Starting phenix.real_space_refine on Sun Feb 18 10:10:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk3_22360/02_2024/7jk3_22360_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk3_22360/02_2024/7jk3_22360.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk3_22360/02_2024/7jk3_22360.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk3_22360/02_2024/7jk3_22360.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk3_22360/02_2024/7jk3_22360_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk3_22360/02_2024/7jk3_22360_updated.pdb" } resolution = 3.4 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 78 5.49 5 Mg 4 5.21 5 S 111 5.16 5 C 13529 2.51 5 N 3818 2.21 5 O 4121 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 326": "OE1" <-> "OE2" Residue "B GLU 371": "OE1" <-> "OE2" Residue "B GLU 420": "OE1" <-> "OE2" Residue "B GLU 580": "OE1" <-> "OE2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C GLU 51": "OE1" <-> "OE2" Residue "C GLU 52": "OE1" <-> "OE2" Residue "C ARG 70": "NH1" <-> "NH2" Residue "C GLU 88": "OE1" <-> "OE2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C ARG 179": "NH1" <-> "NH2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C ARG 344": "NH1" <-> "NH2" Residue "C GLU 412": "OE1" <-> "OE2" Residue "C GLU 446": "OE1" <-> "OE2" Residue "C GLU 458": "OE1" <-> "OE2" Residue "C GLU 476": "OE1" <-> "OE2" Residue "C GLU 485": "OE1" <-> "OE2" Residue "C GLU 496": "OE1" <-> "OE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 699": "OE1" <-> "OE2" Residue "D ARG 27": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D GLU 191": "OE1" <-> "OE2" Residue "D GLU 332": "OE1" <-> "OE2" Residue "D GLU 347": "OE1" <-> "OE2" Residue "D GLU 389": "OE1" <-> "OE2" Residue "D GLU 398": "OE1" <-> "OE2" Residue "D ARG 401": "NH1" <-> "NH2" Residue "D GLU 404": "OE1" <-> "OE2" Residue "D GLU 425": "OE1" <-> "OE2" Residue "E GLU 16": "OE1" <-> "OE2" Residue "E GLU 24": "OE1" <-> "OE2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 144": "NH1" <-> "NH2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "E GLU 223": "OE1" <-> "OE2" Residue "E GLU 246": "OE1" <-> "OE2" Residue "E ARG 293": "NH1" <-> "NH2" Residue "E ARG 345": "NH1" <-> "NH2" Residue "F GLU 223": "OE1" <-> "OE2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A GLU 576": "OE1" <-> "OE2" Residue "A GLU 623": "OE1" <-> "OE2" Residue "A ARG 676": "NH1" <-> "NH2" Residue "A ARG 692": "NH1" <-> "NH2" Residue "A ARG 725": "NH1" <-> "NH2" Residue "A ARG 785": "NH1" <-> "NH2" Residue "A GLU 795": "OE1" <-> "OE2" Residue "A ARG 827": "NH1" <-> "NH2" Residue "A ARG 880": "NH1" <-> "NH2" Residue "G GLU 271": "OE1" <-> "OE2" Residue "G GLU 286": "OE1" <-> "OE2" Residue "G ARG 322": "NH1" <-> "NH2" Residue "G GLU 343": "OE1" <-> "OE2" Residue "G GLU 353": "OE1" <-> "OE2" Residue "G GLU 377": "OE1" <-> "OE2" Residue "G ARG 385": "NH1" <-> "NH2" Residue "G GLU 427": "OE1" <-> "OE2" Residue "G GLU 445": "OE1" <-> "OE2" Residue "G GLU 455": "OE1" <-> "OE2" Residue "G ARG 480": "NH1" <-> "NH2" Residue "G ARG 498": "NH1" <-> "NH2" Residue "G GLU 625": "OE1" <-> "OE2" Residue "G GLU 637": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21661 Number of models: 1 Model: "" Number of chains: 13 Chain: "B" Number of atoms: 2290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2290 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 4 Chain: "C" Number of atoms: 4934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4934 Classifications: {'peptide': 614} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 590} Chain breaks: 6 Chain: "D" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3549 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 11, 'TRANS': 429} Chain breaks: 2 Chain: "E" Number of atoms: 3161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3161 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 386} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 143 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "A" Number of atoms: 3129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3129 Classifications: {'peptide': 401} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 383} Chain: "G" Number of atoms: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2974 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 13, 'TRANS': 358} Chain breaks: 2 Chain: "H" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 684 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "I" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 669 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.92, per 1000 atoms: 0.55 Number of scatterers: 21661 At special positions: 0 Unit cell: (128.14, 162.54, 120.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 111 16.00 P 78 15.00 Mg 4 11.99 O 4121 8.00 N 3818 7.00 C 13529 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: 9.01 Conformation dependent library (CDL) restraints added in 3.8 seconds 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4840 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 129 helices and 11 sheets defined 53.9% alpha, 6.4% beta 32 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 9.88 Creating SS restraints... Processing helix chain 'B' and resid 281 through 284 No H-bonds generated for 'chain 'B' and resid 281 through 284' Processing helix chain 'B' and resid 324 through 349 removed outlier: 4.375A pdb=" N TYR B 339 " --> pdb=" O GLU B 335 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N PHE B 340 " --> pdb=" O TYR B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.693A pdb=" N GLU B 349 " --> pdb=" O CYS B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 371 Processing helix chain 'B' and resid 390 through 399 Processing helix chain 'B' and resid 411 through 422 Processing helix chain 'B' and resid 445 through 454 Processing helix chain 'B' and resid 471 through 474 removed outlier: 3.509A pdb=" N LEU B 474 " --> pdb=" O THR B 471 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 471 through 474' Processing helix chain 'B' and resid 477 through 482 Processing helix chain 'B' and resid 517 through 523 Processing helix chain 'B' and resid 528 through 543 Processing helix chain 'B' and resid 555 through 564 Processing helix chain 'B' and resid 571 through 583 Processing helix chain 'B' and resid 605 through 615 removed outlier: 3.705A pdb=" N GLN B 615 " --> pdb=" O PHE B 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 