158": "OE1" <-> "OE2" Residue "5 PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 186": "NH1" <-> "NH2" Residue "5 ARG 207": "NH1" <-> "NH2" Residue "5 PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 241": "OE1" <-> "OE2" Residue "5 ASP 297": "OD1" <-> "OD2" Residue "5 TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 68": "NH1" <-> "NH2" Residue "7 GLU 80": "OE1" <-> "OE2" Residue "7 PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 104": "OE1" <-> "OE2" Residue "7 ASP 145": "OD1" <-> "OD2" Residue "7 ASP 149": "OD1" <-> "OD2" Residue "7 GLU 156": "OE1" <-> "OE2" Residue "7 ARG 160": "NH1" <-> "NH2" Residue "7 ASP 179": "OD1" <-> "OD2" Residue "7 ASP 248": "OD1" <-> "OD2" Residue "7 ASP 252": "OD1" <-> "OD2" Residue "7 ASP 262": "OD1" <-> "OD2" Residue "7 TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 346": "NH1" <-> "NH2" Residue "7 GLU 350": "OE1" <-> "OE2" Residue "7 TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 446": "NH1" <-> "NH2" Residue "7 GLU 455": "OE1" <-> "OE2" Residue "7 TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 530": "OE1" <-> "OE2" Residue "7 GLU 533": "OE1" <-> "OE2" Residue "7 ASP 578": "OD1" <-> "OD2" Residue "7 TYR 595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 652": "OE1" <-> "OE2" Residue "7 GLU 658": "OE1" <-> "OE2" Residue "7 ASP 676": "OD1" <-> "OD2" Residue "7 PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 680": "OD1" <-> "OD2" Residue "7 ASP 701": "OD1" <-> "OD2" Residue "7 ASP 704": "OD1" <-> "OD2" Residue "7 ASP 713": "OD1" <-> "OD2" Residue "8 ARG 14": "NH1" <-> "NH2" Residue "8 ARG 42": "NH1" <-> "NH2" Residue "8 ASP 56": "OD1" <-> "OD2" Residue "8 GLU 67": "OE1" <-> "OE2" Residue "8 ARG 110": "NH1" <-> "NH2" Residue "8 ARG 117": "NH1" <-> "NH2" Residue "8 ARG 129": "NH1" <-> "NH2" Residue "8 TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 223": "NH1" <-> "NH2" Residue "8 ARG 228": "NH1" <-> "NH2" Residue "8 PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 277": "OE1" <-> "OE2" Residue "8 GLU 290": "OE1" <-> "OE2" Residue "8 GLU 313": "OE1" <-> "OE2" Residue "8 ASP 326": "OD1" <-> "OD2" Residue "8 ARG 333": "NH1" <-> "NH2" Residue "8 PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 337": "NH1" <-> "NH2" Residue "8 PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 371": "NH1" <-> "NH2" Residue "8 TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 429": "NH1" <-> "NH2" Residue "8 PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ASP 462": "OD1" <-> "OD2" Residue "8 GLU 478": "OE1" <-> "OE2" Residue "9 PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 7": "NH1" <-> "NH2" Residue "9 PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 50": "NH1" <-> "NH2" Residue "9 PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 66": "OE1" <-> "OE2" Residue "9 ARG 75": "NH1" <-> "NH2" Residue "9 TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 149": "NH1" <-> "NH2" Residue "9 GLU 165": "OE1" <-> "OE2" Residue "9 ARG 173": "NH1" <-> "NH2" Residue "9 ARG 189": "NH1" <-> "NH2" Residue "9 PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 284": "OD1" <-> "OD2" Residue "9 TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 298": "OE1" <-> "OE2" Residue "9 ASP 351": "OD1" <-> "OD2" Residue "9 TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 362": "OD1" <-> "OD2" Residue "9 PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 499": "OE1" <-> "OE2" Residue "9 ARG 514": "NH1" <-> "NH2" Residue "9 PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 528": "NH1" <-> "NH2" Residue "9 PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 600": "NH1" <-> "NH2" Residue "9 PHE 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 608": "OD1" <-> "OD2" Residue "9 GLU 615": "OE1" <-> "OE2" Residue "9 GLU 622": "OE1" <-> "OE2" Residue "9 TYR 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 TYR 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 647": "OE1" <-> "OE2" Residue "9 ASP 650": "OD1" <-> "OD2" Residue "9 ARG 656": "NH1" <-> "NH2" Residue "9 GLU 660": "OE1" <-> "OE2" Residue "9 GLU 664": "OE1" <-> "OE2" Residue "9 ARG 669": "NH1" <-> "NH2" Residue "9 ARG 679": "NH1" <-> "NH2" Residue "9 TYR 703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 715": "OE1" <-> "OE2" Residue "9 PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 765": "OE1" <-> "OE2" Residue "9 ASP 804": "OD1" <-> "OD2" Residue "3 ASP 46": "OD1" <-> "OD2" Residue "3 PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 117": "OD1" <-> "OD2" Residue "3 ARG 121": "NH1" <-> "NH2" Residue "3 PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 31676 Number of models: 1 Model: "" Number of chains: 11 Chain: "0" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 421 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "1" Number of atoms: 3767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3767 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 29, 'TRANS': 456} Chain breaks: 3 Chain: "2" Number of atoms: 5145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5145 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 22, 'TRANS': 636} Chain breaks: 4 Chain: "4" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3156 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 10, 'TRANS': 380} Chain breaks: 1 Chain: "5" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2411 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 9, 'TRANS': 290} Chain breaks: 2 Chain: "7" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 5575 Classifications: {'peptide': 706} Link IDs: {'PTRANS': 26, 'TRANS': 679} Chain breaks: 2 Chain: "8" Number of atoms: 3797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3797 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 20, 'TRANS': 454} Chain breaks: 2 Chain: "9" Number of atoms: 6034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 6034 Classifications: {'peptide': 764} Link IDs: {'PTRANS': 31, 'TRANS': 732} Chain breaks: 5 Chain: "3" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1336 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain: "2" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.95, per 1000 atoms: 0.54 Number of scatterers: 31676 At special positions: 0 Unit cell: (153.7, 182.32, 187.62, 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) Ca 2 19.99 S 155 16.00 P 3 15.00 O 5923 8.00 N 5414 7.00 C 20179 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.11 Conformation dependent library (CDL) restraints added in 6.5 seconds 