Starting phenix.real_space_refine on Thu Apr 11 05:57:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk4_22361/04_2024/7jk4_22361_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk4_22361/04_2024/7jk4_22361.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/7jk4_22361/04_2024/7jk4_22361.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk4_22361/04_2024/7jk4_22361.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk4_22361/04_2024/7jk4_22361_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk4_22361/04_2024/7jk4_22361_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 80 5.49 5 Mg 4 5.21 5 S 111 5.16 5 C 13572 2.51 5 N 3813 2.21 5 O 4137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 279": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 419": "OE1" <-> "OE2" Residue "B GLU 421": "OE1" <-> "OE2" Residue "B ARG 591": "NH1" <-> "NH2" Residue "B GLU 613": "OE1" <-> "OE2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C GLU 153": "OE1" <-> "OE2" Residue "C ARG 179": "NH1" <-> "NH2" Residue "C GLU 354": "OE1" <-> "OE2" Residue "C PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 428": "OE1" <-> "OE2" Residue "C GLU 443": "OE1" <-> "OE2" Residue "C ARG 469": "NH1" <-> "NH2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C GLU 476": "OE1" <-> "OE2" Residue "C GLU 485": "OE1" <-> "OE2" Residue "C GLU 496": "OE1" <-> "OE2" Residue "C GLU 592": "OE1" <-> "OE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 699": "OE1" <-> "OE2" Residue "D GLU 7": "OE1" <-> "OE2" Residue "D ARG 27": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D GLU 45": "OE1" <-> "OE2" Residue "D PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D GLU 191": "OE1" <-> "OE2" Residue "D GLU 213": "OE1" <-> "OE2" Residue "D GLU 236": "OE1" <-> "OE2" Residue "D GLU 298": "OE1" <-> "OE2" Residue "D PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 398": "OE1" <-> "OE2" Residue "D GLU 404": "OE1" <-> "OE2" Residue "D GLU 425": "OE1" <-> "OE2" Residue "E GLU 2": "OE1" <-> "OE2" Residue "E GLU 20": "OE1" <-> "OE2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 144": "NH1" <-> "NH2" Residue "E GLU 223": "OE1" <-> "OE2" Residue "E TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 293": "NH1" <-> "NH2" Residue "E GLU 320": "OE1" <-> "OE2" Residue "E ARG 345": "NH1" <-> "NH2" Residue "E GLU 395": "OE1" <-> "OE2" Residue "E ARG 431": "NH1" <-> "NH2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A GLU 551": "OE1" <-> "OE2" Residue "A GLU 557": "OE1" <-> "OE2" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A GLU 631": "OE1" <-> "OE2" Residue "A GLU 639": "OE1" <-> "OE2" Residue "A ARG 676": "NH1" <-> "NH2" Residue "A ARG 725": "NH1" <-> "NH2" Residue "A GLU 762": "OE1" <-> "OE2" Residue "A GLU 767": "OE1" <-> "OE2" Residue "A ARG 785": "NH1" <-> "NH2" Residue "A ARG 880": "NH1" <-> "NH2" Residue "A GLU 894": "OE1" <-> "OE2" Residue "G GLU 279": "OE1" <-> "OE2" Residue "G GLU 286": "OE1" <-> "OE2" Residue "G GLU 343": "OE1" <-> "OE2" Residue "G GLU 358": "OE1" <-> "OE2" Residue "G ARG 385": "NH1" <-> "NH2" Residue "G GLU 455": "OE1" <-> "OE2" Residue "G ARG 498": "NH1" <-> "NH2" Residue "G GLU 574": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 21717 Number of models: 1 Model: "" Number of chains: 13 Chain: "B" Number of atoms: 2321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2321 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 11, 'TRANS': 278} Chain breaks: 3 Chain: "C" Number of atoms: 4918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4918 Classifications: {'peptide': 612} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 588} Chain breaks: 7 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: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 693 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "I" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 701 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} 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: 11.82, per 1000 atoms: 0.54 Number of scatterers: 21717 At special positions: 0 Unit cell: (117.82, 161.68, 124.7, 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 80 15.00 Mg 4 11.99 O 4137 8.00 N 3813 7.00 C 13572 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: 9.00 Conformation dependent library (CDL) restraints added in 4.1 seconds 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4844 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 13 sheets defined 55.9% alpha, 6.8% beta 33 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 9.38 Creating SS restraints... Processing helix chain 'B' and resid 280 through 284 Processing helix chain 'B' and resid 324 through 338 Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'B' and resid 362 through 371 Processing helix chain 'B' and resid 390 through 400 Processing helix chain 'B' and resid 411 through 423 Processing helix chain 'B' and resid 445 through 455 Processing helix chain 'B' and resid 471 through 473 No H-bonds generated for 'chain 'B' and resid 471 through 473' Processing helix chain 'B' and resid 477 through 482 Processing helix chain 'B' and resid 516 through 523 Processing helix chain 'B' and resid 528 through 544 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 614 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 88 removed outlier: 5.136A pdb=" N ARG C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N THR C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 123 removed outlier: 3.572A pdb=" N LEU C 111 " --> pdb=" O PRO C 108 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER C 112 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 121 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS C 122 " --> pdb=" O GLN C 119 " (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 185 through 198 removed outlier: 3.995A pdb=" N ASP C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N SER C 198 " --> pdb=" O ASN C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 214 No H-bonds generated for 'chain 'C' and resid 212 through 214' 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: 4.118A 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: 4.563A pdb=" N GLY C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 333 No H-bonds generated for 'chain 'C' and resid 330 through 333' Processing helix chain 'C' and resid 338 through 347 Processing helix