Starting phenix.real_space_refine on Sun Sep 29 07:53:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgs_22330/09_2024/7jgs_22330.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgs_22330/09_2024/7jgs_22330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgs_22330/09_2024/7jgs_22330.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgs_22330/09_2024/7jgs_22330.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgs_22330/09_2024/7jgs_22330.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgs_22330/09_2024/7jgs_22330.cif" } resolution = 3.2 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= 0.003 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 82 5.49 5 Mg 4 5.21 5 S 111 5.16 5 C 13591 2.51 5 N 3810 2.21 5 O 4145 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 21743 Number of models: 1 Model: "" Number of chains: 13 Chain: "B" Number of atoms: 2290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2290 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 4 Chain: "C" Number of atoms: 4934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4934 Classifications: {'peptide': 614} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 590} Chain breaks: 6 Chain: "D" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3549 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 11, 'TRANS': 429} Chain breaks: 2 Chain: "E" Number of atoms: 3161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3161 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 386} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 143 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "A" Number of atoms: 3129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3129 Classifications: {'peptide': 401} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 383} Chain: "G" Number of atoms: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2974 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 13, 'TRANS': 358} Chain breaks: 2 Chain: "H" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 700 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "I" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 735 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} 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: 11.72, per 1000 atoms: 0.54 Number of scatterers: 21743 At special positions: 0 Unit cell: (123.981, 162.129, 119.646, 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 82 15.00 Mg 4 11.99 O 4145 8.00 N 3810 7.00 C 13591 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 - 3.00 Amino acid : True - 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: 4.69 Conformation dependent library (CDL) restraints added in 2.5 seconds 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4840 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 14 sheets defined 64.8% alpha, 7.0% beta 35 base pairs and 68 stacking pairs defined. Time for finding SS restraints: 6.86 Creating SS restraints... Processing helix chain 'B' and resid 280 through 285 Processing helix chain 'B' and resid 324 through 338 Processing helix chain 'B' and resid 339 through 349 removed outlier: 3.610A pdb=" N GLU B 349 " --> pdb=" O CYS B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 372 Processing helix chain 'B' and resid 389 through 401 Processing helix chain 'B' and resid 410 through 423 Processing helix chain 'B' and resid 444 through 456 removed outlier: 3.653A pdb=" N GLN B 448 " --> pdb=" O ASN B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 474 Processing helix chain 'B' and resid 476 through 483 Processing helix chain 'B' and resid 516 through 524 Processing helix chain 'B' and resid 527 through 544 Processing helix chain 'B' and resid 554 through 565 Processing helix chain 'B' and resid 570 through 584 removed outlier: 3.845A pdb=" N LEU B 574 " --> pdb=" O SER B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 615 Processing helix chain 'C' and resid 41 through 46 removed outlier: 3.615A pdb=" N VAL C 45 " --> pdb=" O GLY C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 89 removed outlier: 3.510A pdb=" N GLU C 51 " --> pdb=" O GLN C 47 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ARG C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N THR C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG C 89 " --> pdb=" O GLY C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 109 Processing helix chain 'C' and resid 110 through 124 removed outlier: 3.574A pdb=" N GLN C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 137 removed outlier: 3.555A pdb=" N CYS C 137 " --> pdb=" O SER C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 159 removed outlier: 3.608A pdb=" N GLU C 159 " --> pdb=" O ASN C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 183 