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7536 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 49 sheets defined 31.4% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.03 Creating SS restraints... Processing helix chain '0' and resid 39 through 57 removed outlier: 3.536A pdb=" N ALA 0 51 " --> pdb=" O MET 0 47 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN 0 52 " --> pdb=" O GLN 0 48 " (cutoff:3.500A) Processing helix chain '1' and resid 432 through 443 Processing helix chain '1' and resid 445 through 473 Processing helix chain '2' and resid 36 through 38 No H-bonds generated for 'chain '2' and resid 36 through 38' Processing helix chain '2' and resid 340 through 358 Processing helix chain '2' and resid 491 through 493 No H-bonds generated for 'chain '2' and resid 491 through 493' Processing helix chain '2' and resid 507 through 516 Processing helix chain '2' and resid 561 through 574 Processing helix chain '2' and resid 587 through 634 removed outlier: 3.685A pdb=" N GLU 2 592 " --> pdb=" O VAL 2 588 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASP 2 601 " --> pdb=" O LEU 2 597 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU 2 602 " --> pdb=" O VAL 2 598 " (cutoff:3.500A) Processing helix chain '2' and resid 637 through 685 Processing helix chain '2' and resid 688 through 702 removed outlier: 4.267A pdb=" N GLN 2 693 " --> pdb=" O PRO 2 690 " (cutoff:3.500A) Processing helix chain '2' and resid 707 through 715 Processing helix chain '4' and resid 36 through 44 Processing helix chain '4' and resid 50 through 62 Processing helix chain '4' and resid 69 through 79 removed outlier: 3.552A pdb=" N GLN 4 73 " --> pdb=" O ALA 4 69 " (cutoff:3.500A) Processing helix chain '4' and resid 85 through 96 Processing helix chain '4' and resid 101 through 113 Processing helix chain '4' and resid 118 through 128 removed outlier: 3.751A pdb=" N GLU 4 126 " --> pdb=" O GLU 4 122 " (cutoff:3.500A) Processing helix chain '4' and resid 135 through 147 Processing helix chain '4' and resid 151 through 164 Processing helix chain '4' and resid 168 through 181 Processing helix chain '4' and resid 184 through 196 removed outlier: 4.611A pdb=" N GLU 4 189 " --> pdb=" O ASP 4 185 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE 4 190 " --> pdb=" O LYS 4 186 " (cutoff:3.500A) Processing helix chain '4' and resid 202 through 214 Processing helix chain '4' and resid 219 through 231 removed outlier: 3.664A pdb=" N TYR 4 231 " --> pdb=" O ASN 4 227 " (cutoff:3.500A) Processing helix chain '4' and resid 236 through 248 removed outlier: 3.980A pdb=" N ALA 4 241 " --> pdb=" O LYS 4 237 " (cutoff:3.500A) Processing helix chain '4' and resid 252 through 262 removed outlier: 3.806A pdb=" N VAL 4 262 " --> pdb=" O LYS 4 258 " (cutoff:3.500A) Processing helix chain '4' and resid 270 through 282 Processing helix chain '4' and resid 286 through 298 removed outlier: 3.903A pdb=" N CYS 4 292 " --> pdb=" O ALA 4 288 " (cutoff:3.500A) Processing helix chain '4' and resid 304 through 316 Processing helix chain '4' and resid 322 through 333 Processing helix chain '4' and resid 339 through 349 Processing helix chain '4' and resid 354 through 367 Processing helix chain '4' and resid 372 through 384 Processing helix chain '4' and resid 390 through 401 Processing helix chain '4' and resid 411 through 422 Proline residue: 4 415 - end of helix Processing helix chain '5' and resid 73 through 75 No H-bonds generated for 'chain '5' and resid 73 through 75' Processing helix chain '5' and resid 119 through 132 removed outlier: 4.484A pdb=" N LEU 5 124 " --> pdb=" O TYR 5 121 " (cutoff:3.500A) Processing helix chain '5' and resid 240 through 259 Processing helix chain '5' and resid 299 through 301 No H-bonds generated for 'chain '5' and resid 299 through 301' Processing helix chain '5' and resid 333 through 336 No H-bonds generated for 'chain '5' and resid 333 through 336' Processing helix chain '7' and resid 337 through 367 Processing helix chain '7' and resid 517 through 527 Processing helix chain '7' and resid 570 through 587 Processing helix chain '7' and resid 601 through 633 Proline residue: 7 611 - end of helix removed outlier: 3.868A pdb=" N LEU 7 625 " --> pdb=" O LYS 7 621 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ASP 7 627 " --> pdb=" O VAL 7 623 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ALA 7 628 " --> pdb=" O GLN 7 624 " (cutoff:3.500A) Processing helix chain '7' and resid 636 through 638 No H-bonds generated for 'chain '7' and resid 636 through 638' Processing helix chain '7' and resid 644 through 683 removed outlier: 3.813A pdb=" N ILE 7 649 " --> pdb=" O GLU 7 645 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU 7 651 " --> pdb=" O ARG 7 647 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU 7 652 " --> pdb=" O CYS 7 648 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ASP 7 654 " --> pdb=" O LEU 7 650 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N HIS 7 655 " --> pdb=" O GLU 7 651 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS 7 661 " --> pdb=" O GLN 7 657 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS 7 662 " --> pdb=" O GLU 7 658 " (cutoff:3.500A) Proline residue: 7 664 - end of helix Processing helix chain '7' and resid 693 through 702 Processing helix chain '7' and resid 705 through 714 Processing helix chain '8' and resid 3 through 12 Processing helix chain '8' and resid 18 through 29 Processing helix chain '8' and resid 34 through 47 Processing helix chain '8' and resid 52 through 54 No H-bonds generated for 'chain '8' and resid 52 through 54' Processing helix chain '8' and resid 61 through 64 No H-bonds generated for 'chain '8' and resid 61 through 64' Processing helix chain '8' and resid 121 through 125 Processing helix chain '8' and resid 168 through 171 No H-bonds generated for 'chain '8' and resid 168 through 171' Processing helix chain '8' and resid 175 through 187 removed outlier: 4.263A pdb=" N ALA 8 180 " --> pdb=" O LYS 8 176 " (cutoff:3.500A) Processing helix chain '8' and resid 192 through 205 Processing helix chain '8' and resid 211 through 224 Processing helix chain '8' and resid 228 through 240 removed outlier: 3.928A pdb=" N GLN 8 233 " --> pdb=" O GLU 8 229 " (cutoff:3.500A) Processing helix chain '8' and resid 244 through 256 Processing helix chain '8' and resid 260 through 273 Processing helix chain '8' and resid 278 through 290 Processing helix chain '8' and resid 294 through 307 removed outlier: 4.313A pdb=" N GLU 8 299 " --> pdb=" O SER 8 295 " (cutoff:3.500A) Processing