chain 'C' and resid 351 through 357 Processing helix chain 'C' and resid 360 through 367 Proline residue: C 364 - end of helix Processing helix chain 'C' and resid 373 through 379 Processing helix chain 'C' and resid 383 through 415 Proline residue: C 390 - end of helix removed outlier: 4.666A pdb=" N GLU C 412 " --> pdb=" O GLU C 408 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU C 413 " --> pdb=" O PHE C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 435 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 584 through 586 No H-bonds generated for 'chain 'C' and resid 584 through 586' 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 599 through 606 Processing helix chain 'C' and resid 610 through 619 Processing helix chain 'C' and resid 621 through 625 removed outlier: 4.093A pdb=" N MET C 625 " --> pdb=" O HIS C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 653 removed outlier: 3.522A 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 688 through 702 Processing helix chain 'D' and resid 4 through 20 removed outlier: 3.742A pdb=" N LEU D 8 " --> pdb=" O ALA D 4 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL D 9 " --> pdb=" O ASP D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 45 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 154 removed outlier: 3.772A pdb=" N ALA D 154 " --> pdb=" O ASP D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 168 removed outlier: 5.983A pdb=" N LEU D 160 " --> pdb=" O ASN D 157 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE D 165 " --> pdb=" O TYR D 162 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL D 167 " --> pdb=" O LEU D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 212 through 223 removed outlier: 3.532A pdb=" N LEU D 223 " --> pdb=" O CYS D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 243 Processing helix chain 'D' and resid 251 through 254 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 282 through 294 Processing helix chain 'D' and resid 298 through 311 removed outlier: 4.071A 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 337 through 340 No H-bonds generated for 'chain 'D' and resid 337 through 340' Processing helix chain 'D' and resid 345 through 361 Processing helix chain 'D' and resid 368 through 379 removed outlier: 3.722A 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: 3.569A pdb=" N GLN D 441 " --> pdb=" O HIS D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 455 removed outlier: 3.820A pdb=" N GLN D 455 " --> pdb=" O ALA D 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 9 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 93 through 95 No H-bonds generated for 'chain 'E' and resid 93 through 95' Processing helix chain 'E' and resid 101 through 111 removed outlier: 3.722A pdb=" N GLN E 111 " --> pdb=" O GLN E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 133 removed outlier: 3.753A pdb=" N ARG E 132 " --> pdb=" O GLU E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 149 removed outlier: 3.536A pdb=" N ARG E 144 " --> pdb=" O PRO E 140 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLN E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLU E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) 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: 4.302A pdb=" N ASP E 195 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N PHE E 196 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N GLN E 197 " --> pdb=" O GLY E 193 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLN E 198 " --> pdb=" O SER E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 218 Processing helix chain 'E' and resid 223 through 237 removed outlier: 4.107A pdb=" N VAL E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 258 removed outlier: 4.299A 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 289 Proline residue: E 282 - end of helix removed outlier: 3.584A pdb=" N SER E 285 " --> pdb=" O GLY E 281 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR E 288 " --> pdb=" O ARG E 284 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN E 289 " --> pdb=" O SER E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 337 Processing helix chain 'E' and resid 343 through 347 Processing helix chain 'E' and resid 382 through 393 Processing helix chain 'E' and resid 401 through 412 Processing helix chain 'E' and resid 438 through 448 Processing helix chain 'E' and resid 452 through 455 Processing helix chain 'F' and resid 225 through 237 Processing helix chain 'A' and resid 520 through 528 Processing helix chain 'A' and resid 546 through 548 No H-bonds generated for 'chain 'A' and resid 546 through 548' Processing helix chain 'A' and resid 551 through 558 Processing helix chain 'A' and resid 572 through 587 Processing helix chain 'A' and resid 604 through 620 Processing helix chain 'A' and resid 640 through 651 removed outlier: 3.525A pdb=" N ALA A 643 " --> pdb=" O PRO A 640 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE A 647 " --> pdb=" O TYR A 644 " (cutoff:3.500A) removed outlier: 4.029A 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 689 Processing helix chain 'A' and resid 695 through 702 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 735 Processing helix chain 'A' and resid 747 through 757 removed outlier: 3.860A pdb=" N GLN A 751 " --> pdb=" O HIS A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 777 Processing helix chain 'A' and resid 783 through 799 removed outlier: 3.619A pdb=" N ARG A 791 " --> pdb=" O LEU A 787 " (cutoff:3.500A) removed outlier: 3.509A 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 823 through 827 Processing helix chain 'A' and resid 831 through 847 removed outlier: 3.652A pdb=" N ALA A 841 " --> pdb=" O LEU A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 868 Processing helix chain 'A' and resid 875 through 887 removed outlier: 3.823A pdb=" N ARG A 880 " --> pdb=" O GLY A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 917 removed outlier: 3.734A 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 272 through 286 Processing helix chain 'G' and resid 303 through 310 Processing helix chain 'G' and resid 314 through 319 Processing helix chain 'G' and resid 333 through 344 removed outlier: 3.850A pdb=" N VAL G 336 " --> pdb=" O VAL G 333 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TYR G 337 " --> pdb=" O GLY G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 