Processing helix chain 'C' and resid 184 through 196 Processing helix chain 'C' and resid 216 through 230 Processing helix chain 'C' and resid 245 through 253 removed outlier: 4.090A pdb=" N VAL C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 259 removed outlier: 3.608A pdb=" N SER C 259 " --> pdb=" O TYR C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 282 Processing helix chain 'C' and resid 293 through 307 Processing helix chain 'C' and resid 310 through 327 Processing helix chain 'C' and resid 328 through 335 removed outlier: 5.844A pdb=" N ALA C 331 " --> pdb=" O GLY C 328 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS C 335 " --> pdb=" O PHE C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 349 through 358 removed outlier: 3.989A pdb=" N MET C 353 " --> pdb=" O THR C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 368 removed outlier: 3.950A pdb=" N TYR C 365 " --> pdb=" O SER C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 380 removed outlier: 3.962A pdb=" N ILE C 375 " --> pdb=" O ASP C 371 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 376 " --> pdb=" O CYS C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 415 Proline residue: C 390 - end of helix Processing helix chain 'C' and resid 425 through 436 removed outlier: 3.710A pdb=" N LEU C 429 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG C 436 " --> pdb=" O ASN C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 453 removed outlier: 3.524A pdb=" N LYS C 445 " --> pdb=" O THR C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 477 Processing helix chain 'C' and resid 484 through 508 Proline residue: C 493 - end of helix Processing helix chain 'C' and resid 563 through 581 removed outlier: 3.664A pdb=" N LYS C 567 " --> pdb=" O ARG C 563 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N GLN C 578 " --> pdb=" O THR C 574 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASP C 579 " --> pdb=" O GLN C 575 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 581 " --> pdb=" O VAL C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 607 Processing helix chain 'C' and resid 609 through 620 Processing helix chain 'C' and resid 621 through 626 Processing helix chain 'C' and resid 643 through 654 removed outlier: 3.588A pdb=" N VAL C 647 " --> pdb=" O PRO C 643 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL C 648 " --> pdb=" O ASP C 644 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU C 654 " --> pdb=" O LYS C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 672 Processing helix chain 'C' and resid 688 through 703 removed outlier: 3.510A pdb=" N LEU C 703 " --> pdb=" O GLU C 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 21 removed outlier: 3.936A pdb=" N LEU D 8 " --> pdb=" O ALA D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 47 removed outlier: 3.537A pdb=" N ARG D 33 " --> pdb=" O TYR D 29 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 74 Processing helix chain 'D' and resid 75 through 77 No H-bonds generated for 'chain 'D' and resid 75 through 77' Processing helix chain 'D' and resid 95 through 107 Processing helix chain 'D' and resid 120 through 135 removed outlier: 3.640A pdb=" N GLY D 135 " --> pdb=" O CYS D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 153 removed outlier: 3.847A pdb=" N PHE D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS D 153 " --> pdb=" O PHE D 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 148 through 153' Processing helix chain 'D' and resid 155 through 157 No H-bonds generated for 'chain 'D' and resid 155 through 157' Processing helix chain 'D' and resid 158 through 169 removed outlier: 3.780A pdb=" N SER D 168 " --> pdb=" O LEU D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 189 removed outlier: 3.668A pdb=" N GLU D 188 " --> pdb=" O ASP D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 198 Processing helix chain 'D' and resid 211 through 222 Processing helix chain 'D' and resid 227 through 244 removed outlier: 3.949A pdb=" N ILE D 244 " --> pdb=" O ASN D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 254 removed outlier: 4.213A pdb=" N ARG D 253 " --> pdb=" O TYR D 250 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN D 254 " --> pdb=" O PHE D 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 250 through 254' Processing helix chain 'D' and resid 264 through 280 Processing helix chain 'D' and resid 281 through 295 removed outlier: 3.658A pdb=" N ARG D 285 " --> pdb=" O THR D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 310 removed outlier: 3.645A pdb=" N LEU D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 333 removed outlier: 3.570A pdb=" N GLY D 333 " --> pdb=" O SER D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 341 