helix chain '8' and resid 312 through 324 Processing helix chain '8' and resid 328 through 340 removed outlier: 3.690A pdb=" N LEU 8 338 " --> pdb=" O PHE 8 334 " (cutoff:3.500A) Processing helix chain '8' and resid 347 through 358 Processing helix chain '8' and resid 366 through 375 Processing helix chain '8' and resid 380 through 396 Processing helix chain '8' and resid 399 through 412 Processing helix chain '8' and resid 417 through 430 Processing helix chain '8' and resid 433 through 446 Processing helix chain '8' and resid 452 through 464 Processing helix chain '8' and resid 467 through 480 removed outlier: 3.734A pdb=" N LYS 8 476 " --> pdb=" O ALA 8 472 " (cutoff:3.500A) Processing helix chain '8' and resid 486 through 497 Processing helix chain '9' and resid 65 through 67 No H-bonds generated for 'chain '9' and resid 65 through 67' Processing helix chain '9' and resid 207 through 212 Processing helix chain '9' and resid 378 through 395 Processing helix chain '9' and resid 531 through 533 No H-bonds generated for 'chain '9' and resid 531 through 533' Processing helix chain '9' and resid 559 through 562 No H-bonds generated for 'chain '9' and resid 559 through 562' Processing helix chain '9' and resid 608 through 626 removed outlier: 4.093A pdb=" N ILE 9 612 " --> pdb=" O ASP 9 608 " (cutoff:3.500A) Processing helix chain '9' and resid 646 through 685 removed outlier: 3.656A pdb=" N GLU 9 668 " --> pdb=" O GLU 9 664 " (cutoff:3.500A) Processing helix chain '9' and resid 695 through 741 Processing helix chain '9' and resid 746 through 756 Processing helix chain '9' and resid 768 through 782 Processing helix chain '9' and resid 788 through 793 Processing helix chain '9' and resid 806 through 820 Processing helix chain '3' and resid 30 through 35 Processing helix chain '3' and resid 74 through 76 No H-bonds generated for 'chain '3' and resid 74 through 76' Processing helix chain '3' and resid 78 through 84 removed outlier: 3.776A pdb=" N TYR 3 83 " --> pdb=" O TRP 3 80 " (cutoff:3.500A) Processing helix chain '3' and resid 102 through 113 Processing helix chain '3' and resid 140 through 147 Processing helix chain '3' and resid 170 through 182 Processing sheet with id= A, first strand: chain '1' and resid 21 through 25 removed outlier: 3.959A pdb=" N SER 1 58 " --> pdb=" O VAL 1 50 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LYS 1 52 " --> pdb=" O LEU 1 56 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU 1 56 " --> pdb=" O LYS 1 52 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '1' and resid 66 through 72 removed outlier: 6.727A pdb=" N ALA 1 87 " --> pdb=" O ALA 1 67 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA 1 69 " --> pdb=" O ALA 1 85 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA 1 85 " --> pdb=" O ALA 1 69 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR 1 71 " --> pdb=" O ALA 1 83 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ALA 1 83 " --> pdb=" O THR 1 71 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '1' and resid 200 through 207 removed outlier: 6.569A pdb=" N GLY 1 222 " --> pdb=" O THR 1 201 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N MET 1 203 " --> pdb=" O VAL 1 220 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL 1 220 " --> pdb=" O MET 1 203 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR 1 205 " --> pdb=" O CYS 1 218 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N CYS 1 218 " --> pdb=" O THR 1 205 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU 1 219 " --> pdb=" O LEU 1 231 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU 1 227 " --> pdb=" O THR 1 223 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '1' and resid 285 through 287 removed outlier: 4.412A pdb=" N SER 1 271 " --> pdb=" O CYS 1 267 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '1' and resid 292 through 297 removed outlier: 6.488A pdb=" N GLY 1 305 " --> pdb=" O VAL 1 293 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LEU 1 295 " --> pdb=" O VAL 1 303 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL 1 303 " --> pdb=" O LEU 1 295 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N GLY 1 297 " --> pdb=" O VAL 1 301 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL 1 301 " --> pdb=" O GLY 1 297 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER 1 310 " --> pdb=" O SER 1 306 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N THR 1 315 " --> pdb=" O ARG 1 320 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ARG 1 320 " --> pdb=" O THR 1 315 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '1' and resid 335 through 338 Processing sheet with id= G, first strand: chain '1' and resid 487 through 493 Processing sheet with id= H, first strand: chain '1' and resid 534 through 536 Processing sheet with id= I, first strand: chain '1' and resid 3 through 9 removed outlier: 6.612A pdb=" N ILE 1 399 " --> pdb=" O SER 1 6 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER 1 8 " --> pdb=" O LEU 1 397 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU 1 397 " --> pdb=" O SER 1 8 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LEU 1 397 " --> pdb=" O MET 1 390 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N MET 1 390 " --> pdb=" O LEU 1 397 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE 1 399 " --> pdb=" O LEU 1 388 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU 1 388 " --> pdb=" O ILE 1 399 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER 1 375 " --> pdb=" O THR 1 391 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '2' and resid 6 through 9 removed outlier: 4.767A pdb=" N GLU 2 313 " --> pdb=" O SER 2 309 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '2' and resid 19 through 22 removed outlier: 3.889A pdb=" N LYS 2 39 " --> pdb=" O THR 2 35 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '2' and resid 75 through 81 removed outlier: 6.494A pdb=" N GLY 2 95 " --> pdb=" O SER 2 76 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU 2 78 " --> pdb=" O LEU 2 93 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU 2 93 " --> pdb=" O LEU 2 78 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA 2 80 " --> pdb=" O ALA 2 91 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ALA 2 91 " --> pdb=" O ALA 2 80 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE 2 112 " --> pdb=" O ALA 2 102 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP 2 104 " --> pdb=" O ASP 2 110 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASP 2 110 " --> pdb=" O ASP 2 104 