365 Processing helix chain 'G' and resid 378 through 381 Processing helix chain 'G' and resid 387 through 393 Processing helix chain 'G' and resid 414 through 418 Processing helix chain 'G' and resid 420 through 424 removed outlier: 3.632A pdb=" N ALA G 424 " --> pdb=" O ARG G 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 440 through 453 removed outlier: 3.616A pdb=" N ALA G 452 " --> pdb=" O LYS G 448 " (cutoff:3.500A) Processing helix chain 'G' and resid 457 through 459 No H-bonds generated for 'chain 'G' and resid 457 through 459' Processing helix chain 'G' and resid 462 through 475 removed outlier: 3.671A pdb=" N ALA G 470 " --> pdb=" O GLN G 466 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA G 474 " --> pdb=" O ALA G 470 " (cutoff:3.500A) Processing helix chain 'G' and resid 479 through 497 removed outlier: 3.798A pdb=" N VAL G 490 " --> pdb=" O GLY G 486 " (cutoff:3.500A) removed outlier: 3.691A 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 573 Processing helix chain 'G' and resid 581 through 594 removed outlier: 3.796A pdb=" N VAL G 587 " --> pdb=" O ARG G 583 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG G 590 " --> pdb=" O GLU G 586 " (cutoff:3.500A) Processing helix chain 'G' and resid 602 through 615 removed outlier: 4.034A pdb=" N GLY G 607 " --> pdb=" O ALA G 603 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR G 614 " --> pdb=" O ASP G 610 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG G 615 " --> pdb=" O LEU G 611 " (cutoff:3.500A) Processing helix chain 'G' and resid 626 through 628 No H-bonds generated for 'chain 'G' and resid 626 through 628' Processing helix chain 'G' and resid 637 through 644 removed outlier: 3.767A pdb=" N ALA G 642 " --> pdb=" O GLU G 638 " (cutoff:3.500A) Processing helix chain 'G' and resid 647 through 654 removed outlier: 3.648A pdb=" N SER G 652 " --> pdb=" O GLN G 648 " (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 485 through 488 removed outlier: 6.265A pdb=" N ASN B 352 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N TRP B 488 " --> pdb=" O ASN B 352 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU B 354 " --> pdb=" O TRP B 488 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU B 430 " --> pdb=" O HIS B 461 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU B 463 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU B 432 " --> pdb=" O LEU B 463 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N SER B 465 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL B 434 " --> pdb=" O SER B 465 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR B 377 " --> pdb=" O PHE B 431 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ILE B 433 " --> pdb=" O THR B 377 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU B 379 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N HIS B 435 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 6.663A 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 591 Processing sheet with id= C, first strand: chain 'C' and resid 261 through 267 removed outlier: 7.321A pdb=" N LEU C 96 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ARG C 264 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N THR C 98 " --> pdb=" O ARG C 264 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N PHE C 266 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA C 100 " --> pdb=" O PHE C 266 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 127 through 131 removed outlier: 6.072A pdb=" N GLN C 204 " --> pdb=" O MET C 128 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N CYS C 130 " --> pdb=" O GLN C 204 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL C 206 " --> pdb=" O CYS C 130 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 658 through 660 Processing sheet with id= F, first strand: chain 'D' and resid 50 through 55 Processing sheet with id= G, first strand: chain 'D' and resid 83 through 89 removed outlier: 6.254A pdb=" N SER D 141 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL D 86 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE D 143 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LEU D 88 " --> pdb=" O ILE D 143 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE D 145 " --> pdb=" O LEU D 88 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'D' and resid 406 through 408 Processing sheet with id= I, first strand: chain 'E' and resid 176 through 180 removed outlier: 8.009A pdb=" N ILE E 37 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL E 155 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU E 39 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU E 157 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N GLY E 41 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N SER E 159 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE E 121 " --> pdb=" O CYS E 154 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ILE E 156 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE E 123 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU E 158 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL E 125 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ARG E 65 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ALA E 124 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA E 67 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ASP E 126 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU E 69 " --> pdb=" O ASP E 126 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 739 through 742 removed outlier: 8.961A pdb=" N LEU A 740 " --> pdb=" O CYS A 593 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TYR A 595 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N PHE A 742 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N SER A 597 " --> pdb=" O PHE A 742 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR A 679 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL A 714 " --> pdb=" O THR A 679 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU A 681 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE A 716 " --> pdb=" O LEU A 681 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A 683 " --> pdb=" O ILE A 716 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 851 through 853 removed outlier: 3.532A pdb=" N THR A 852 " --> pdb=" O ILE A 904 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 431 through 435 removed outlier: 6.031A pdb=" N LEU G 371 " --> pdb=" O LEU G 404 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL G 406 " --> pdb=" O LEU G 371 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU G 373 " --> pdb=" O VAL G 406 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE G 408 " --> pdb=" O LEU G 373 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU G 375 " --> pdb=" O ILE G 408 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 618 through 621 895 hydrogen bonds defined for protein. 