Processing helix chain 'D' and resid 344 through 361 Processing helix chain 'D' and resid 367 through 380 removed outlier: 3.787A pdb=" N PHE D 378 " --> pdb=" O ARG D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 403 removed outlier: 3.580A pdb=" N VAL D 393 " --> pdb=" O GLU D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 443 removed outlier: 3.612A pdb=" N ILE D 436 " --> pdb=" O THR D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 456 removed outlier: 3.830A pdb=" N GLN D 455 " --> pdb=" O ALA D 451 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER D 456 " --> pdb=" O GLN D 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 12 Proline residue: E 10 - end of helix Processing helix chain 'E' and resid 15 through 27 Processing helix chain 'E' and resid 47 through 62 removed outlier: 3.555A pdb=" N THR E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 89 removed outlier: 3.818A pdb=" N MET E 80 " --> pdb=" O THR E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 96 removed outlier: 3.673A pdb=" N ALA E 95 " --> pdb=" O GLN E 92 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU E 96 " --> pdb=" O GLY E 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 92 through 96' Processing helix chain 'E' and resid 100 through 110 removed outlier: 3.743A pdb=" N ARG E 110 " --> pdb=" O GLU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 134 removed outlier: 3.918A pdb=" N ARG E 132 " --> pdb=" O GLU E 129 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET E 134 " --> pdb=" O LEU E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 143 Processing helix chain 'E' and resid 144 through 150 Processing helix chain 'E' and resid 162 through 166 Processing helix chain 'E' and resid 184 through 194 Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.590A pdb=" N GLU E 205 " --> pdb=" O ASN E 201 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN E 206 " --> pdb=" O GLN E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 220 removed outlier: 3.807A pdb=" N GLU E 219 " --> pdb=" O GLU E 215 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA E 220 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 238 removed outlier: 3.977A pdb=" N VAL E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 259 removed outlier: 4.000A pdb=" N LYS E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 265 Processing helix chain 'E' and resid 275 through 288 Proline residue: E 282 - end of helix removed outlier: 3.987A pdb=" N THR E 288 " --> pdb=" O ARG E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 338 Processing helix chain 'E' and resid 342 through 348 removed outlier: 3.958A pdb=" N VAL E 348 " --> pdb=" O LYS E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 394 removed outlier: 4.433A pdb=" N GLU E 394 " --> pdb=" O TYR E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 413 removed outlier: 4.171A pdb=" N LEU E 404 " --> pdb=" O THR E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 449 removed outlier: 3.594A pdb=" N VAL E 441 " --> pdb=" O GLY E 437 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 238 Processing helix chain 'A' and resid 520 through 529 Processing helix chain 'A' and resid 545 through 549 removed outlier: 3.571A pdb=" N SER A 548 " --> pdb=" O LYS A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 571 through 589 Processing helix chain 'A' and resid 603 through 621 removed outlier: 3.616A pdb=" N THR A 607 " --> pdb=" O GLY A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 637 No H-bonds generated for 'chain 'A' and resid 635 through 637' Processing helix chain 'A' and resid 639 through 641 No H-bonds generated for 'chain 'A' and resid 639 through 641' Processing helix chain 'A' and resid 642 through 650 removed outlier: 3.504A pdb=" N GLN A 650 " --> pdb=" O GLN A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 670 Processing helix chain 'A' and resid 685 through 690 removed outlier: 3.980A pdb=" N LEU A 689 " --> pdb=" O GLU A 685 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS A 690 " --> pdb=" O LEU A 686 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 685 through 690' Processing helix chain 'A' and resid 695 through 703 Processing helix chain 'A' and resid 704 through 706 No H-bonds generated for 'chain 'A' and resid 704 through 706' Processing helix chain 'A' and resid 721 through 726 removed outlier: 3.541A pdb=" N LEU A 726 " --> pdb=" O LEU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 736 removed outlier: 3.576A pdb=" N GLY A 736 " --> pdb=" O THR A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 759 removed outlier: 3.781A pdb=" N VAL A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A 759 " --> pdb=" O THR A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 