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '2' and resid 163 through 169 removed outlier: 6.746A pdb=" N GLY 2 182 " --> pdb=" O HIS 2 164 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU 2 166 " --> pdb=" O LEU 2 180 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU 2 180 " --> pdb=" O LEU 2 166 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LEU 2 168 " --> pdb=" O GLU 2 178 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLU 2 178 " --> pdb=" O LEU 2 168 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP 2 187 " --> pdb=" O SER 2 183 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA 2 198 " --> pdb=" O VAL 2 190 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '2' and resid 208 through 211 removed outlier: 3.943A pdb=" N SER 2 208 " --> pdb=" O ALA 2 220 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '2' and resid 246 through 250 removed outlier: 3.553A pdb=" N SER 2 246 " --> pdb=" O GLY 2 263 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '2' and resid 269 through 271 Processing sheet with id= Q, first strand: chain '2' and resid 383 through 390 Processing sheet with id= R, first strand: chain '2' and resid 427 through 430 removed outlier: 4.422A pdb=" N ILE 2 417 " --> pdb=" O HIS 2 428 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL 2 415 " --> pdb=" O VAL 2 430 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE 2 460 " --> pdb=" O ARG 2 413 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL 2 415 " --> pdb=" O LYS 2 458 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LYS 2 458 " --> pdb=" O VAL 2 415 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ILE 2 417 " --> pdb=" O HIS 2 456 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N HIS 2 456 " --> pdb=" O ILE 2 417 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain '2' and resid 485 through 487 removed outlier: 3.596A pdb=" N ALA 2 485 " --> pdb=" O THR 2 536 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N CYS 2 534 " --> pdb=" O THR 2 487 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain '2' and resid 143 through 147 removed outlier: 3.961A pdb=" N PHE 2 155 " --> pdb=" O GLY 2 146 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain '5' and resid 13 through 15 removed outlier: 3.521A pdb=" N ASP 5 32 " --> pdb=" O VAL 5 52 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain '5' and resid 37 through 40 removed outlier: 3.517A pdb=" N ASN 5 78 " --> pdb=" O LEU 5 98 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LYS 5 100 " --> pdb=" O ILE 5 76 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ILE 5 76 " --> pdb=" O LYS 5 100 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain '5' and resid 199 through 202 removed outlier: 4.103A pdb=" N ARG 5 186 " --> pdb=" O THR 5 183 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN 5 162 " --> pdb=" O ILE 5 182 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain '5' and resid 314 through 316 Processing sheet with id= Y, first strand: chain '5' and resid 206 through 210 removed outlier: 6.886A pdb=" N GLU 5 223 " --> pdb=" O ARG 5 207 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL 5 209 " --> pdb=" O VAL 5 221 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL 5 221 " --> pdb=" O VAL 5 209 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain '7' and resid 6 through 9 removed outlier: 3.618A pdb=" N SER 7 291 " --> pdb=" O SER 7 308 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain '7' and resid 21 through 24 removed outlier: 3.797A pdb=" N LYS 7 34 " --> pdb=" O LEU 7 24 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain '7' and resid 69 through 72 removed outlier: 3.652A pdb=" N LEU 7 101 " --> pdb=" O GLY 7 92 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain '7' and resid 114 through 117 removed outlier: 6.264A pdb=" N CYS 7 133 " --> pdb=" O ASP 7 137 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ASP 7 137 " --> pdb=" O CYS 7 133 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain '7' and resid 147 through 152 removed outlier: 7.047A pdb=" N ALA 7 166 " --> pdb=" O ASN 7 148 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL 7 150 " --> pdb=" O VAL 7 164 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL 7 164 " --> pdb=" O VAL 7 150 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL 7 171 " --> pdb=" O CYS 7 167 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR 7 182 " --> pdb=" O VAL 7 174 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLN 7 176 " --> pdb=" O VAL 7 180 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N VAL 7 180 " --> pdb=" O GLN 7 176 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain '7' and resid 215 through 217 removed outlier: 4.037A pdb=" N LYS 7 215 " --> pdb=" O THR 7 211 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain '7' and resid 244 through 247 removed outlier: 3.766A pdb=" N PHE 7 281 " --> pdb=" O VAL 7 268 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLY 7 270 " --> pdb=" O LEU 7 279 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU 7 279 " --> pdb=" O GLY 7 270 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain '7' and resid 384 through 387 removed outlier: 4.261A pdb=" N THR 7 386 " --> pdb=" O SER 7 395 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain '7' and resid 442 through 446 removed outlier: 3.566A pdb=" N ILE 7 409 " --> pdb=" O ALA 7 443 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N THR 7 473 " --> pdb=" O ASP 7 405 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL 7 407 " --> pdb=" O TYR 7 471 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TYR 7 471 " --> pdb=" O VAL 7 407 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE 7 409 " --> pdb=" O GLN 7 469 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLN 7 469 " --> pdb=" O ILE 7 409 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N SER 7 411 " --> pdb=" O THR 7 467 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N THR 7 467 " --> pdb=" O SER 7 411 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain '7' and resid 592 through 595 removed outlier: 3.729A pdb=" N LEU 7 509 " --> pdb=" O PHE 7 565 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU 7 562 " --> pdb=" O ARG 7 559 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain '9' and resid 6 through 8 Processing sheet with id= AK, first strand: chain '9' and resid 11 through 13 Processing sheet with id= AL, first strand: chain '9' and resid 26 through 28 removed outlier: 3.575A pdb=" N ALA 9 28 " --> pdb=" O