2544 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 73 hydrogen bonds 146 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 8.20 Time building geometry restraints manager: 9.54 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: 5882 1.34 - 1.46: 4713 1.46 - 1.58: 11322 1.58 - 1.70: 152 1.70 - 1.82: 164 Bond restraints: 22233 Sorted by residual: bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.09e+01 bond pdb=" C4 ATP E 901 " pdb=" C5 ATP E 901 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.81e+01 bond pdb=" C4 ATP A1001 " pdb=" C5 ATP A1001 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.76e+01 bond pdb=" C4 ATP G 901 " pdb=" C5 ATP G 901 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.51e+01 bond pdb=" C5 ATP E 901 " pdb=" C6 ATP E 901 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.27e+01 ... (remaining 22228 not shown) Histogram of bond angle deviations from ideal: 98.15 - 105.68: 718 105.68 - 113.22: 12264 113.22 - 120.75: 10659 120.75 - 128.29: 6498 128.29 - 135.82: 210 Bond angle restraints: 30349 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 139.87 118.71 21.16 1.00e+00 1.00e+00 4.48e+02 angle pdb=" PB ATP E 901 " pdb=" O3B ATP E 901 " pdb=" PG ATP E 901 " ideal model delta sigma weight residual 139.87 121.02 18.85 1.00e+00 1.00e+00 3.55e+02 angle pdb=" PB ATP G 901 " pdb=" O3B ATP G 901 " pdb=" PG ATP G 901 " ideal model delta sigma weight residual 139.87 121.44 18.43 1.00e+00 1.00e+00 3.40e+02 angle pdb=" PA ATP D 901 " pdb=" O3A ATP D 901 " pdb=" PB ATP D 901 " ideal model delta sigma weight residual 136.83 119.65 17.18 1.00e+00 1.00e+00 2.95e+02 angle pdb=" PB ATP A1001 " pdb=" O3B ATP A1001 " pdb=" PG ATP A1001 " ideal model delta sigma weight residual 139.87 122.92 16.95 1.00e+00 1.00e+00 2.87e+02 ... (remaining 30344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 11568 17.93 - 35.87: 1277 35.87 - 53.80: 494 53.80 - 71.74: 113 71.74 - 89.67: 26 Dihedral angle restraints: 13478 sinusoidal: 6058 harmonic: 7420 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 180.00 150.57 29.43 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA GLN C 347 " pdb=" C GLN C 347 " pdb=" N LEU C 348 " pdb=" CA LEU C 348 " ideal model delta harmonic sigma weight residual -180.00 -156.12 -23.88 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA SER G 349 " pdb=" C SER G 349 " pdb=" N GLY G 350 " pdb=" CA GLY G 350 " ideal model delta harmonic sigma weight residual 180.00 156.46 23.54 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 13475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2828 0.063 - 0.126: 575 0.126 - 0.188: 95 0.188 - 0.251: 4 0.251 - 0.314: 1 Chirality restraints: 3503 Sorted by residual: chirality pdb=" CG LEU C 275 " pdb=" CB LEU C 275 " pdb=" CD1 LEU C 275 " pdb=" CD2 LEU C 275 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CB VAL E 221 " pdb=" CA VAL E 221 " pdb=" CG1 VAL E 221 " pdb=" CG2 VAL E 221 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB ILE C 356 " pdb=" CA ILE C 356 " pdb=" CG1 ILE C 356 " pdb=" CG2 ILE C 356 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 3500 not shown) Planarity restraints: 3607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 872 " -0.057 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO A 873 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 873 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 873 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 150 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.95e+00 pdb=" CG ASN E 150 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN E 150 " 0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN E 150 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY E 281 " -0.038 5.00e-02 4.00e+02 5.80e-02 5.38e+00 pdb=" N PRO E 282 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO E 282 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 282 " -0.032 5.00e-02 4.00e+02 ... (remaining 3604 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 305 2.66 - 3.22: 18807 3.22 - 3.78: 34807 3.78 - 4.34: 47125 4.34 - 4.90: 76370 Nonbonded interactions: 177414 Sorted by model distance: nonbonded pdb=" OG1 THR G 304 " pdb="MG MG G 902 " model vdw 2.102 2.170 nonbonded pdb=" OG1 THR D 63 " pdb="MG MG D 902 " model vdw 2.115 2.170 nonbonded pdb=" O2B ATP G 901 " pdb="MG MG G 902 " model vdw 2.129 2.170 nonbonded pdb=" O3G ATP E 901 " pdb="MG MG E 902 " model vdw 2.139 2.170 nonbonded pdb=" O3G ATP G 901 " pdb="MG MG G 902 " model vdw 2.162 2.170 ... (remaining 177409 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 6.860 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 64.490 Find NCS groups from input model: 0.690 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 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 : 0.006 0.097 22233 Z= 0.366 Angle : 0.952 21.164 30349 Z= 0.589 Chirality : 0.052 0.314 3503 Planarity : 0.006 0.087 3607 Dihedral : 17.944 89.669 8634 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.32 % Allowed : 5.00 % Favored : 94.68 % 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: -2.88 (0.14), residues: 2481 helix: -2.59 (0.08), residues: 1477 sheet: -2.74 (0.28), residues: 233 loop : 0.52 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 57 HIS 0.006 0.001 HIS E 278 PHE 0.026 0.003 PHE C 215 TYR 0.027 0.002 TYR E 258 ARG 0.009 0.001 ARG G 480 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 260 time to evaluate : 2.669 Fit side-chains revert: symmetry clash REVERT: B 333 MET cc_start: 0.8758 (mmm) cc_final: 0.8494 (mmm) REVERT: B 575 ARG cc_start: 0.8983 (mtt-85) cc_final: 0.8783 (mtt-85) REVERT: B 588 LYS cc_start: 0.9428 (mmtm) cc_final: 0.9225 (mmmt) REVERT: C 387 LYS cc_start: 0.9712 (tttt) cc_final: 0.9208 (ptpt) REVERT: C 443 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8152 (mm-30) REVERT: C 654 