777 removed outlier: 3.590A pdb=" N VAL A 769 " --> pdb=" O LYS A 765 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 800 removed outlier: 3.867A pdb=" N ALA A 786 " --> pdb=" O ASP A 782 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG A 791 " --> pdb=" O LEU A 787 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 799 " --> pdb=" O GLU A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 818 removed outlier: 3.514A pdb=" N VAL A 810 " --> pdb=" O THR A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 828 Processing helix chain 'A' and resid 830 through 848 removed outlier: 3.531A pdb=" N ALA A 841 " --> pdb=" O LEU A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 869 Processing helix chain 'A' and resid 874 through 888 removed outlier: 3.527A pdb=" N GLU A 888 " --> pdb=" O LYS A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 918 removed outlier: 3.580A pdb=" N ILE A 913 " --> pdb=" O SER A 909 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 260 removed outlier: 4.145A pdb=" N ASN G 260 " --> pdb=" O ARG G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 287 removed outlier: 3.507A pdb=" N SER G 287 " --> pdb=" O ASN G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 310 Processing helix chain 'G' and resid 313 through 319 Processing helix chain 'G' and resid 332 through 334 No H-bonds generated for 'chain 'G' and resid 332 through 334' Processing helix chain 'G' and resid 335 through 345 Processing helix chain 'G' and resid 352 through 366 removed outlier: 3.530A pdb=" N HIS G 356 " --> pdb=" O THR G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 378 through 382 removed outlier: 3.537A pdb=" N CYS G 382 " --> pdb=" O ASP G 379 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 393 Processing helix chain 'G' and resid 394 through 398 Processing helix chain 'G' and resid 413 through 418 Processing helix chain 'G' and resid 419 through 425 removed outlier: 3.527A pdb=" N ARG G 425 " --> pdb=" O LEU G 422 " (cutoff:3.500A) Processing helix chain 'G' and resid 439 through 453 removed outlier: 3.503A pdb=" N ILE G 443 " --> pdb=" O SER G 439 " (cutoff:3.500A) Processing helix chain 'G' and resid 456 through 460 removed outlier: 3.584A pdb=" N VAL G 459 " --> pdb=" O VAL G 456 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE G 460 " --> pdb=" O LEU G 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 456 through 460' Processing helix chain 'G' and resid 461 through 476 removed outlier: 3.566A pdb=" N LEU G 465 " --> pdb=" O PRO G 461 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA G 470 " --> pdb=" O GLN G 466 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA G 474 " --> pdb=" O ALA G 470 " (cutoff:3.500A) Processing helix chain 'G' and resid 478 through 498 removed outlier: 3.806A pdb=" N ALA G 482 " --> pdb=" O ASP G 478 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL G 490 " --> pdb=" O GLY G 486 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN G 495 " --> pdb=" O GLU G 491 " (cutoff:3.500A) Processing helix chain 'G' and resid 530 through 542 removed outlier: 3.519A pdb=" N VAL G 534 " --> pdb=" O GLN G 530 " (cutoff:3.500A) Processing helix chain 'G' and resid 557 through 574 Processing helix chain 'G' and resid 581 through 595 removed outlier: 3.613A pdb=" N VAL G 587 " --> pdb=" O ARG G 583 " (cutoff:3.500A) Processing helix chain 'G' and resid 601 through 614 removed outlier: 3.817A pdb=" N GLY G 607 " --> pdb=" O ALA G 603 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR G 614 " --> pdb=" O ASP G 610 " (cutoff:3.500A) Processing helix chain 'G' and resid 625 through 628 Processing helix chain 'G' and resid 636 through 645 removed outlier: 3.667A pdb=" N SER G 645 " --> pdb=" O HIS G 641 " (cutoff:3.500A) Processing helix chain 'G' and resid 646 through 655 removed outlier: 3.728A pdb=" N SER G 652 " --> pdb=" O GLN G 648 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER G 655 " --> pdb=" O ALA G 651 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 485 through 488 removed outlier: 6.196A pdb=" N ASN B 352 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TRP B 488 " --> pdb=" O ASN B 352 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU B 354 " --> pdb=" O TRP B 488 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR B 377 " --> pdb=" O PHE B 431 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE B 433 " --> pdb=" O THR B 377 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU B 379 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N HIS B 435 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B 381 " --> pdb=" O HIS B 435 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 588 through 590 Processing sheet with id=AA3, first strand: chain 