LYS 9 39 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain '9' and resid 82 through 84 removed outlier: 3.656A pdb=" N LEU 9 95 " --> pdb=" O TYR 9 106 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR 9 127 " --> pdb=" O VAL 9 105 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain '9' and resid 108 through 111 Processing sheet with id= AO, first strand: chain '9' and resid 138 through 141 Processing sheet with id= AP, first strand: chain '9' and resid 184 through 187 Processing sheet with id= AQ, first strand: chain '9' and resid 245 through 251 removed outlier: 7.193A pdb=" N LEU 9 263 " --> pdb=" O ILE 9 246 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ILE 9 248 " --> pdb=" O PHE 9 261 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N PHE 9 261 " --> pdb=" O ILE 9 248 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ILE 9 250 " --> pdb=" O SER 9 259 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N SER 9 259 " --> pdb=" O ILE 9 250 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain '9' and resid 287 through 291 removed outlier: 6.730A pdb=" N GLY 9 306 " --> pdb=" O SER 9 288 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE 9 290 " --> pdb=" O LEU 9 304 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU 9 304 " --> pdb=" O PHE 9 290 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N MET 9 311 " --> pdb=" O ASN 9 307 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLN 9 316 " --> pdb=" O LEU 9 320 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU 9 320 " --> pdb=" O GLN 9 316 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain '9' and resid 411 through 417 Processing sheet with id= AT, first strand: chain '9' and resid 471 through 474 Processing sheet with id= AU, first strand: chain '9' and resid 535 through 537 Processing sheet with id= AV, first strand: chain '3' and resid 20 through 23 removed outlier: 6.310A pdb=" N ALA 3 89 " --> pdb=" O LEU 3 21 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU 3 23 " --> pdb=" O ALA 3 89 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE 3 91 " --> pdb=" O LEU 3 23 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N PHE 3 92 " --> pdb=" O PRO 3 124 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU 3 126 " --> pdb=" O PHE 3 92 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE 3 94 " --> pdb=" O LEU 3 126 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N PHE 3 128 " --> pdb=" O ILE 3 94 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain '3' and resid 56 through 59 1355 hydrogen bonds defined for protein. 3822 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.68 Time building geometry restraints manager: 13.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5289 1.31 - 1.43: 8270 1.43 - 1.56: 18493 1.56 - 1.69: 5 1.69 - 1.82: 232 Bond restraints: 32289 Sorted by residual: bond pdb=" CA SER 7 428 " pdb=" CB SER 7 428 " ideal model delta sigma weight residual 1.527 1.451 0.076 7.60e-03 1.73e+04 1.00e+02 bond pdb=" C ALA 8 20 " pdb=" O ALA 8 20 " ideal model delta sigma weight residual 1.237 1.177 0.059 1.17e-02 7.31e+03 2.58e+01 bond pdb=" CA SER 2 254 " pdb=" CB SER 2 254 " ideal model delta sigma weight residual 1.530 1.465 0.065 1.50e-02 4.44e+03 1.87e+01 bond pdb=" CA SER 7 430 " pdb=" CB SER 7 430 " ideal model delta sigma weight residual 1.529 1.458 0.071 1.70e-02 3.46e+03 1.75e+01 bond pdb=" N VAL 1 373 " pdb=" CA VAL 1 373 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.20e-02 6.94e+03 1.34e+01 ... (remaining 32284 not shown) Histogram of bond angle deviations from ideal: 99.49 - 106.40: 855 106.40 - 113.32: 17766 113.32 - 120.23: 11614 120.23 - 127.14: 13144 127.14 - 134.06: 321 Bond angle restraints: 43700 Sorted by residual: angle pdb=" C ASP 2 172 " pdb=" CA ASP 2 172 " pdb=" CB ASP 2 172 " ideal model delta sigma weight residual 109.83 118.15 -8.32 9.90e-01 1.02e+00 7.06e+01 angle pdb=" C ASP 2 251 " pdb=" CA ASP 2 251 " pdb=" CB ASP 2 251 " ideal model delta sigma weight residual 111.70 103.13 8.57 1.48e+00 4.57e-01 3.35e+01 angle pdb=" N ALA 8 20 " pdb=" CA ALA 8 20 " pdb=" C ALA 8 20 " ideal model delta sigma weight residual 111.28 105.16 6.12 1.09e+00 8.42e-01 3.15e+01 angle pdb=" C ASP 9 362 " pdb=" CA ASP 9 362 " pdb=" CB ASP 9 362 " ideal model delta sigma weight residual 110.71 102.25 8.46 1.53e+00 4.27e-01 3.05e+01 angle pdb=" N GLN 8 25 " pdb=" CA GLN 8 25 " pdb=" C GLN 8 25 " ideal model delta sigma weight residual 110.97 104.95 6.02 1.09e+00 8.42e-01 3.05e+01 ... (remaining 43695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.20: 18924 31.20 - 62.39: 542 62.39 - 93.59: 55 93.59 - 124.78: 3 124.78 - 155.98: 2 Dihedral angle restraints: 19526 sinusoidal: 7873 harmonic: 11653 Sorted by residual: dihedral pdb=" C8 GTP 3 201 " pdb=" C1' GTP 3 201 " pdb=" N9 GTP 3 201 " pdb=" O4' GTP 3 201 " ideal model delta sinusoidal sigma weight residual 104.59 -51.39 155.98 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" C5' GTP 3 201 " pdb=" O5' GTP 3 201 " pdb=" PA GTP 3 201 " pdb=" O3A GTP 3 201 " ideal model delta sinusoidal sigma weight residual 69.27 -150.42 -140.31 1 2.00e+01 2.50e-03 4.25e+01 dihedral pdb=" O3B GTP 3 201 " pdb=" O3A GTP 3 201 " pdb=" PB GTP 3 201 " pdb=" PA GTP 3 201 " ideal model delta sinusoidal sigma weight residual -68.92 55.24 -124.16 1 2.00e+01 2.50e-03 3.75e+01 ... (remaining 19523 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4658 0.096 - 0.192: 275 0.192 - 0.288: 28 0.288 - 0.384: 10 0.384 - 0.480: 3 Chirality restraints: 4974 Sorted by residual: chirality pdb=" CA ASP 2 172 " pdb=" N ASP 2 172 " pdb=" C ASP 2 172 " pdb=" CB ASP 2 172 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.75e+00 chirality pdb=" CA PHE 2 171 " pdb=" N PHE 2 171 " pdb=" C PHE 2 171 " pdb=" CB PHE 2 171 " both_signs ideal model delta sigma weight residual False 2.51 2.98 -0.47 2.00e-01 2.50e+01 5.55e+00 chirality pdb=" CA GLU 2 259 " pdb=" N GLU 2 259 " pdb=" C GLU 2 259 " pdb=" CB GLU 2 259 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.86e+00 ... (remaining 4971 not shown) Planarity restraints: 5596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL 7 427 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C VAL 7 427 " 0.062 2.00e-02 2.50e+03 pdb=" O VAL 7 427 " -0.024 2.00e-02 2.50e+03 pdb=" N SER 7 428 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE 8 16 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C PHE 8 16 " 0.058 2.00e-02 2.50e+03 pdb=" O PHE 8 16 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN 8 17 