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8220 (tm-30) REVERT: D 116 LYS cc_start: 0.9161 (mmtt) cc_final: 0.8890 (mmtp) REVERT: D 185 ASP cc_start: 0.8333 (p0) cc_final: 0.7880 (p0) REVERT: D 347 GLU cc_start: 0.8382 (mp0) cc_final: 0.8104 (mp0) REVERT: E 169 LYS cc_start: 0.8814 (mttm) cc_final: 0.8459 (mtpt) REVERT: E 198 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8524 (tm-30) REVERT: E 337 HIS cc_start: 0.8196 (t-90) cc_final: 0.7884 (t-90) REVERT: F 226 GLU cc_start: 0.9546 (mt-10) cc_final: 0.9326 (mt-10) REVERT: A 577 ASN cc_start: 0.8919 (t0) cc_final: 0.8653 (m-40) REVERT: A 903 LYS cc_start: 0.9269 (mttm) cc_final: 0.8969 (mtpp) REVERT: A 915 TYR cc_start: 0.9110 (t80) cc_final: 0.8770 (t80) outliers start: 7 outliers final: 2 residues processed: 267 average time/residue: 0.4513 time to fit residues: 175.3773 Evaluate side-chains 156 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain E residue 45 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 217 optimal weight: 8.9990 chunk 194 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 104 optimal weight: 0.3980 chunk 201 optimal weight: 0.6980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.1980 chunk 149 optimal weight: 4.9990 chunk 233 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 HIS B 436 ASN B 498 ASN B 577 GLN B 598 GLN B 609 GLN C 113 GLN C 194 ASN C 250 HIS C 391 GLN C 605 ASN D 330 GLN E 127 ASN ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 414 ASN E 433 GLN A 622 ASN A 749 GLN A 828 ASN A 838 GLN G 386 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22233 Z= 0.184 Angle : 0.531 6.952 30349 Z= 0.285 Chirality : 0.038 0.174 3503 Planarity : 0.004 0.059 3607 Dihedral : 17.610 81.030 3664 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.08 % Allowed : 8.65 % Favored : 90.27 % 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: -0.69 (0.16), residues: 2481 helix: -0.24 (0.12), residues: 1476 sheet: -2.28 (0.28), residues: 241 loop : 0.20 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 276 HIS 0.004 0.001 HIS C 652 PHE 0.016 0.001 PHE D 366 TYR 0.018 0.001 TYR A 579 ARG 0.005 0.000 ARG C 604 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 171 time to evaluate : 2.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 387 LYS cc_start: 0.9726 (tttt) cc_final: 0.9190 (ptpt) REVERT: C 443 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8159 (mm-30) REVERT: C 654 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8331 (tm-30) REVERT: C 699 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8092 (mt-10) REVERT: D 116 LYS cc_start: 0.9190 (mmtt) cc_final: 0.8956 (mmtm) REVERT: D 185 ASP cc_start: 0.8398 (p0) cc_final: 0.7711 (p0) REVERT: D 188 GLU cc_start: 0.8075 (pt0) cc_final: 0.7426 (pt0) REVERT: D 347 GLU cc_start: 0.8391 (mp0) cc_final: 0.7980 (mp0) REVERT: D 426 MET cc_start: 0.8921 (mmm) cc_final: 0.8402 (mmm) REVERT: E 1 MET cc_start: 0.7729 (ppp) cc_final: 0.7431 (ptm) REVERT: E 82 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7978 (mt-10) REVERT: E 276 TRP cc_start: 0.8405 (t-100) cc_final: 0.8155 (t-100) REVERT: E 337 HIS cc_start: 0.8256 (t-90) cc_final: 0.7929 (t-90) REVERT: A 577 ASN cc_start: 0.8952 (t0) cc_final: 0.8676 (m-40) REVERT: A 915 TYR cc_start: 0.9110 (t80) cc_final: 0.8759 (t80) REVERT: G 575 ARG cc_start: 0.7545 (mmp-170) cc_final: 0.7217 (mmp-170) outliers start: 24 outliers final: 14 residues processed: 186 average time/residue: 0.3421 time to fit residues: 101.7147 Evaluate side-chains 159 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 144 time to evaluate : 2.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 699 GLU Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 456 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 129 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 194 optimal weight: 0.5980 chunk 158 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 233 optimal weight: 5.9990 chunk 252 optimal weight: 8.9990 chunk 208 optimal weight: 0.8980 chunk 231 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 HIS E 63 ASN ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 22233 Z= 0.148 Angle : 0.485 7.997 30349 Z= 0.258 Chirality : 0.037 0.170 3503 Planarity : 0.003 0.049 3607 Dihedral : 17.473 77.734 3664 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.53 % Allowed : 9.73 % Favored : 88.74 % 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: 0.25 (0.17), residues: 2481 helix: 0.71 (0.13), residues: 1485 sheet: -1.81 (0.30), residues: 233 loop : 0.03 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 276 HIS 0.004 0.000 HIS G 284 PHE 0.011 0.001 PHE C 49 TYR 0.012 0.001 TYR E 258 ARG 0.003 0.000 ARG E 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 164 time to evaluate : 2.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 588 LYS cc_start: 0.9405 (mmmt) cc_final: 0.9104 (mmtm) REVERT: C 387 LYS cc_start: 0.9729 (tttt) cc_final: 0.9192 (ptpt) REVERT: C 443 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8212 (mm-30) REVERT: C 453 PHE cc_start: 0.7553 (m-10) cc_final: 0.7275 (m-10) REVERT: C 654 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8274 (tm-30) REVERT: C 699 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8160 (mt-10) REVERT: D 185 ASP cc_start: 0.8404 (p0) cc_final: 0.7144 (p0) REVERT: D 188 GLU cc_start: 0.8066 (pt0) cc_final: 0.7423 (pt0) REVERT: D 347 GLU cc_start: 0.8379 (mp0) cc_final: 0.7985 (mp0) REVERT: D 426 MET cc_start: 0.8956 (mmm) cc_final: 0.8380 (mmm) REVERT: E 82 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7955 (mt-10) REVERT: E 337 HIS cc_start: 0.8281 (t-90) cc_final: 0.7976 (t-90) REVERT: A 577 ASN cc_start: 0.8940 (t0) cc_final: 0.8671 (m-40) REVERT: A 915 TYR cc_start: 0.9115 (t80) cc_final: 0.8810 (t80) REVERT: G 320 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8958 (pp) REVERT: G 575 ARG cc_start: 0.7641 (mmp-170) cc_final: 0.7411 (mmp-170) REVERT: G 618 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9343 (mt) REVERT: G 621 MET cc_start: 0.8353 (ttp) cc_final: 0.8024 (ttm) outliers start: 34 outliers final: 16 residues processed: 188 average time/residue: 0.3457 time to fit residues: 102.2094 Evaluate side-chains 167 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 148 time to evaluate : 2.