45 No H-bonds generated for 'chain 'C' and resid 42 through 45' Processing helix chain 'C' and resid 48 through 87 removed outlier: 5.111A pdb=" N ARG C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N THR C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 121 removed outlier: 5.721A pdb=" N SER C 112 " --> pdb=" O PRO C 108 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLN C 113 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE C 114 " --> pdb=" O HIS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 136 No H-bonds generated for 'chain 'C' and resid 134 through 136' Processing helix chain 'C' and resid 140 through 158 Processing helix chain 'C' and resid 180 through 182 No H-bonds generated for 'chain 'C' and resid 180 through 182' Processing helix chain 'C' and resid 185 through 195 Processing helix chain 'C' and resid 217 through 229 Processing helix chain 'C' and resid 246 through 252 Processing helix chain 'C' and resid 255 through 260 removed outlier: 4.414A pdb=" N LYS C 260 " --> pdb=" O HIS C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 281 Processing helix chain 'C' and resid 294 through 306 Processing helix chain 'C' and resid 311 through 328 removed outlier: 4.196A pdb=" N GLY C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 334 removed outlier: 3.537A pdb=" N LEU C 334 " --> pdb=" O ALA C 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 331 through 334' Processing helix chain 'C' and resid 338 through 345 Processing helix chain 'C' and resid 350 through 356 removed outlier: 3.814A pdb=" N GLU C 354 " --> pdb=" O HIS C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 366 No H-bonds generated for 'chain 'C' and resid 363 through 366' Processing helix chain 'C' and resid 373 through 380 removed outlier: 3.618A pdb=" N THR C 380 " --> pdb=" O ILE C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 415 Proline residue: C 390 - end of helix Processing helix chain 'C' and resid 426 through 435 Processing helix chain 'C' and resid 438 through 440 No H-bonds generated for 'chain 'C' and resid 438 through 440' Processing helix chain 'C' and resid 442 through 452 Processing helix chain 'C' and resid 456 through 476 Processing helix chain 'C' and resid 485 through 507 Proline residue: C 493 - end of helix Processing helix chain 'C' and resid 564 through 575 Processing helix chain 'C' and resid 577 through 580 No H-bonds generated for 'chain 'C' and resid 577 through 580' Processing helix chain 'C' and resid 591 through 593 No H-bonds generated for 'chain 'C' and resid 591 through 593' Processing helix chain 'C' and resid 600 through 606 Processing helix chain 'C' and resid 610 through 619 Processing helix chain 'C' and resid 621 through 625 removed outlier: 4.327A pdb=" N MET C 625 " --> pdb=" O HIS C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 652 removed outlier: 3.638A pdb=" N VAL C 648 " --> pdb=" O ASP C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 671 Processing helix chain 'C' and resid 689 through 702 Processing helix chain 'D' and resid 4 through 19 removed outlier: 3.820A pdb=" N LEU D 8 " --> pdb=" O ALA D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 44 Processing helix chain 'D' and resid 63 through 76 Proline residue: D 75 - end of helix Processing helix chain 'D' and resid 96 through 106 Processing helix chain 'D' and resid 121 through 133 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 159 through 164 Processing helix chain 'D' and resid 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 212 through 221 Processing helix chain 'D' and resid 228 through 243 Processing helix chain 'D' and resid 258 through 260 No H-bonds generated for 'chain 'D' and resid 258 through 260' Processing helix chain 'D' and resid 265 through 279 Processing helix chain 'D' and resid 283 through 294 Processing helix chain 'D' and resid 298 through 311 removed outlier: 4.135A pdb=" N HIS D 311 " --> pdb=" O ARG D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 332 Processing helix chain 'D' and resid 336 through 342 removed outlier: 4.069A pdb=" N GLY D 342 " --> pdb=" O GLU D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 361 Processing helix chain 'D' and resid 368 through 379 removed outlier: 3.850A pdb=" N PHE D 378 " --> pdb=" O ARG D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 402 Processing helix chain 'D' and resid 433 through 442 removed outlier: 3.621A pdb=" N GLN D 441 " --> pdb=" O HIS D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 455 removed outlier: 3.551A pdb=" N GLN D 455 " --> pdb=" O ALA D 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 8 Processing helix chain 'E' and resid 16 through 25 Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 77 through 88 Processing helix chain 'E' and resid 101 through 111 removed outlier: 4.027A pdb=" N GLN E 111 " --> pdb=" O GLN E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 130 No H-bonds generated for 'chain 'E' and resid 128 through 130' Processing helix chain 'E' and resid 139 through 143 Processing helix chain 'E' and resid 145 through 149 Processing helix chain 'E' and resid 163 through 165 No H-bonds generated for 'chain 'E' and resid 163 through 165' Processing helix chain 'E' and resid 185 through 204 removed outlier: 4.390A pdb=" N ASP E 195 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N PHE E 196 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLN E 197 " --> pdb=" O GLY E 193 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N GLN E 198 " --> pdb=" O SER E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 217 Processing helix chain 'E' and resid 223 through 237 removed outlier: 4.015A pdb=" N VAL E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 258 removed outlier: 4.033A pdb=" N LYS E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 263 No H-bonds generated for 'chain 'E' and resid 260 through 263' Processing helix chain 'E' and resid 276 through 287 Proline residue: E 282 - end of helix Processing helix chain 'E' and resid 323 through 336 Processing helix chain 'E' and resid 343 through 346 No H-bonds generated for 'chain 'E' and resid 343 through 346' Processing helix chain 'E' and resid 382 through 393 Processing helix chain 'E' and resid 401 through 411 Processing helix chain 'E' and resid 439 through 448 Processing helix chain 'F' and resid 225 through 237 Processing helix chain 'A' and resid 520 through 528 