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE 2 250 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C PHE 2 250 " -0.055 2.00e-02 2.50e+03 pdb=" O PHE 2 250 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP 2 251 " 0.018 2.00e-02 2.50e+03 ... (remaining 5593 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 475 2.64 - 3.20: 28863 3.20 - 3.77: 48224 3.77 - 4.33: 67834 4.33 - 4.90: 112445 Nonbonded interactions: 257841 Sorted by model distance: nonbonded pdb=" O SER 7 428 " pdb=" OG SER 7 428 " model vdw 2.070 2.440 nonbonded pdb=" OD2 ASP 7 433 " pdb=" OG SER 7 436 " model vdw 2.200 2.440 nonbonded pdb=" O HIS 7 323 " pdb=" OG SER 3 140 " model vdw 2.201 2.440 nonbonded pdb=" OG1 THR 5 83 " pdb=" OE1 GLU 5 93 " model vdw 2.208 2.440 nonbonded pdb=" ND2 ASN 7 148 " pdb=" O PRO 7 190 " model vdw 2.212 2.520 ... (remaining 257836 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 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: 0.040 Extract box with map and model: 8.970 Check model and map are aligned: 0.440 Set scattering table: 0.270 Process input model: 88.840 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.140 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 32289 Z= 0.271 Angle : 0.714 10.033 43700 Z= 0.424 Chirality : 0.052 0.480 4974 Planarity : 0.004 0.050 5596 Dihedral : 15.128 155.981 11990 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.20 % Favored : 92.72 % Rotamer: Outliers : 0.72 % Allowed : 6.87 % Favored : 92.42 % Cbeta Deviations : 0.16 % 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: -3.09 (0.12), residues: 3944 helix: -0.62 (0.12), residues: 1352 sheet: -2.24 (0.15), residues: 991 loop : -3.14 (0.13), residues: 1601 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 3495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 799 time to evaluate : 3.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 10 residues processed: 814 average time/residue: 0.4476 time to fit residues: 571.2391 Evaluate side-chains 429 residues out of total 3495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 419 time to evaluate : 3.993 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2900 time to fit residues: 10.9770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 334 optimal weight: 0.9990 chunk 300 optimal weight: 1.9990 chunk 166 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 202 optimal weight: 0.0670 chunk 160 optimal weight: 9.9990 chunk 310 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 188 optimal weight: 10.0000 chunk 231 optimal weight: 0.0170 chunk 359 optimal weight: 5.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 15 HIS 1 45 GLN 1 54 HIS ** 1 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 291 GLN 1 365 ASN 1 449 HIS 1 545 ASN 2 3 GLN 2 28 HIS ** 2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 223 ASN 2 343 GLN ** 2 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 358 ASN 2 384 HIS ** 2 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 516 GLN 2 532 GLN 2 540 ASN 2 543 GLN 2 656 ASN 2 684 HIS 4 35 GLN 4 40 HIS 4 58 GLN 4 91 GLN 4 140 ASN 4 167 HIS 4 224 HIS ** 4 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 275 ASN 5 44 ASN 5 176 ASN 5 190 HIS 5 205 GLN 5 251 ASN 5 334 GLN ** 7 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 99 GLN ** 7 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 228 HIS 7 477 GLN ** 7 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 502 HIS 7 610 HIS 7 624 GLN 7 635 HIS 8 216 GLN 8 233 GLN 8 307 GLN 8 322 HIS 8 350 ASN 8 351 ASN 8 360 GLN 8 388 ASN 8 422 ASN 8 454 HIS 8 456 ASN 9 22 GLN ** 9 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 201 GLN 9 276 GLN 9 309 ASN 9 652 HIS 9 693 GLN ** 9 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 778 HIS 3 43 GLN 3 120 HIS Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 32289 Z= 0.196 Angle : 0.597 9.471 43700 Z= 0.304 Chirality : 0.043 0.222 4974 Planarity : 0.004 0.065 5596 Dihedral : 6.371 161.494 4309 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 2.23 % Allowed : 14.33 % Favored : 83.43 % 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: -1.84 (0.13), residues: 3944 helix: 0.73 (0.14), residues: 1346 sheet: -1.70 (0.16), residues: 1001 loop : -2.61 (0.14), residues: 1597 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 468 time to evaluate : 3.933 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 45 residues processed: 520 average time/residue: 0.4405 time to fit residues: 370.9637 Evaluate side-chains 438 residues out of total 3495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 393 time to evaluate : 3.620 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.2920 time to fit residues: 29.6007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 199 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 299 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 99 optimal weight: 0.0670 chunk 360 optimal weight: 10.0000 chunk 389 optimal weight: 6.9990 chunk 320 optimal weight: 7.9990 chunk 357 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 289 optimal weight: 2.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 308 GLN 1 426 ASN 1 545 ASN ** 1 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 343 GLN ** 2 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 91 GLN 4 103 ASN 4 275 ASN 5 60 HIS 5 251 ASN 7 6 ASN 7 99 GLN ** 7 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 382 ASN 8 188 HIS ** 8 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 484 HIS ** 9 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 53 ASN 9 73 HIS ** 9 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 309 ASN 9 694 HIS ** 3 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 32289 Z= 0.371 Angle : 0.683 10.546 43700 Z= 0.346 Chirality : 0.046 0.162 4974 Planarity : 0.005 0.053 5596 Dihedral : 6.364 156.380 4309 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 2.89 % Allowed : 17.40 % Favored : 79.71 % 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: -1.55 (0.13), residues: 3944 helix: 0.87 (0.14), residues: 1347 sheet: -1.48 (0.16), residues: 969 loop : -2.38 (0.15), residues: 1628 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 421 time to evaluate : 3.634 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 101 outliers final: 59 residues processed: 501 average time/residue: 0.4512 time to fit residues: 365.7296 Evaluate side-chains 413 residues out of total 3495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 354 time to evaluate : 3.728 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 0 residues processed: 59 average time/residue: 0.3106 time to fit residues: 38.7117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 355 optimal weight: 0.0170 chunk 270 optimal weight: 4.9990 chunk 186 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 171 optimal weight: 0.9980 chunk 241 optimal weight: 3.9990 chunk 361 optimal weight: 3.9990 chunk 382 optimal weight: 6.9990 chunk 188 optimal weight: 7.9990 chunk 342 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 overall best weight: 2.