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 699 GLU Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 422 LYS Chi-restraints excluded: chain E residue 412 HIS Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 618 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 231 optimal weight: 8.9990 chunk 175 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 156 optimal weight: 4.9990 chunk 234 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 222 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 325 HIS C 605 ASN E 63 ASN ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 273 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 22233 Z= 0.359 Angle : 0.567 9.042 30349 Z= 0.295 Chirality : 0.040 0.164 3503 Planarity : 0.004 0.048 3607 Dihedral : 17.536 84.034 3663 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.67 % Allowed : 10.54 % Favored : 87.79 % 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: 0.75 (0.17), residues: 2481 helix: 1.18 (0.14), residues: 1486 sheet: -1.61 (0.30), residues: 241 loop : 0.08 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 57 HIS 0.005 0.001 HIS E 278 PHE 0.012 0.001 PHE D 304 TYR 0.020 0.001 TYR E 258 ARG 0.004 0.000 ARG E 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 151 time to evaluate : 2.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 588 LYS cc_start: 0.9420 (mmmt) cc_final: 0.9184 (mmtm) REVERT: C 387 LYS cc_start: 0.9737 (tttt) cc_final: 0.9195 (ptpt) REVERT: C 443 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8412 (mm-30) REVERT: C 654 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8284 (tm-30) REVERT: D 95 ASP cc_start: 0.8276 (t0) cc_final: 0.8037 (t0) REVERT: D 185 ASP cc_start: 0.8489 (p0) cc_final: 0.7314 (p0) REVERT: D 188 GLU cc_start: 0.8074 (pt0) cc_final: 0.7473 (pt0) REVERT: D 347 GLU cc_start: 0.8421 (mp0) cc_final: 0.7975 (mp0) REVERT: D 425 GLU cc_start: 0.8500 (tt0) cc_final: 0.8103 (pt0) REVERT: D 426 MET cc_start: 0.8932 (mmm) cc_final: 0.8317 (mmm) REVERT: E 337 HIS cc_start: 0.8381 (t-90) cc_final: 0.8092 (t-90) REVERT: A 650 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.7844 (mp10) REVERT: A 915 TYR cc_start: 0.9151 (t80) cc_final: 0.8816 (t80) REVERT: G 320 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8956 (pp) REVERT: G 575 ARG cc_start: 0.7719 (mmp-170) cc_final: 0.7508 (mmp-170) REVERT: G 621 MET cc_start: 0.8423 (ttp) cc_final: 0.8099 (ttt) outliers start: 37 outliers final: 17 residues processed: 181 average time/residue: 0.3437 time to fit residues: 97.9513 Evaluate side-chains 158 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 139 time to evaluate : 2.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 401 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain G residue 456 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 206 optimal weight: 0.7980 chunk 141 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 184 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 chunk 211 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 126 optimal weight: 0.8980 chunk 222 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 325 HIS C 58 ASN C 605 ASN E 63 ASN ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 22233 Z= 0.146 Angle : 0.470 9.270 30349 Z= 0.248 Chirality : 0.036 0.169 3503 Planarity : 0.003 0.046 3607 Dihedral : 17.364 84.453 3663 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.99 % Allowed : 12.03 % Favored : 86.98 % 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: 1.11 (0.17), residues: 2481 helix: 1.49 (0.14), residues: 1473 sheet: -1.26 (0.31), residues: 233 loop : 0.09 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 276 HIS 0.004 0.000 HIS G 284 PHE 0.011 0.001 PHE C 49 TYR 0.012 0.001 TYR B 534 ARG 0.002 0.000 ARG G 619 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 160 time to evaluate : 2.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 588 LYS cc_start: 0.9409 (mmmt) cc_final: 0.9182 (mmtm) REVERT: C 387 LYS cc_start: 0.9738 (tttt) cc_final: 0.9210 (ptpt) REVERT: C 443 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8186 (mm-30) REVERT: C 654 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8250 (tm-30) REVERT: D 185 ASP cc_start: 0.8465 (p0) cc_final: 0.7774 (p0) REVERT: D 188 GLU cc_start: 0.8051 (pt0) cc_final: 0.7723 (pt0) REVERT: D 347 GLU cc_start: 0.8387 (mp0) cc_final: 0.7977 (mp0) REVERT: D 425 GLU cc_start: 0.8467 (tt0) cc_final: 0.8118 (pt0) REVERT: D 426 MET cc_start: 0.8936 (mmm) cc_final: 0.8391 (mmm) REVERT: E 337 HIS cc_start: 0.8387 (t-90) cc_final: 0.8118 (t-90) REVERT: A 577 ASN cc_start: 0.8900 (t0) cc_final: 0.8650 (m-40) REVERT: A 915 TYR cc_start: 0.9125 (t80) cc_final: 0.8797 (t80) REVERT: G 621 MET cc_start: 0.8372 (ttp) cc_final: 0.8058 (ttt) outliers start: 22 outliers final: 15 residues processed: 176 average time/residue: 0.3787 time to fit residues: 102.6547 Evaluate side-chains 161 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 146 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 699 GLU Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 422 LYS Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 456 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 83 optimal weight: 0.9990 chunk 223 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 145 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 248 optimal weight: 5.9990 chunk 206 optimal weight: 2.9990 chunk 115 optimal weight: 0.4980 chunk 20 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 325 HIS C 605 ASN E 63 ASN ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22233 Z= 0.182 Angle : 0.478 7.608 30349 Z= 0.252 Chirality : 0.037 0.164 3503 Planarity : 0.003 0.045 3607 Dihedral : 17.234 87.458 3663 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.40 % Allowed : 12.66 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.36 (0.17), residues: 2481 helix: 1.70 (0.14), residues: 1476 sheet: -1.03 (0.32), residues: 234 loop : 0.12 (0.23), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 276 HIS 0.004 0.001 HIS G 284 PHE 0.012 0.001 PHE A 867 TYR 0.014 0.001 TYR A 629 ARG 0.007 0.000 ARG B 556 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 153 time to evaluate : 2.