'C' and resid 98 through 99 removed outlier: 6.188A pdb=" N MET C 128 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE C 208 " --> pdb=" O MET C 128 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N CYS C 130 " --> pdb=" O ILE C 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA5, first strand: chain 'C' and resid 291 through 292 removed outlier: 7.814A pdb=" N HIS C 291 " --> pdb=" O PHE C 596 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 658 through 659 removed outlier: 3.616A pdb=" N HIS C 715 " --> pdb=" O SER C 709 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 83 through 89 removed outlier: 6.692A pdb=" N VAL D 142 " --> pdb=" O CYS D 176 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU D 178 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N PHE D 144 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N VAL D 180 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU D 146 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN D 50 " --> pdb=" O ILE D 175 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 406 through 408 Processing sheet with id=AA9, first strand: chain 'E' and resid 64 through 70 removed outlier: 6.672A pdb=" N PHE E 121 " --> pdb=" O CYS E 154 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ILE E 156 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE E 123 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU E 158 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL E 125 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE E 37 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N SER E 159 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU E 39 " --> pdb=" O SER E 159 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ALA E 36 " --> pdb=" O VAL E 176 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N LEU E 178 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N TYR E 38 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU E 180 " --> pdb=" O TYR E 38 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE E 40 " --> pdb=" O LEU E 180 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 416 through 420 removed outlier: 7.032A pdb=" N ARG E 431 " --> pdb=" O VAL E 419 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 627 through 633 removed outlier: 6.489A pdb=" N GLY A 592 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N THR A 715 " --> pdb=" O GLY A 592 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N MET A 594 " --> pdb=" O THR A 715 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ALA A 717 " --> pdb=" O MET A 594 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL A 596 " --> pdb=" O ALA A 717 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N LEU A 740 " --> pdb=" O CYS A 593 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TYR A 595 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N PHE A 742 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER A 597 " --> pdb=" O PHE A 742 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 852 through 853 Processing sheet with id=AB4, first strand: chain 'G' and resid 320 through 326 removed outlier: 6.795A pdb=" N LEU G 293 " --> pdb=" O GLY G 407 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N ALA G 409 " --> pdb=" O LEU G 293 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL G 295 " --> pdb=" O ALA G 409 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TYR G 294 " --> pdb=" O MET G 433 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N PHE G 435 " --> pdb=" O TYR G 294 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N SER G 296 " --> pdb=" O PHE G 435 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 579 through 580 removed outlier: 4.453A pdb=" N ILE G 579 " --> pdb=" O VAL G 631 " (cutoff:3.500A) 1069 hydrogen bonds defined for protein. 3126 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 68 stacking parallelities Total time for adding SS restraints: 7.84 Time building geometry restraints manager: 5.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5797 1.33 - 1.46: 4953 1.46 - 1.58: 11194 1.58 - 1.70: 157 1.70 - 1.83: 163 Bond restraints: 22264 Sorted by residual: bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.34e+01 bond pdb=" C4 ATP E 901 " pdb=" C5 ATP E 901 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.07e+01 bond pdb=" C4 ATP A1001 " pdb=" C5 ATP A1001 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.02e+01 bond pdb=" C4 ATP G 901 " pdb=" C5 ATP G 901 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.93e+01 bond pdb=" C5 ATP E 901 " pdb=" C6 ATP E 901 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.39e+01 ... (remaining 22259 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.86: 30182 3.86 - 7.72: 184 7.72 - 11.58: 27 