Processing helix chain 'A' and resid 551 through 558 Processing helix chain 'A' and resid 572 through 588 Processing helix chain 'A' and resid 605 through 620 Processing helix chain 'A' and resid 634 through 636 No H-bonds generated for 'chain 'A' and resid 634 through 636' Processing helix chain 'A' and resid 640 through 650 removed outlier: 4.122A pdb=" N ILE A 647 " --> pdb=" O TYR A 644 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR A 648 " --> pdb=" O VAL A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 669 Processing helix chain 'A' and resid 686 through 688 No H-bonds generated for 'chain 'A' and resid 686 through 688' Processing helix chain 'A' and resid 696 through 705 Proline residue: A 704 - end of helix Processing helix chain 'A' and resid 722 through 725 No H-bonds generated for 'chain 'A' and resid 722 through 725' Processing helix chain 'A' and resid 729 through 734 Processing helix chain 'A' and resid 747 through 758 removed outlier: 3.677A pdb=" N GLN A 751 " --> pdb=" O HIS A 747 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 776 Processing helix chain 'A' and resid 783 through 799 removed outlier: 3.807A pdb=" N ARG A 791 " --> pdb=" O LEU A 787 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR A 799 " --> pdb=" O GLU A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 817 Processing helix chain 'A' and resid 824 through 827 No H-bonds generated for 'chain 'A' and resid 824 through 827' Processing helix chain 'A' and resid 831 through 847 Processing helix chain 'A' and resid 854 through 868 Processing helix chain 'A' and resid 875 through 887 removed outlier: 4.242A pdb=" N ARG A 880 " --> pdb=" O GLY A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 917 removed outlier: 3.883A pdb=" N HIS A 914 " --> pdb=" O ALA A 910 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 259 Processing helix chain 'G' and resid 273 through 286 Processing helix chain 'G' and resid 303 through 312 removed outlier: 3.992A pdb=" N LEU G 311 " --> pdb=" O LEU G 307 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG G 312 " --> pdb=" O SER G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 319 Processing helix chain 'G' and resid 333 through 344 removed outlier: 3.892A pdb=" N VAL G 336 " --> pdb=" O VAL G 333 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N TYR G 337 " --> pdb=" O GLY G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 365 removed outlier: 3.759A pdb=" N LYS G 365 " --> pdb=" O GLN G 361 " (cutoff:3.500A) Processing helix chain 'G' and resid 378 through 380 No H-bonds generated for 'chain 'G' and resid 378 through 380' Processing helix chain 'G' and resid 387 through 397 removed outlier: 3.846A pdb=" N TRP G 395 " --> pdb=" O THR G 391 " (cutoff:3.500A) Proline residue: G 396 - end of helix Processing helix chain 'G' and resid 414 through 417 No H-bonds generated for 'chain 'G' and resid 414 through 417' Processing helix chain 'G' and resid 421 through 424 Processing helix chain 'G' and resid 440 through 452 Processing helix chain 'G' and resid 462 through 475 removed outlier: 3.913A pdb=" N ALA G 474 " --> pdb=" O ALA G 470 " (cutoff:3.500A) Processing helix chain 'G' and resid 479 through 497 removed outlier: 3.956A pdb=" N VAL G 490 " --> pdb=" O GLY G 486 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN G 495 " --> pdb=" O GLU G 491 " (cutoff:3.500A) Processing helix chain 'G' and resid 531 through 541 Processing helix chain 'G' and resid 558 through 572 Processing helix chain 'G' and resid 581 through 594 removed outlier: 3.579A pdb=" N ARG G 590 " --> pdb=" O GLU G 586 " (cutoff:3.500A) Processing helix chain 'G' and resid 602 through 615 removed outlier: 4.014A pdb=" N GLY G 607 " --> pdb=" O ALA G 603 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR G 614 " --> pdb=" O ASP G 610 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG G 615 " --> pdb=" O LEU G 611 " (cutoff:3.500A) Processing helix chain 'G' and resid 637 through 644 Processing helix chain 'G' and resid 647 through 655 removed outlier: 3.709A pdb=" N SER G 652 " --> pdb=" O GLN G 648 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU G 654 " --> pdb=" O ILE G 650 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER G 655 " --> pdb=" O ALA G 651 " (cutoff:3.500A) Processing helix chain 'G' and resid 657 through 659 No H-bonds generated for 'chain 'G' and resid 657 through 659' Processing sheet with id= A, first strand: chain 'B' and resid 353 through 355 removed outlier: 6.559A pdb=" N LEU B 430 " --> pdb=" O HIS B 461 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N LEU B 463 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU B 432 " --> pdb=" O LEU B 463 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N SER B 465 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL B 434 " --> pdb=" O SER B 465 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR B 377 " --> pdb=" O PHE B 431 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ILE B 433 " --> pdb=" O THR B 377 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU B 379 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N HIS B 435 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL B 381 " --> pdb=" O HIS B 435 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 588 through 590 Processing sheet with id= C, first strand: chain 'C' and resid 264 through 267 removed outlier: 5.807A pdb=" N LEU C 205 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL C 239 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL C 207 " --> pdb=" O VAL C 239 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 658 through 660 Processing sheet with id= E, first strand: chain 'D' and resid 50 through 55 Processing sheet with id= F, first strand: chain 'D' and resid 406 through 408 Processing sheet with id= G, first strand: chain 'E' and resid 176 through 179 removed outlier: 8.153A pdb=" N ILE E 37 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL E 155 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEU E 39 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LEU E 157 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N PHE E 121 " --> pdb=" O CYS E 154 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ILE E 156 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE E 123 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU E 158 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL E 125 