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 535 MET cc_start: 0.8453 (mmm) cc_final: 0.8196 (tpp) REVERT: B 588 LYS cc_start: 0.9412 (mmmt) cc_final: 0.9180 (mmtm) REVERT: C 387 LYS cc_start: 0.9736 (tttt) cc_final: 0.9214 (ptpt) REVERT: C 443 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8190 (mm-30) REVERT: C 654 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8258 (tm-30) REVERT: D 185 ASP cc_start: 0.8503 (p0) cc_final: 0.7996 (p0) REVERT: D 188 GLU cc_start: 0.8048 (pt0) cc_final: 0.7629 (pt0) REVERT: D 347 GLU cc_start: 0.8430 (mp0) cc_final: 0.8002 (mp0) REVERT: D 425 GLU cc_start: 0.8496 (tt0) cc_final: 0.8121 (pt0) REVERT: D 426 MET cc_start: 0.8929 (mmm) cc_final: 0.8345 (mmm) REVERT: E 337 HIS cc_start: 0.8367 (t-90) cc_final: 0.8117 (t-90) REVERT: F 224 ASP cc_start: 0.8919 (t0) cc_final: 0.8618 (t0) REVERT: A 650 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.7869 (mp10) REVERT: A 915 TYR cc_start: 0.9132 (t80) cc_final: 0.8768 (t80) REVERT: G 320 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8904 (pp) REVERT: G 575 ARG cc_start: 0.7930 (mmp-170) cc_final: 0.7717 (mmp-170) REVERT: G 621 MET cc_start: 0.8370 (ttp) cc_final: 0.8058 (ttt) outliers start: 31 outliers final: 16 residues processed: 175 average time/residue: 0.3526 time to fit residues: 96.4580 Evaluate side-chains 162 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 144 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 422 LYS Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 456 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 239 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 209 optimal weight: 9.9990 chunk 138 optimal weight: 8.9990 chunk 247 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 63 ASN ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 22233 Z= 0.447 Angle : 0.610 9.792 30349 Z= 0.313 Chirality : 0.041 0.170 3503 Planarity : 0.004 0.045 3607 Dihedral : 17.368 86.883 3663 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.49 % Allowed : 13.42 % Favored : 85.09 % 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: 1.22 (0.17), residues: 2481 helix: 1.60 (0.14), residues: 1491 sheet: -1.27 (0.31), residues: 244 loop : 0.11 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 57 HIS 0.005 0.001 HIS E 278 PHE 0.015 0.001 PHE D 304 TYR 0.022 0.001 TYR A 629 ARG 0.005 0.000 ARG B 556 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 140 time to evaluate : 2.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 535 MET cc_start: 0.8436 (mmm) cc_final: 0.8211 (mmp) REVERT: B 588 LYS cc_start: 0.9425 (mmmt) cc_final: 0.9185 (mmtm) REVERT: C 387 LYS cc_start: 0.9740 (tttt) cc_final: 0.9198 (ptpt) REVERT: C 443 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8266 (mm-30) REVERT: C 654 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8242 (tm-30) REVERT: D 185 ASP cc_start: 0.8523 (p0) cc_final: 0.8304 (p0) REVERT: D 347 GLU cc_start: 0.8452 (mp0) cc_final: 0.7997 (mp0) REVERT: D 425 GLU cc_start: 0.8514 (tt0) cc_final: 0.8121 (pt0) REVERT: D 426 MET cc_start: 0.8917 (mmm) cc_final: 0.8335 (mmm) REVERT: E 337 HIS cc_start: 0.8409 (t-90) cc_final: 0.8156 (t-90) REVERT: F 224 ASP cc_start: 0.8957 (t0) cc_final: 0.8630 (t0) REVERT: A 650 GLN cc_start: 0.9172 (OUTLIER) cc_final: 0.7982 (mp10) REVERT: A 915 TYR cc_start: 0.9144 (t80) cc_final: 0.8797 (t80) REVERT: G 320 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8929 (pp) REVERT: G 563 MET cc_start: 0.8272 (tmm) cc_final: 0.7942 (tmm) REVERT: G 621 MET cc_start: 0.8433 (ttp) cc_final: 0.8120 (ttt) outliers start: 33 outliers final: 23 residues processed: 166 average time/residue: 0.3698 time to fit residues: 95.3209 Evaluate side-chains 161 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 2.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 456 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 153 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 chunk 147 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 194 optimal weight: 4.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 230 HIS C 570 GLN E 63 ASN ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22233 Z= 0.194 Angle : 0.495 8.742 30349 Z= 0.259 Chirality : 0.037 0.183 3503 Planarity : 0.003 0.048 3607 Dihedral : 17.272 88.966 3663 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.49 % Allowed : 13.78 % Favored : 84.73 % 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: 1.44 (0.18), residues: 2481 helix: 1.80 (0.14), residues: 1481 sheet: -1.03 (0.31), residues: 239 loop : 0.08 (0.24), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 191 HIS 0.004 0.001 HIS G 284 PHE 0.011 0.001 PHE C 49 TYR 0.015 0.001 TYR A 629 ARG 0.006 0.000 ARG G 417 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 152 time to evaluate : 2.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 588 LYS cc_start: 0.9405 (mmmt) cc_final: 0.9169 (mmtm) REVERT: C 145 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8082 (mm-30) REVERT: C 387 LYS cc_start: 0.9731 (tttt) cc_final: 0.9221 (ptpt) REVERT: C 443 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8217 (mm-30) REVERT: C 654 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8192 (tm-30) REVERT: D 185 ASP cc_start: 0.8490 (p0) cc_final: 0.8064 (p0) REVERT: D 188 GLU cc_start: 0.7998 (pt0) cc_final: 0.7545 (pt0) REVERT: D 347 GLU cc_start: 0.8415 (mp0) cc_final: 0.7949 (mp0) REVERT: D 425 GLU cc_start: 0.8501 (tt0) cc_final: 0.8146 (pt0) REVERT: D 426 MET cc_start: 0.8937 (mmm) cc_final: 0.8349 (mmm) REVERT: E 337 HIS cc_start: 0.8405 (t-90) cc_final: 0.8162 (t-90) REVERT: F 224 ASP cc_start: 0.8987 (t0) cc_final: 0.8668 (t0) REVERT: A 650 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.7945 (mp10) REVERT: A 915 TYR cc_start: 0.9115 (t80) cc_final: 0.8770 (t80) REVERT: G 320 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8890 (pp) REVERT: G 563 MET cc_start: 0.8213 (tmm) cc_final: 0.7720 (tmm) REVERT: G 621 MET cc_start: 0.8385 (ttp) cc_final: 0.8069 (ttt) outliers start: 33 outliers final: 23 residues processed: 178 average time/residue: 0.3567 time to fit residues: 99.3414 Evaluate side-chains 172 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 147 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 456 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 225 optimal weight: 3.9990 chunk 237 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 chunk 230 optimal weight: 0.0370 chunk 138 optimal weight: 9.9990 chunk 100 optimal weight: 0.0970 chunk 181 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 208 optimal weight: 0.9990 chunk 218 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 overall best weight: 0.