11.58 - 15.44: 3 15.44 - 19.30: 4 Bond angle restraints: 30400 Sorted by residual: angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 120.57 19.30 1.00e+00 1.00e+00 3.72e+02 angle pdb=" PB ATP G 901 " pdb=" O3B ATP G 901 " pdb=" PG ATP G 901 " ideal model delta sigma weight residual 139.87 121.67 18.20 1.00e+00 1.00e+00 3.31e+02 angle pdb=" PA ATP A1001 " pdb=" O3A ATP A1001 " pdb=" PB ATP A1001 " ideal model delta sigma weight residual 136.83 119.26 17.57 1.00e+00 1.00e+00 3.09e+02 angle pdb=" PB ATP E 901 " pdb=" O3B ATP E 901 " pdb=" PG ATP E 901 " ideal model delta sigma weight residual 139.87 124.37 15.50 1.00e+00 1.00e+00 2.40e+02 angle pdb=" PA ATP E 901 " pdb=" O3A ATP E 901 " pdb=" PB ATP E 901 " ideal model delta sigma weight residual 136.83 121.59 15.24 1.00e+00 1.00e+00 2.32e+02 ... (remaining 30395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 11482 17.97 - 35.94: 1379 35.94 - 53.91: 527 53.91 - 71.89: 102 71.89 - 89.86: 36 Dihedral angle restraints: 13526 sinusoidal: 6113 harmonic: 7413 Sorted by residual: dihedral pdb=" CA LEU G 259 " pdb=" C LEU G 259 " pdb=" N ASN G 260 " pdb=" CA ASN G 260 " ideal model delta harmonic sigma weight residual 180.00 149.83 30.17 0 5.00e+00 4.00e-02 3.64e+01 dihedral pdb=" CA MET E 134 " pdb=" C MET E 134 " pdb=" N ASP E 135 " pdb=" CA ASP E 135 " ideal model delta harmonic sigma weight residual -180.00 -150.35 -29.65 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA MET C 128 " pdb=" C MET C 128 " pdb=" N VAL C 129 " pdb=" CA VAL C 129 " ideal model delta harmonic sigma weight residual -180.00 -156.62 -23.38 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 13523 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2320 0.042 - 0.084: 876 0.084 - 0.127: 233 0.127 - 0.169: 63 0.169 - 0.211: 16 Chirality restraints: 3508 Sorted by residual: chirality pdb=" CB ILE C 590 " pdb=" CA ILE C 590 " pdb=" CG1 ILE C 590 " pdb=" CG2 ILE C 590 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+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 -2.42 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB ILE C 5 " pdb=" CA ILE C 5 " pdb=" CG1 ILE C 5 " pdb=" CG2 ILE C 5 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 3505 not shown) Planarity restraints: 3607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 872 " 0.059 5.00e-02 4.00e+02 8.90e-02 1.27e+01 pdb=" N PRO A 873 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 873 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 873 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 587 " -0.057 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO C 588 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO C 588 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 588 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 9 " -0.050 5.00e-02 4.00e+02 7.48e-02 8.96e+00 pdb=" N PRO E 10 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO E 10 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 10 " -0.042 5.00e-02 4.00e+02 ... (remaining 3604 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.09: 7 2.09 - 2.80: 5303 2.80 - 3.50: 27585 3.50 - 4.20: 52196 4.20 - 4.90: 91105 Nonbonded interactions: 176196 Sorted by model distance: nonbonded pdb=" NH1 ARG C 711 " pdb=" C4' DA I 44 " model vdw 1.392 3.550 nonbonded pdb=" NH1 ARG C 711 " pdb=" O3' DA I 44 " model vdw 1.479 3.120 nonbonded pdb=" NH1 ARG C 711 " pdb=" C3' DA I 44 " model vdw 1.628 3.550 nonbonded pdb=" OG SER C 709 " pdb=" O HIS C 715 " model vdw 2.031 3.040 nonbonded pdb=" OG1 THR E 48 " pdb="MG MG E 902 " model vdw 2.068 2.170 ... (remaining 176191 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.830 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 49.550 Find NCS groups from input model: 0.310 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: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 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 0.080 22264 Z= 0.340 Angle : 0.938 19.298 30400 Z= 0.583 Chirality : 0.049 0.211 3508 Planarity : 0.007 0.089 3607 Dihedral : 18.330 89.857 8686 Min Nonbonded Distance : 1.392 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.18 % Allowed : 6.18 % Favored : 93.64 % 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: -3.49 (0.13), residues: 2478 helix: -2.42 (0.09), residues: 1450 sheet: -2.18 (0.28), residues: 228 loop : -1.65 (0.18), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 664 HIS 0.009 0.001 HIS C 652 PHE 0.019 0.002 PHE G 447 TYR 0.021 0.002 TYR E 323 ARG 0.010 0.001 ARG G 322 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 306 time to evaluate : 2.