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP E 126 " --> pdb=" O LEU E 69 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 739 through 742 removed outlier: 8.819A pdb=" N LEU A 740 " --> pdb=" O CYS A 593 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR A 595 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N PHE A 742 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N SER A 597 " --> pdb=" O PHE A 742 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR A 679 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL A 714 " --> pdb=" O THR A 679 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU A 681 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE A 716 " --> pdb=" O LEU A 681 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL A 683 " --> pdb=" O ILE A 716 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 891 through 893 Processing sheet with id= J, first strand: chain 'G' and resid 431 through 435 removed outlier: 3.683A pdb=" N ARG G 431 " --> pdb=" O SER G 292 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU G 405 " --> pdb=" O GLY G 291 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 618 through 621 882 hydrogen bonds defined for protein. 2574 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 84 hydrogen bonds 164 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 8.42 Time building geometry restraints manager: 9.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5825 1.34 - 1.46: 4252 1.46 - 1.58: 11782 1.58 - 1.70: 150 1.70 - 1.82: 163 Bond restraints: 22172 Sorted by residual: bond pdb=" C4 ATP A1001 " pdb=" C5 ATP A1001 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.52e+01 bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.51e+01 bond pdb=" C4 ATP G 901 " pdb=" C5 ATP G 901 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.37e+01 bond pdb=" C4 ATP E 901 " pdb=" C5 ATP E 901 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.25e+01 bond pdb=" C5 ATP G 901 " pdb=" C6 ATP G 901 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.67e+01 ... (remaining 22167 not shown) Histogram of bond angle deviations from ideal: 97.46 - 105.20: 614 105.20 - 112.93: 12047 112.93 - 120.66: 10413 120.66 - 128.40: 6991 128.40 - 136.13: 193 Bond angle restraints: 30258 Sorted by residual: angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 120.08 19.79 1.00e+00 1.00e+00 3.92e+02 angle pdb=" PB ATP E 901 " pdb=" O3B ATP E 901 " pdb=" PG ATP E 901 " ideal model delta sigma weight residual 139.87 120.96 18.91 1.00e+00 1.00e+00 3.57e+02 angle pdb=" PB ATP A1001 " pdb=" O3B ATP A1001 " pdb=" PG ATP A1001 " ideal model delta sigma weight residual 139.87 120.99 18.88 1.00e+00 1.00e+00 3.56e+02 angle pdb=" PB ATP G 901 " pdb=" O3B ATP G 901 " pdb=" PG ATP G 901 " ideal model delta sigma weight residual 139.87 122.02 17.85 1.00e+00 1.00e+00 3.19e+02 angle pdb=" PA ATP E 901 " pdb=" O3A ATP E 901 " pdb=" PB ATP E 901 " ideal model delta sigma weight residual 136.83 119.72 17.11 1.00e+00 1.00e+00 2.93e+02 ... (remaining 30253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 11510 17.95 - 35.91: 1282 35.91 - 53.86: 458 53.86 - 71.82: 113 71.82 - 89.77: 27 Dihedral angle restraints: 13390 sinusoidal: 5977 harmonic: 7413 Sorted by residual: dihedral pdb=" CA LEU G 259 " pdb=" C LEU G 259 " pdb=" N ASN G 260 " pdb=" CA ASN G 260 " ideal model delta harmonic sigma weight residual 180.00 153.30 26.70 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA MET E 134 " pdb=" C MET E 134 " pdb=" N ASP E 135 " pdb=" CA ASP E 135 " ideal model delta harmonic sigma weight residual -180.00 -158.08 -21.92 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ASP E 135 " pdb=" C ASP E 135 " pdb=" N ALA E 136 " pdb=" CA ALA E 136 " ideal model delta harmonic sigma weight residual 180.00 158.56 21.44 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 13387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2487 0.044 - 0.089: 774 0.089 - 0.133: 188 0.133 - 0.178: 36 0.178 - 0.222: 7 Chirality restraints: 3492 Sorted by residual: chirality pdb=" CA ASP C 714 " pdb=" N ASP C 714 " pdb=" C ASP C 714 " pdb=" CB ASP C 714 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB THR A 679 " pdb=" CA THR A 679 " pdb=" OG1 THR A 679 " pdb=" CG2 THR A 679 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA GLU E 260 " pdb=" N GLU E 260 " pdb=" C GLU E 260 " pdb=" CB GLU E 260 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 3489 not shown) Planarity restraints: 3603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 712 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.40e+00 pdb=" C LYS C 712 " 0.053 2.00e-02 2.50e+03 pdb=" O LYS C 712 " -0.020 2.00e-02 2.50e+03 pdb=" N THR C 713 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP G 395 " 0.050 5.00e-02 4.00e+02 7.56e-02 9.15e+00 pdb=" N PRO G 396 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO G 396 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 396 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 74 " 0.049 5.00e-02 4.00e+02 7.35e-02 8.64e+00 pdb=" N PRO D 75 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " 0.042 5.00e-02 4.00e+02 ... (remaining 3600 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 23 2.35 - 2.99: 9295 2.99 - 3.62: 31680 3.62 - 4.26: 48852 4.26 - 4.90: 81990 Nonbonded interactions: 171840 Sorted by model distance: nonbonded pdb=" NH1 ARG C 711 " pdb=" O3' DA I 43 " model vdw 1.709 2.520 nonbonded pdb=" OG1 THR G 304 " pdb="MG MG G 902 " model vdw 2.106 2.170 nonbonded pdb=" OG1 THR D 63 " pdb="MG MG D 902 " model vdw 2.117 2.170 nonbonded pdb=" O2B ATP A1001 " pdb="MG MG A1002 " model vdw 2.122 2.170 nonbonded pdb=" OG1 THR E 48 " pdb="MG MG E 902 " model vdw 2.128 2.170 ... (remaining 171835 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 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: 0.020 Extract box with map and model: 6.980 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 65.760 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.080 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 22172 Z= 0.282 Angle : 0.866 19.789 30258 Z= 0.553 Chirality : 0.046 0.222 3492 Planarity : 0.007 0.076 3603 Dihedral : 17.808 89.771 8550 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.18 % Allowed : 5.82 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -3.87 (0.13), residues: 2478 helix: -2.55 (0.09), residues: 1448 sheet: -1.77 (0.30), residues: 228 loop : -2.42 (0.17), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 57 HIS 0.011 0.001 HIS G 629 PHE 0.019 0.002 PHE D 256 TYR 0.015 0.001 TYR E 258 ARG 0.007 0.000 ARG A 675 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 208 time to evaluate : 2.