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 343 GLN ** 2 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 384 HIS 2 436 HIS 4 91 GLN ** 7 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 309 ASN 9 515 ASN 3 27 ASN ** 3 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 145 GLN 3 158 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 32289 Z= 0.302 Angle : 0.631 10.868 43700 Z= 0.320 Chirality : 0.044 0.186 4974 Planarity : 0.004 0.052 5596 Dihedral : 6.110 152.812 4309 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 2.32 % Allowed : 20.11 % Favored : 77.57 % 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: -1.31 (0.13), residues: 3944 helix: 1.12 (0.14), residues: 1338 sheet: -1.35 (0.17), residues: 959 loop : -2.27 (0.15), residues: 1647 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 393 time to evaluate : 3.809 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 41 residues processed: 455 average time/residue: 0.4465 time to fit residues: 327.1778 Evaluate side-chains 393 residues out of total 3495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 352 time to evaluate : 3.767 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.2777 time to fit residues: 27.0427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 318 optimal weight: 8.9990 chunk 217 optimal weight: 1.9990 chunk 5 optimal weight: 0.0670 chunk 285 optimal weight: 2.9990 chunk 157 optimal weight: 8.9990 chunk 326 optimal weight: 2.9990 chunk 264 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 195 optimal weight: 9.9990 chunk 343 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 343 GLN 2 468 GLN 4 91 GLN 4 224 HIS ** 5 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 6 ASN ** 7 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 241 GLN ** 8 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 22 GLN ** 9 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 309 ASN 9 453 GLN 3 27 ASN ** 3 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 158 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 32289 Z= 0.252 Angle : 0.603 10.538 43700 Z= 0.307 Chirality : 0.043 0.190 4974 Planarity : 0.004 0.050 5596 Dihedral : 5.821 147.126 4309 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 1.83 % Allowed : 20.97 % Favored : 77.20 % 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: -1.12 (0.14), residues: 3944 helix: 1.28 (0.14), residues: 1343 sheet: -1.24 (0.17), residues: 941 loop : -2.17 (0.15), residues: 1660 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 394 time to evaluate : 3.706 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 30 residues processed: 438 average time/residue: 0.4605 time to fit residues: 325.2701 Evaluate side-chains 385 residues out of total 3495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 355 time to evaluate : 3.672 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.3077 time to fit residues: 22.4561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 128 optimal weight: 1.9990 chunk 344 optimal weight: 0.5980 chunk 75 optimal weight: 6.9990 chunk 224 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 383 optimal weight: 8.9990 chunk 318 optimal weight: 10.0000 chunk 177 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 201 optimal weight: 9.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 343 GLN ** 2 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 91 GLN 5 102 ASN ** 5 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 6 ASN ** 7 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 309 ASN 9 448 ASN 9 515 ASN ** 3 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 158 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 32289 Z= 0.333 Angle : 0.649 10.800 43700 Z= 0.329 Chirality : 0.045 0.250 4974 Planarity : 0.004 0.052 5596 Dihedral : 5.871 142.568 4309 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 2.12 % Allowed : 21.63 % Favored : 76.25 % 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: -1.16 (0.14), residues: 3944 helix: 1.21 (0.14), residues: 1344 sheet: -1.28 (0.17), residues: 955 loop : -2.14 (0.15), residues: 1645 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 384 time to evaluate : 3.729 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 36 residues processed: 430 average time/residue: 0.4404 time to fit residues: 302.8017 Evaluate side-chains 398 residues out of total 3495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 362 time to evaluate : 3.554 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.2748 time to fit residues: 23.4798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 369 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 218 optimal weight: 9.9990 chunk 279 optimal weight: 0.8980 chunk 216 optimal weight: 5.9990 chunk 322 optimal weight: 6.9990 chunk 213 optimal weight: 6.9990 chunk 381 optimal weight: 10.0000 chunk 238 optimal weight: 8.9990 chunk 232 optimal weight: 6.9990 chunk 176 optimal weight: 6.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 308 GLN 1 359 HIS ** 1 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 343 GLN ** 2 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 664 ASN ** 4 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 74 ASN ** 5 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 350 ASN 8 388 ASN 8 484 HIS ** 9 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 309 ASN 9 328 HIS 9 605 GLN ** 3 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 145 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 32289 Z= 0.481 Angle : 0.742 10.898 43700 Z= 0.378 Chirality : 0.048 0.220 4974 Planarity : 0.005 0.054 5596 Dihedral : 6.246 137.566 4309 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.38 % Favored : 90.59 % Rotamer: Outliers : 1.80 % Allowed : 22.43 % Favored : 75.77 % 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: -1.47 (0.13), residues: 3944 helix: 0.83 (0.14), residues: 1346 sheet: -1.33 (0.17), residues: 954 loop : -2.29 (0.15), residues: 1644 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 382 time to evaluate : 4.