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 540 TYR cc_start: 0.7672 (t80) cc_final: 0.7307 (t80) REVERT: B 562 CYS cc_start: 0.8065 (m) cc_final: 0.7777 (m) REVERT: B 583 ASP cc_start: 0.8326 (t70) cc_final: 0.7846 (m-30) REVERT: B 584 HIS cc_start: 0.8122 (m90) cc_final: 0.7880 (m170) REVERT: C 398 LEU cc_start: 0.8588 (tp) cc_final: 0.8335 (tt) REVERT: C 435 ASN cc_start: 0.9079 (m-40) cc_final: 0.8838 (t0) REVERT: C 443 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7903 (mm-30) REVERT: C 450 MET cc_start: 0.8680 (mtp) cc_final: 0.7823 (mtp) REVERT: C 451 LEU cc_start: 0.9276 (mt) cc_final: 0.8723 (pp) REVERT: C 457 ASP cc_start: 0.8536 (p0) cc_final: 0.8297 (p0) REVERT: C 699 GLU cc_start: 0.8014 (tt0) cc_final: 0.7453 (mt-10) REVERT: D 185 ASP cc_start: 0.8212 (p0) cc_final: 0.8007 (p0) REVERT: D 347 GLU cc_start: 0.9057 (mp0) cc_final: 0.8577 (mp0) REVERT: D 389 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8001 (mt-10) REVERT: D 426 MET cc_start: 0.8648 (mmm) cc_final: 0.8291 (mmm) REVERT: E 414 ASN cc_start: 0.8993 (t0) cc_final: 0.8636 (p0) REVERT: E 417 SER cc_start: 0.9075 (t) cc_final: 0.8689 (p) REVERT: F 224 ASP cc_start: 0.8881 (t70) cc_final: 0.8235 (p0) REVERT: F 226 GLU cc_start: 0.9235 (mm-30) cc_final: 0.8876 (mp0) REVERT: F 231 ARG cc_start: 0.9049 (ttp80) cc_final: 0.8734 (ttp80) REVERT: F 232 MET cc_start: 0.9345 (tpt) cc_final: 0.9068 (tpp) REVERT: A 618 MET cc_start: 0.8498 (mtp) cc_final: 0.8135 (mtt) REVERT: G 345 GLN cc_start: 0.8993 (mp10) cc_final: 0.8744 (mp10) REVERT: G 570 MET cc_start: 0.7777 (mtp) cc_final: 0.7518 (mtp) outliers start: 4 outliers final: 1 residues processed: 310 average time/residue: 0.4201 time to fit residues: 187.4888 Evaluate side-chains 171 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 170 time to evaluate : 2.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 1.9990 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 232 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 325 HIS B 366 GLN B 429 HIS B 436 ASN B 544 ASN B 609 GLN C 46 GLN C 133 GLN C 194 ASN C 370 ASN C 449 GLN ** C 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN C 666 GLN D 202 GLN ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 HIS ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 838 GLN G 260 ASN G 356 HIS G 410 ASN G 530 GLN G 573 ASN G 585 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22264 Z= 0.160 Angle : 0.552 9.545 30400 Z= 0.299 Chirality : 0.038 0.168 3508 Planarity : 0.005 0.061 3607 Dihedral : 17.469 87.625 3716 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.08 % Allowed : 9.60 % Favored : 89.31 % 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: -0.91 (0.16), residues: 2478 helix: -0.12 (0.12), residues: 1456 sheet: -1.67 (0.30), residues: 238 loop : -0.89 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 664 HIS 0.004 0.001 HIS C 715 PHE 0.021 0.001 PHE C 459 TYR 0.019 0.001 TYR C 255 ARG 0.008 0.000 ARG C 419 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 187 time to evaluate : 2.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 519 MET cc_start: 0.8257 (tmm) cc_final: 0.8036 (tmm) REVERT: B 540 TYR cc_start: 0.7626 (t80) cc_final: 0.7361 (t80) REVERT: B 564 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8623 (mm-30) REVERT: B 584 HIS cc_start: 0.8021 (m90) cc_final: 0.7496 (m-70) REVERT: C 185 MET cc_start: 0.8605 (mmm) cc_final: 0.8221 (mmm) REVERT: C 435 ASN cc_start: 0.9105 (m-40) cc_final: 0.8823 (t0) REVERT: C 457 ASP cc_start: 0.8502 (p0) cc_final: 0.8265 (p0) REVERT: C 699 GLU cc_start: 0.7842 (tt0) cc_final: 0.7091 (mt-10) REVERT: D 185 ASP cc_start: 0.8153 (p0) cc_final: 0.7896 (p0) REVERT: D 347 GLU cc_start: 0.9114 (mp0) cc_final: 0.8769 (mp0) REVERT: D 389 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7972 (mt-10) REVERT: D 426 MET cc_start: 0.8740 (mmm) cc_final: 0.8367 (mmm) REVERT: E 254 CYS cc_start: 0.8372 (m) cc_final: 0.7866 (t) REVERT: E 417 SER cc_start: 0.8802 (t) cc_final: 0.8262 (p) REVERT: E 455 TYR cc_start: 0.8730 (m-80) cc_final: 0.8493 (m-80) REVERT: F 227 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8007 (pt) REVERT: A 775 LYS cc_start: 0.9116 (mttt) cc_final: 0.8848 (mptt) REVERT: G 345 GLN cc_start: 0.9013 (mp10) cc_final: 0.8723 (mp10) outliers start: 24 outliers final: 14 residues processed: 203 average time/residue: 0.3578 time to fit residues: 112.1584 Evaluate side-chains 172 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 157 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 75 TYR Chi-restraints excluded: chain E residue 412 HIS Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain G residue 464 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 0.0770 chunk 72 optimal weight: 5.9990 chunk 193 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 232 optimal weight: 3.9990 chunk 251 optimal weight: 8.9990 chunk 207 optimal weight: 