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 562 CYS cc_start: 0.9246 (m) cc_final: 0.8941 (p) REVERT: C 52 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8212 (mm-30) REVERT: C 353 MET cc_start: 0.9122 (mmt) cc_final: 0.8864 (mmm) REVERT: C 383 ASP cc_start: 0.9088 (m-30) cc_final: 0.8859 (p0) REVERT: C 454 LEU cc_start: 0.7557 (tp) cc_final: 0.6884 (tt) REVERT: C 699 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7537 (mt-10) REVERT: D 426 MET cc_start: 0.8449 (mmm) cc_final: 0.8221 (mmp) REVERT: F 224 ASP cc_start: 0.9297 (t0) cc_final: 0.8988 (t70) REVERT: F 226 GLU cc_start: 0.9523 (mm-30) cc_final: 0.9253 (mp0) REVERT: A 622 ASN cc_start: 0.9018 (t0) cc_final: 0.8797 (t0) REVERT: A 631 GLU cc_start: 0.8033 (pp20) cc_final: 0.7828 (pm20) REVERT: A 788 ASP cc_start: 0.8471 (m-30) cc_final: 0.8229 (m-30) REVERT: A 817 MET cc_start: 0.8916 (mmm) cc_final: 0.8200 (mmm) REVERT: G 491 GLU cc_start: 0.8308 (tt0) cc_final: 0.7859 (pt0) REVERT: G 563 MET cc_start: 0.8404 (tmm) cc_final: 0.7867 (tmm) REVERT: G 592 CYS cc_start: 0.9046 (m) cc_final: 0.8460 (m) outliers start: 4 outliers final: 0 residues processed: 212 average time/residue: 0.3881 time to fit residues: 124.5157 Evaluate side-chains 134 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 2.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 8.9990 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 232 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 325 HIS B 330 ASN B 374 HIS B 498 ASN B 577 GLN C 133 GLN C 368 GLN C 432 ASN C 578 GLN C 652 HIS D 50 ASN D 82 ASN D 138 HIS D 455 GLN E 414 ASN E 433 GLN A 621 GLN A 718 ASN A 747 HIS A 749 GLN A 838 GLN A 902 GLN G 265 GLN G 284 HIS ** G 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 634 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22172 Z= 0.142 Angle : 0.507 11.344 30258 Z= 0.265 Chirality : 0.037 0.166 3492 Planarity : 0.004 0.050 3603 Dihedral : 17.309 88.344 3578 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.68 % Allowed : 9.92 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -1.69 (0.15), residues: 2478 helix: -0.59 (0.13), residues: 1451 sheet: -1.41 (0.31), residues: 222 loop : -1.77 (0.19), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 276 HIS 0.004 0.000 HIS C 715 PHE 0.010 0.001 PHE E 104 TYR 0.015 0.001 TYR A 629 ARG 0.009 0.000 ARG C 604 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 147 time to evaluate : 2.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 ASN cc_start: 0.9353 (m-40) cc_final: 0.8987 (m110) REVERT: B 562 CYS cc_start: 0.9219 (m) cc_final: 0.8892 (m) REVERT: C 324 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8212 (tm-30) REVERT: C 383 ASP cc_start: 0.9129 (m-30) cc_final: 0.8807 (p0) REVERT: C 435 ASN cc_start: 0.9350 (t0) cc_final: 0.9099 (p0) REVERT: C 699 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7468 (mt-10) REVERT: D 440 MET cc_start: 0.8594 (mmp) cc_final: 0.8269 (mmm) REVERT: E 249 LEU cc_start: 0.9292 (mt) cc_final: 0.8916 (tt) REVERT: F 231 ARG cc_start: 0.9527 (mtp-110) cc_final: 0.9294 (ttp-110) REVERT: A 622 ASN cc_start: 0.9070 (t0) cc_final: 0.8700 (t0) REVERT: A 631 GLU cc_start: 0.8059 (pp20) cc_final: 0.7818 (pm20) REVERT: A 788 ASP cc_start: 0.8551 (m-30) cc_final: 0.8309 (m-30) REVERT: A 817 MET cc_start: 0.8932 (mmm) cc_final: 0.8198 (mmm) REVERT: G 370 MET cc_start: 0.8628 (tpp) cc_final: 0.8233 (tpp) REVERT: G 491 GLU cc_start: 0.8336 (tt0) cc_final: 0.7861 (pt0) REVERT: G 592 CYS cc_start: 0.8968 (m) cc_final: 0.8470 (m) outliers start: 15 outliers final: 10 residues processed: 156 average time/residue: 0.3380 time to fit residues: 83.9841 Evaluate side-chains 137 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 127 time to evaluate : 2.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain G residue 382 CYS Chi-restraints excluded: chain G residue 426 CYS Chi-restraints excluded: chain G residue 456 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 0.0470 chunk 72 optimal weight: 8.9990 chunk 193 optimal weight: 8.9990 chunk 158 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 232 optimal weight: 4.9990 chunk 251 optimal weight: 10.0000 chunk 207 optimal weight: 0.9990 chunk 230 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 652 HIS D 82 ASN D 311 HIS E 150 ASN A 809 HIS ** G 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22172 Z= 0.207 Angle : 0.508 8.305 30258 Z= 0.262 Chirality : 0.037 0.152 3492 Planarity : 0.004 0.081 3603 Dihedral : 17.252 88.976 3578 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.17 % Allowed : 11.18 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -0.52 (0.17), residues: 2478 helix: 0.40 (0.14), residues: 1451 sheet: -1.17 (0.31), residues: 223 loop : -1.32 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 276 HIS 0.003 0.001 HIS G 629 PHE 0.008 0.001 PHE D 121 TYR 0.012 0.001 TYR C 255 ARG 0.019 0.000 ARG G 322 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 2.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 ASN cc_start: 0.9362 (m-40) cc_final: 0.8988 (m110) REVERT: B 344 MET cc_start: 0.8931 (mmm) cc_final: 0.8704 (mmm) REVERT: B 562 CYS cc_start: 0.9214 (m) cc_final: 0.8821 (p) REVERT: C 324 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8276 (tm-30) REVERT: C 383 ASP cc_start: 0.9109 (m-30) cc_final: 0.8794 (p0) REVERT: C 435 ASN cc_start: 0.9377 (t0) cc_final: 0.9079 (p0) REVERT: C 699 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7515 (mt-10) REVERT: D 131 CYS cc_start: 0.9166 (t) cc_final: 0.8850 (t) REVERT: E 1 MET cc_start: 0.7570 (ppp) cc_final: 0.7357 (tmm) REVERT: E 249 LEU cc_start: 0.9270 (mt) cc_final: 0.8914 (tt) REVERT: E 276 TRP cc_start: 0.8277 (t-100) cc_final: 0.7864 (t-100) REVERT: A 622 ASN cc_start: 0.9100 (t0) cc_final: 0.8753 (t0) REVERT: A 635 MET cc_start: 0.8766 (tpp) cc_final: 0.8455 (mmm) REVERT: A 817 MET cc_start: 0.8967 (mmm) cc_final: 0.7865 (mmm) REVERT: G 491 GLU cc_start: 0.8342 (tt0) cc_final: 0.7841 (pt0) REVERT: G 592 CYS cc_start: 0.8903 (m) cc_final: 0.8469 (m) outliers start: 26 outliers final: 17 residues processed: 152 average time/residue: 0.3215 time to fit residues: 79.2000 Evaluate side-chains 138 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 2.