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 34 residues processed: 429 average time/residue: 0.4426 time to fit residues: 306.1583 Evaluate side-chains 386 residues out of total 3495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 352 time to evaluate : 3.718 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.3289 time to fit residues: 25.3993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 236 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 242 optimal weight: 5.9990 chunk 260 optimal weight: 5.9990 chunk 188 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 300 optimal weight: 0.6980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 359 HIS ** 1 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 343 GLN ** 2 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 383 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 309 ASN 9 515 ASN ** 3 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 32289 Z= 0.285 Angle : 0.644 10.698 43700 Z= 0.328 Chirality : 0.044 0.204 4974 Planarity : 0.004 0.050 5596 Dihedral : 5.992 138.679 4309 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.48 % Favored : 92.49 % Rotamer: Outliers : 0.94 % Allowed : 23.52 % Favored : 75.54 % 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: -1.23 (0.14), residues: 3944 helix: 1.07 (0.14), residues: 1354 sheet: -1.32 (0.17), residues: 969 loop : -2.13 (0.15), residues: 1621 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 384 time to evaluate : 3.897 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 19 residues processed: 403 average time/residue: 0.4579 time to fit residues: 299.3152 Evaluate side-chains 368 residues out of total 3495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 349 time to evaluate : 3.731 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2966 time to fit residues: 15.8295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 347 optimal weight: 3.9990 chunk 365 optimal weight: 5.9990 chunk 333 optimal weight: 1.9990 chunk 355 optimal weight: 5.9990 chunk 214 optimal weight: 7.9990 chunk 154 optimal weight: 10.0000 chunk 279 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 321 optimal weight: 3.9990 chunk 336 optimal weight: 3.9990 chunk 354 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 343 GLN ** 2 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 436 HIS ** 4 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 385 GLN ** 5 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 309 ASN ** 3 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 32289 Z= 0.274 Angle : 0.643 12.943 43700 Z= 0.326 Chirality : 0.044 0.229 4974 Planarity : 0.004 0.050 5596 Dihedral : 5.889 139.733 4309 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.54 % Allowed : 24.58 % Favored : 74.88 % 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: -1.12 (0.14), residues: 3944 helix: 1.19 (0.14), residues: 1351 sheet: -1.25 (0.17), residues: 960 loop : -2.09 (0.15), residues: 1633 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 371 time to evaluate : 3.937 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 384 average time/residue: 0.4585 time to fit residues: 285.4392 Evaluate side-chains 362 residues out of total 3495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 353 time to evaluate : 3.647 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2888 time to fit residues: 9.9496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 233 optimal weight: 0.9980 chunk 376 optimal weight: 4.9990 chunk 229 optimal weight: 9.9990 chunk 178 optimal weight: 20.0000 chunk 261 optimal weight: 0.8980 chunk 394 optimal weight: 9.9990 chunk 363 optimal weight: 7.9990 chunk 314 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 242 optimal weight: 6.9990 chunk 192 optimal weight: 4.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 545 ASN ** 1 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 115 HIS ** 7 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 663 GLN ** 9 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 309 ASN 9 353 HIS ** 3 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 32289 Z= 0.413 Angle : 0.720 12.550 43700 Z= 0.364 Chirality : 0.047 0.231 4974 Planarity : 0.005 0.051 5596 Dihedral : 6.102 138.906 4309 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 0.49 % Allowed : 24.92 % Favored : 74.59 % 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: -1.30 (0.13), residues: 3944 helix: 0.93 (0.14), residues: 1353 sheet: -1.26 (0.17), residues: 960 loop : -2.15 (0.15), residues: 1631 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 353 time to evaluate : 3.829 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 363 average time/residue: 0.4673 time to fit residues: 273.0254 Evaluate side-chains 358 residues out of total 3495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 347 time to evaluate : 4.041 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3593 time to fit residues: 12.4774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 249 optimal weight: 0.8980 chunk 334 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 chunk 289 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 314 optimal weight: 8.9990 chunk 131 optimal weight: 0.9980 chunk 323 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 343 GLN ** 2 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 91 GLN ** 4 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 205 GLN ** 7 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 309 ASN ** 3 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.162240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.139461 restraints weight = 48381.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.139214 restraints weight = 59751.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.140488 restraints weight = 49151.128| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 32289 Z= 0.196 Angle : 0.623 14.058 43700 Z= 0.314 Chirality : 0.043 0.213 4974 Planarity : 0.004 0.092 5596 Dihedral : 5.721 142.450 4309 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.49 % Favored : 93.48 % Rotamer: Outliers : 0.43 % Allowed : 24.84 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.14), residues: 3944 helix: 1.37 (0.14), residues: 1352 sheet: -1.08 (0.17), residues: 944 loop : -1.96 (0.15), residues: 1648 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6859.13 seconds wall clock time: 128 minutes 4.59 seconds (7684.59 seconds total)