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 605 ASN E 63 ASN ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22233 Z= 0.136 Angle : 0.482 9.650 30349 Z= 0.251 Chirality : 0.036 0.183 3503 Planarity : 0.003 0.048 3607 Dihedral : 17.044 83.323 3663 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.13 % Allowed : 14.01 % Favored : 84.86 % 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: 1.56 (0.18), residues: 2481 helix: 1.90 (0.14), residues: 1487 sheet: -0.80 (0.32), residues: 239 loop : 0.03 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 191 HIS 0.005 0.000 HIS G 284 PHE 0.012 0.001 PHE C 49 TYR 0.012 0.001 TYR A 629 ARG 0.005 0.000 ARG B 556 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 154 time to evaluate : 2.526 Fit side-chains revert: symmetry clash REVERT: B 588 LYS cc_start: 0.9401 (mmmt) cc_final: 0.9200 (mmtm) REVERT: C 387 LYS cc_start: 0.9720 (tttt) cc_final: 0.9227 (ptpt) REVERT: C 443 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8207 (mm-30) REVERT: C 654 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8147 (tm-30) REVERT: D 347 GLU cc_start: 0.8419 (mp0) cc_final: 0.8026 (mp0) REVERT: D 425 GLU cc_start: 0.8483 (tt0) cc_final: 0.8211 (pt0) REVERT: D 426 MET cc_start: 0.8898 (mmm) cc_final: 0.8378 (mmm) REVERT: E 337 HIS cc_start: 0.8404 (t-90) cc_final: 0.8171 (t-90) REVERT: F 224 ASP cc_start: 0.8992 (t0) cc_final: 0.8661 (t0) REVERT: A 577 ASN cc_start: 0.8889 (t0) cc_final: 0.8620 (t0) REVERT: A 915 TYR cc_start: 0.9112 (t80) cc_final: 0.8729 (t80) REVERT: G 320 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8830 (pp) REVERT: G 563 MET cc_start: 0.8207 (tmm) cc_final: 0.7699 (tmm) REVERT: G 621 MET cc_start: 0.8359 (ttp) cc_final: 0.8035 (ttm) outliers start: 25 outliers final: 19 residues processed: 172 average time/residue: 0.3612 time to fit residues: 96.7503 Evaluate side-chains 170 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 150 time to evaluate : 2.538 ------------------------------------------------------------------------------- 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 336 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 456 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 244 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 115 optimal weight: 10.0000 chunk 169 optimal weight: 9.9990 chunk 256 optimal weight: 10.0000 chunk 235 optimal weight: 2.9990 chunk 203 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 605 ASN ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 451 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22233 Z= 0.211 Angle : 0.502 9.610 30349 Z= 0.259 Chirality : 0.037 0.192 3503 Planarity : 0.003 0.047 3607 Dihedral : 17.018 81.992 3663 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.99 % Allowed : 14.46 % Favored : 84.55 % 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: 1.66 (0.18), residues: 2481 helix: 1.98 (0.14), residues: 1484 sheet: -0.73 (0.32), residues: 238 loop : 0.05 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 276 HIS 0.004 0.001 HIS G 284 PHE 0.017 0.001 PHE A 867 TYR 0.014 0.001 TYR A 629 ARG 0.013 0.000 ARG B 591 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 147 time to evaluate : 2.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 588 LYS cc_start: 0.9424 (mmmt) cc_final: 0.9219 (mmtm) REVERT: C 387 LYS cc_start: 0.9722 (tttt) cc_final: 0.9232 (ptpt) REVERT: C 443 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8244 (mm-30) REVERT: C 654 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8138 (tm-30) REVERT: D 185 ASP cc_start: 0.8306 (p0) cc_final: 0.6884 (p0) REVERT: D 188 GLU cc_start: 0.7922 (pt0) cc_final: 0.7520 (pt0) REVERT: D 347 GLU cc_start: 0.8436 (mp0) cc_final: 0.8024 (mp0) REVERT: D 422 LYS cc_start: 0.9302 (ptmt) cc_final: 0.9071 (ptmm) REVERT: D 425 GLU cc_start: 0.8497 (tt0) cc_final: 0.8237 (pt0) REVERT: D 426 MET cc_start: 0.8931 (mmm) cc_final: 0.8335 (mmm) REVERT: E 337 HIS cc_start: 0.8408 (t-90) cc_final: 0.8172 (t-90) REVERT: F 224 ASP cc_start: 0.9011 (t0) cc_final: 0.8566 (t0) REVERT: F 226 GLU cc_start: 0.9561 (mt-10) cc_final: 0.9315 (mt-10) REVERT: A 650 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.7937 (mp10) REVERT: A 915 TYR cc_start: 0.9131 (t80) cc_final: 0.8729 (t80) REVERT: G 320 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8840 (pp) REVERT: G 563 MET cc_start: 0.8221 (tmm) cc_final: 0.7731 (tmm) REVERT: G 621 MET cc_start: 0.8386 (ttp) cc_final: 0.8111 (ttm) outliers start: 22 outliers final: 20 residues processed: 167 average time/residue: 0.3468 time to fit residues: 92.6620 Evaluate side-chains 167 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 2.686 ------------------------------------------------------------------------------- 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 130 CYS Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 320 LEU Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 456 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 217 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 187 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 204 optimal weight: 0.9990 chunk 85 optimal weight: 0.0270 chunk 209 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 0.4980 chunk 179 optimal weight: 0.0770 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 605 ASN D 421 GLN ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.080980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.060321 restraints weight = 58379.289| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 3.05 r_work: 0.2798 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22233 Z= 0.129 Angle : 0.485 9.836 30349 Z= 0.251 Chirality : 0.036 0.179 3503 Planarity : 0.003 0.046 3607 Dihedral : 16.868 78.038 3663 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.86 % Allowed : 14.68 % Favored : 84.46 % 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: 1.70 (0.18), residues: 2481 helix: 2.01 (0.14), residues: 1480 sheet: -0.70 (0.32), residues: 244 loop : 0.08 (0.24), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 276 HIS 0.005 0.000 HIS G 284 PHE 0.012 0.001 PHE C 49 TYR 0.010 0.001 TYR A 629 ARG 0.004 0.000 ARG B 556 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3933.90 seconds wall clock time: 73 minutes 19.25 seconds (4399.25 seconds total)