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain G residue 382 CYS Chi-restraints excluded: chain G residue 426 CYS Chi-restraints excluded: chain G residue 456 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 111 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 233 optimal weight: 10.0000 chunk 247 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 221 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 HIS D 82 ASN ** G 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22172 Z= 0.287 Angle : 0.546 9.465 30258 Z= 0.278 Chirality : 0.038 0.208 3492 Planarity : 0.003 0.064 3603 Dihedral : 17.240 88.345 3578 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.67 % Allowed : 11.90 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.17), residues: 2478 helix: 1.00 (0.14), residues: 1453 sheet: -0.87 (0.31), residues: 227 loop : -0.98 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 57 HIS 0.006 0.001 HIS C 230 PHE 0.011 0.001 PHE E 237 TYR 0.017 0.001 TYR B 540 ARG 0.007 0.000 ARG G 322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 120 time to evaluate : 2.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 ASN cc_start: 0.9371 (m-40) cc_final: 0.8982 (m110) REVERT: B 344 MET cc_start: 0.8970 (mmm) cc_final: 0.8765 (mmm) REVERT: B 540 TYR cc_start: 0.8169 (t80) cc_final: 0.7942 (t80) REVERT: B 562 CYS cc_start: 0.9208 (m) cc_final: 0.8850 (m) REVERT: C 324 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8385 (tm-30) REVERT: C 435 ASN cc_start: 0.9410 (t0) cc_final: 0.9035 (p0) REVERT: C 699 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7575 (mt-10) REVERT: D 131 CYS cc_start: 0.9148 (t) cc_final: 0.8922 (t) REVERT: D 426 MET cc_start: 0.8794 (mmm) cc_final: 0.8555 (mmt) REVERT: E 1 MET cc_start: 0.7679 (ppp) cc_final: 0.7409 (tmm) REVERT: E 249 LEU cc_start: 0.9310 (mt) cc_final: 0.8968 (tt) REVERT: E 276 TRP cc_start: 0.8333 (t-100) cc_final: 0.7967 (t-100) REVERT: A 622 ASN cc_start: 0.9112 (t0) cc_final: 0.8820 (t0) REVERT: A 635 MET cc_start: 0.8927 (tpp) cc_final: 0.8642 (mmm) REVERT: G 491 GLU cc_start: 0.8423 (tt0) cc_final: 0.7948 (pt0) REVERT: G 592 CYS cc_start: 0.8867 (m) cc_final: 0.8561 (m) outliers start: 37 outliers final: 24 residues processed: 148 average time/residue: 0.3250 time to fit residues: 77.9366 Evaluate side-chains 138 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 114 time to evaluate : 2.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 382 CYS Chi-restraints excluded: chain G residue 426 CYS Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain G residue 571 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 184 optimal weight: 10.0000 chunk 102 optimal weight: 0.0980 chunk 211 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 126 optimal weight: 9.9990 chunk 222 optimal weight: 0.0040 chunk 62 optimal weight: 5.9990 overall best weight: 1.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 ASN ** G 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22172 Z= 0.165 Angle : 0.489 11.494 30258 Z= 0.249 Chirality : 0.037 0.219 3492 Planarity : 0.003 0.053 3603 Dihedral : 17.145 88.786 3578 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.40 % Allowed : 12.40 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: 0.62 (0.17), residues: 2478 helix: 1.31 (0.14), residues: 1450 sheet: -0.78 (0.32), residues: 222 loop : -0.80 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 57 HIS 0.017 0.001 HIS C 652 PHE 0.010 0.001 PHE E 237 TYR 0.015 0.001 TYR A 915 ARG 0.005 0.000 ARG F 231 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 124 time to evaluate : 2.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 ASN cc_start: 0.9355 (m-40) cc_final: 0.8968 (m-40) REVERT: B 432 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8877 (pp) REVERT: B 540 TYR cc_start: 0.8073 (t80) cc_final: 0.7868 (t80) REVERT: B 562 CYS cc_start: 0.9200 (m) cc_final: 0.8835 (m) REVERT: C 185 MET cc_start: 0.7990 (mmm) cc_final: 0.7773 (mmm) REVERT: C 324 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8357 (tm-30) REVERT: C 383 ASP cc_start: 0.9069 (m-30) cc_final: 0.8774 (p0) REVERT: C 435 ASN cc_start: 0.9417 (t0) cc_final: 0.9147 (m-40) REVERT: C 699 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7546 (mt-10) REVERT: C 721 TRP cc_start: 0.8497 (p-90) cc_final: 0.8200 (p-90) REVERT: D 426 MET cc_start: 0.8762 (mmm) cc_final: 0.8549 (mmt) REVERT: E 249 LEU cc_start: 0.9302 (mt) cc_final: 0.8958 (tt) REVERT: E 254 CYS cc_start: 0.7974 (m) cc_final: 0.7594 (t) REVERT: E 276 TRP cc_start: 0.8306 (t-100) cc_final: 0.8026 (t-100) REVERT: A 622 ASN cc_start: 0.9102 (t0) cc_final: 0.8818 (t0) REVERT: A 628 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7661 (tm-30) REVERT: A 635 MET cc_start: 0.8906 (tpp) cc_final: 0.8657 (mmm) REVERT: G 491 GLU cc_start: 0.8446 (tt0) cc_final: 0.7932 (pt0) REVERT: G 592 CYS cc_start: 0.8860 (m) cc_final: 0.8550 (m) outliers start: 31 outliers final: 20 residues processed: 148 average time/residue: 0.3184 time to fit residues: 77.1666 Evaluate side-chains 137 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 2.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain G residue 382 CYS Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 571 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 8.9990 chunk 222 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 247 optimal weight: 10.0000 chunk 205 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 ASN ** G 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22172 Z= 0.160 Angle : 0.486 10.285 30258 Z= 0.248 Chirality : 0.037 0.251 3492 Planarity : 0.003 0.048 3603 Dihedral : 16.980 87.887 3578 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.40 % Allowed : 13.39 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: 0.92 (0.18), residues: 2478 helix: 1.54 (0.14), residues: 1453 sheet: -0.63 (0.33), residues: 222 loop : -0.67 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 57 HIS 0.003 0.001 HIS C 230 PHE 0.010 0.001 PHE E 237 TYR 0.014 0.001 TYR A 915 ARG 0.007 0.000 ARG E 284 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 123 time to evaluate : 2.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 ASN cc_start: 0.9343 (m-40) cc_final: 0.8961 (m-40) REVERT: B 432 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8851 (pp) REVERT: B 562 CYS cc_start: 0.9184 (m) cc_final: 0.8825 (m) REVERT: C 324 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8343 (tm-30) REVERT: C 383 ASP cc_start: 0.9070 (m-30) cc_final: 0.8802 (p0) REVERT: C 435 ASN cc_start: 0.9416 (t0) cc_final: 0.9143 (m-40) REVERT: C 699 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7534 (mt-10) REVERT: C 721 TRP cc_start: 0.8536 (p-90) cc_final: 0.8269 (p-90) REVERT: E 249 LEU cc_start: 0.9290 (mt) cc_final: 0.8981 (tt) REVERT: E 254 CYS cc_start: 0.7918 (m) cc_final: 0.7613 (t) REVERT: A 622 ASN cc_start: 0.9092 (t0) cc_final: 0.8818 (t0) REVERT: A 635 MET cc_start: 0.8949 (tpp) cc_final: 0.8687 (mmm) REVERT: G 491 GLU cc_start: 0.8369 (tt0) cc_final: 0.7870 (pt0) REVERT: G 592 CYS cc_start: 0.8838 (m) cc_final: 0.8568 (m) outliers start: 31 outliers final: 25 residues processed: 147 average time/residue: 0.3106 time to fit residues: 74.8762 Evaluate side-chains 143 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 117 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 276 CYS Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 412 HIS Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain G residue 382 CYS Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 464 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 chunk 140 optimal weight: 0.9990 chunk 208 optimal weight: 20.0000 chunk 138 optimal weight: 1.9990 chunk 246 optimal weight: 7.9990 chunk 154 optimal weight: 9.9990 chunk 150 optimal weight: 0.0980 chunk 113 optimal weight: 1.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22172 Z= 0.145 Angle : 0.481 9.659 30258 Z= 0.244 Chirality : 0.037 0.227 3492 Planarity : 0.003 0.042 3603 Dihedral : 16.831 84.405 3578 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.35 % Allowed : 13.66 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 (0.18), residues: 2478 helix: 1.72 (0.14), residues: 1456 sheet: -0.53 (0.33), residues: 222 loop : -0.54 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 276 HIS 0.003 0.000 HIS G 629 PHE 0.010 0.001 PHE E 237 TYR 0.013 0.001 TYR B 540 ARG 0.006 0.000 ARG F 231 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 124 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 ASN cc_start: 0.9326 (m-40) cc_final: 0.8957 (m-40) REVERT: B 432 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8836 (pp) REVERT: B 553 MET cc_start: 0.8379 (ttt) cc_final: 0.8009 (ttt) REVERT: B 562 CYS cc_start: 0.9211 (m) cc_final: 0.8824 (m) REVERT: C 128 MET cc_start: 0.7313 (mtp) cc_final: 0.6904 (mtp) REVERT: C 324 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8305 (tm-30) REVERT: C 383 ASP cc_start: 0.9050 (m-30) cc_final: 0.8800 (p0) REVERT: C 435 ASN cc_start: 0.9428 (t0) cc_final: 0.9148 (m-40) REVERT: C 699 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7520 (mt-10) REVERT: C 721 TRP cc_start: 0.8557 (p-90) cc_final: 0.8261 (p-90) REVERT: E 249 LEU cc_start: 0.9236 (mt) cc_final: 0.8959 (tt) REVERT: E 254 CYS cc_start: 0.7882 (m) cc_final: 0.7622 (t) REVERT: A 622 ASN cc_start: 0.9099 (t0) cc_final: 0.8831 (t0) REVERT: A 635 MET cc_start: 0.8942 (tpp) cc_final: 0.8684 (mmm) REVERT: G 491 GLU cc_start: 0.8373 (tt0) cc_final: 0.7842 (pt0) REVERT: G 592 CYS cc_start: 0.8837 (m) cc_final: 0.8565 (m) outliers start: 30 outliers final: 23 residues processed: 149 average time/residue: 0.3168 time to fit residues: 77.1733 Evaluate side-chains 140 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 116 time to evaluate : 2.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 276 CYS Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 412 HIS Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 464 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 0.0370 chunk 98 optimal weight: 9.9990 chunk 147 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 156 optimal weight: 0.7980 chunk 168 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 193 optimal weight: 6.9990 overall best weight: 1.0860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 652 HIS ** G 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 22172 Z= 0.140 Angle : 0.485 8.484 30258 Z= 0.245 Chirality : 0.036 0.216 3492 Planarity : 0.003 0.044 3603 Dihedral : 16.734 84.091 3578 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.31 % Allowed : 13.89 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 (0.18), residues: 2478 helix: 1.82 (0.14), residues: 1457 sheet: -0.44 (0.33), residues: 222 loop : -0.48 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 276 HIS 0.003 0.000 HIS G 629 PHE 0.010 0.001 PHE E 237 TYR 0.015 0.001 TYR A 915 ARG 0.008 0.000 ARG F 231 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 120 time to evaluate : 2.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 ASN cc_start: 0.9320 (m-40) cc_final: 0.8953 (m-40) REVERT: B 432 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8821 (pp) REVERT: B 553 MET cc_start: 0.8378 (ttt) cc_final: 0.8028 (ttt) REVERT: B 562 CYS cc_start: 0.9207 (m) cc_final: 0.8765 (m) REVERT: C 324 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8292 (tm-30) REVERT: C 383 ASP cc_start: 0.9028 (m-30) cc_final: 0.8824 (p0) REVERT: C 435 ASN cc_start: 0.9430 (t0) cc_final: 0.9152 (m-40) REVERT: C 699 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7502 (mt-10) REVERT: C 721 TRP cc_start: 0.8560 (p-90) cc_final: 0.8307 (p-90) REVERT: E 249 LEU cc_start: 0.9229 (mt) cc_final: 0.8952 (tt) REVERT: E 254 CYS cc_start: 0.7885 (m) cc_final: 0.7630 (t) REVERT: E 426 MET cc_start: 0.7690 (ptm) cc_final: 0.7483 (ptp) REVERT: F 232 MET cc_start: 0.8294 (mmp) cc_final: 0.7864 (mmp) REVERT: A 622 ASN cc_start: 0.9098 (t0) cc_final: 0.8812 (t0) REVERT: A 628 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7445 (tm-30) REVERT: A 635 MET cc_start: 0.8924 (tpp) cc_final: 0.8709 (mmm) REVERT: G 491 GLU cc_start: 0.8371 (tt0) cc_final: 0.7974 (mm-30) REVERT: G 592 CYS cc_start: 0.8816 (m) cc_final: 0.8543 (m) outliers start: 29 outliers final: 27 residues processed: 143 average time/residue: 0.3041 time to fit residues: 72.6630 Evaluate side-chains 144 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 116 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 276 CYS Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 412 HIS Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain G residue 571 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 0.9990 chunk 236 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 229 optimal weight: 10.0000 chunk 138 optimal weight: 0.9990 chunk 100 optimal weight: 0.0870 chunk 180 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 207 optimal weight: 8.9990 chunk 217 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 overall best weight: 0.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 348 ASN ** G 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 22172 Z= 0.129 Angle : 0.481 9.182 30258 Z= 0.242 Chirality : 0.036 0.212 3492 Planarity : 0.003 0.041 3603 Dihedral : 16.666 83.968 3578 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.31 % Allowed : 13.93 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: 1.40 (0.18), residues: 2478 helix: 1.89 (0.14), residues: 1457 sheet: -0.37 (0.33), residues: 222 loop : -0.44 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 276 HIS 0.005 0.000 HIS C 652 PHE 0.009 0.001 PHE E 237 TYR 0.014 0.001 TYR A 915 ARG 0.008 0.000 ARG F 231 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 121 time to evaluate : 2.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 ASN cc_start: 0.9321 (m-40) cc_final: 0.8952 (m-40) REVERT: B 432 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8820 (pp) REVERT: B 553 MET cc_start: 0.8361 (ttt) cc_final: 0.8008 (ttt) REVERT: B 562 CYS cc_start: 0.9201 (m) cc_final: 0.8755 (m) REVERT: C 324 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8262 (tm-30) REVERT: C 435 ASN cc_start: 0.9428 (t0) cc_final: 0.9151 (m-40) REVERT: C 699 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7487 (mt-10) REVERT: C 721 TRP cc_start: 0.8617 (p-90) cc_final: 0.8370 (p-90) REVERT: E 249 LEU cc_start: 0.9228 (mt) cc_final: 0.8945 (tt) REVERT: E 254 CYS cc_start: 0.7891 (m) cc_final: 0.7628 (t) REVERT: A 622 ASN cc_start: 0.9094 (t0) cc_final: 0.8793 (t0) REVERT: A 628 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7466 (tm-30) REVERT: G 491 GLU cc_start: 0.8359 (tt0) cc_final: 0.7955 (mm-30) REVERT: G 592 CYS cc_start: 0.8817 (m) cc_final: 0.8537 (m) outliers start: 29 outliers final: 27 residues processed: 143 average time/residue: 0.3132 time to fit residues: 74.6773 Evaluate side-chains 146 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 118 time to evaluate : 2.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 276 CYS Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 412 HIS Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain G residue 382 CYS Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain G residue 571 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 0.9990 chunk 148 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 169 optimal weight: 0.0370 chunk 255 optimal weight: 10.0000 chunk 234 optimal weight: 4.9990 chunk 203 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 GLN ** G 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22172 Z= 0.177 Angle : 0.503 9.306 30258 Z= 0.252 Chirality : 0.037 0.213 3492 Planarity : 0.003 0.051 3603 Dihedral : 16.639 83.137 3578 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.40 % Allowed : 14.11 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: 1.50 (0.18), residues: 2478 helix: 1.96 (0.14), residues: 1457 sheet: -0.35 (0.33), residues: 223 loop : -0.36 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 276 HIS 0.003 0.000 HIS G 629 PHE 0.014 0.001 PHE C 196 TYR 0.015 0.001 TYR A 915 ARG 0.008 0.000 ARG F 231 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 116 time to evaluate : 2.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 330 ASN cc_start: 0.9316 (m-40) cc_final: 0.8941 (m-40) REVERT: B 432 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8885 (pp) REVERT: B 553 MET cc_start: 0.8306 (ttt) cc_final: 0.7953 (ttt) REVERT: B 562 CYS cc_start: 0.9197 (m) cc_final: 0.8752 (m) REVERT: C 128 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7726 (mtp) REVERT: C 324 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8306 (tm-30) REVERT: C 435 ASN cc_start: 0.9429 (t0) cc_final: 0.9151 (m-40) REVERT: C 699 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7504 (mt-10) REVERT: C 721 TRP cc_start: 0.8643 (p-90) cc_final: 0.8370 (p-90) REVERT: E 249 LEU cc_start: 0.9245 (mt) cc_final: 0.8956 (tt) REVERT: E 254 CYS cc_start: 0.7921 (m) cc_final: 0.7646 (t) REVERT: F 232 MET cc_start: 0.8259 (mmp) cc_final: 0.7760 (mmp) REVERT: A 622 ASN cc_start: 0.9116 (t0) cc_final: 0.8813 (t0) REVERT: A 628 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7506 (tm-30) REVERT: A 855 MET cc_start: 0.8862 (mmp) cc_final: 0.8580 (mmp) REVERT: G 491 GLU cc_start: 0.8371 (tt0) cc_final: 0.7964 (mm-30) REVERT: G 592 CYS cc_start: 0.8847 (m) cc_final: 0.8572 (m) outliers start: 31 outliers final: 29 residues processed: 140 average time/residue: 0.3331 time to fit residues: 77.9410 Evaluate side-chains 146 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 115 time to evaluate : 2.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 597 SER Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 276 CYS Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain G residue 382 CYS Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 464 THR Chi-restraints excluded: chain G residue 571 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 203 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 208 optimal weight: 20.0000 chunk 25 optimal weight: 0.0670 chunk 37 optimal weight: 5.9990 chunk 178 optimal weight: 5.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 HIS ** G 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.068602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.047741 restraints weight = 74869.044| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 3.67 r_work: 0.2681 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22172 Z= 0.135 Angle : 0.486 9.078 30258 Z= 0.243 Chirality : 0.036 0.204 3492 Planarity : 0.003 0.045 3603 Dihedral : 16.562 83.251 3578 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.44 % Allowed : 14.07 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: 1.57 (0.18), residues: 2478 helix: 2.01 (0.14), residues: 1458 sheet: -0.22 (0.34), residues: 222 loop : -0.35 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 276 HIS 0.005 0.000 HIS C 230 PHE 0.011 0.001 PHE C 196 TYR 0.013 0.001 TYR D 239 ARG 0.009 0.000 ARG F 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3874.51 seconds wall clock time: 71 minutes 40.35 seconds (4300.35 seconds total)