0.8980 chunk 230 optimal weight: 0.4980 chunk 79 optimal weight: 10.0000 chunk 186 optimal weight: 0.6980 overall best weight: 1.2340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN A 553 GLN A 622 ASN ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22264 Z= 0.171 Angle : 0.521 8.473 30400 Z= 0.279 Chirality : 0.037 0.161 3508 Planarity : 0.004 0.052 3607 Dihedral : 17.422 83.488 3716 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.31 % Allowed : 10.87 % Favored : 87.83 % 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: 0.37 (0.17), residues: 2478 helix: 0.98 (0.14), residues: 1465 sheet: -1.25 (0.32), residues: 238 loop : -0.51 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 191 HIS 0.003 0.001 HIS E 278 PHE 0.016 0.001 PHE C 459 TYR 0.020 0.001 TYR C 255 ARG 0.006 0.000 ARG C 419 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 173 time to evaluate : 2.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9199 (tpp) cc_final: 0.8939 (mmm) REVERT: B 391 LYS cc_start: 0.8964 (tptt) cc_final: 0.8401 (tptt) REVERT: B 395 ASP cc_start: 0.8384 (m-30) cc_final: 0.8114 (m-30) REVERT: B 540 TYR cc_start: 0.7555 (t80) cc_final: 0.7351 (t80) REVERT: B 584 HIS cc_start: 0.7955 (m90) cc_final: 0.7324 (m-70) REVERT: C 185 MET cc_start: 0.8850 (mmm) cc_final: 0.8317 (mmm) REVERT: C 323 MET cc_start: 0.8847 (ttp) cc_final: 0.8644 (ttp) REVERT: C 419 ARG cc_start: 0.7365 (ttp80) cc_final: 0.7116 (ttp80) REVERT: C 435 ASN cc_start: 0.9126 (m-40) cc_final: 0.8826 (t0) REVERT: C 446 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8149 (tp30) REVERT: C 457 ASP cc_start: 0.8361 (p0) cc_final: 0.8136 (p0) REVERT: C 699 GLU cc_start: 0.7932 (tt0) cc_final: 0.7159 (mt-10) REVERT: D 347 GLU cc_start: 0.9084 (mp0) cc_final: 0.8793 (mp0) REVERT: D 426 MET cc_start: 0.8721 (mmm) cc_final: 0.8340 (mmm) REVERT: D 440 MET cc_start: 0.8651 (mmm) cc_final: 0.8352 (mmm) REVERT: E 254 CYS cc_start: 0.8357 (m) cc_final: 0.7936 (t) REVERT: E 412 HIS cc_start: 0.8405 (OUTLIER) cc_final: 0.8185 (m-70) REVERT: E 417 SER cc_start: 0.8847 (t) cc_final: 0.8294 (p) REVERT: E 455 TYR cc_start: 0.8791 (m-80) cc_final: 0.8552 (m-80) REVERT: A 775 LYS cc_start: 0.9101 (mttt) cc_final: 0.8848 (mptt) REVERT: G 345 GLN cc_start: 0.9029 (mp10) cc_final: 0.8750 (mp10) outliers start: 29 outliers final: 13 residues processed: 191 average time/residue: 0.3413 time to fit residues: 100.8452 Evaluate side-chains 174 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 160 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 75 TYR Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 412 HIS Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain G residue 464 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 3.9990 chunk 175 optimal weight: 10.0000 chunk 120 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 111 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 233 optimal weight: 1.9990 chunk 247 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 221 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 113 GLN ** C 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 ASN A 622 ASN ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22264 Z= 0.181 Angle : 0.516 13.107 30400 Z= 0.272 Chirality : 0.037 0.159 3508 Planarity : 0.004 0.050 3607 Dihedral : 17.269 80.434 3714 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.40 % Allowed : 11.72 % Favored : 86.88 % 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: 1.07 (0.17), residues: 2478 helix: 1.56 (0.14), residues: 1467 sheet: -0.97 (0.33), residues: 238 loop : -0.27 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 191 HIS 0.003 0.001 HIS G 284 PHE 0.012 0.001 PHE C 459 TYR 0.015 0.001 TYR C 384 ARG 0.006 0.000 ARG D 253 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 166 time to evaluate : 2.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9214 (tpp) cc_final: 0.8959 (mmm) REVERT: B 391 LYS cc_start: 0.8979 (tptt) cc_final: 0.8385 (tptt) REVERT: B 395 ASP cc_start: 0.8379 (m-30) cc_final: 0.7883 (m-30) REVERT: B 540 TYR cc_start: 0.7523 (t80) cc_final: 0.7277 (t80) REVERT: B 584 HIS cc_start: 0.7973 (m90) cc_final: 0.7632 (m-70) REVERT: C 72 TYR cc_start: 0.8312 (t80) cc_final: 0.8102 (t80) REVERT: C 323 MET cc_start: 0.8873 (ttp) cc_final: 0.8653 (ttp) REVERT: C 435 ASN cc_start: 0.9152 (m-40) cc_final: 0.8832 (t0) REVERT: C 446 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8144 (tp30) REVERT: C 450 MET cc_start: 0.8417 (mtp) cc_final: 0.5790 (mtp) REVERT: C 457 ASP cc_start: 0.8281 (p0) cc_final: 0.8011 (p0) REVERT: D 253 ARG cc_start: 0.8377 (tpt90) cc_final: 0.7862 (tpt-90) REVERT: D 347 GLU cc_start: 0.9096 (mp0) cc_final: 0.8780 (mp0) REVERT: D 426 MET cc_start: 0.8743 (mmm) cc_final: 0.8366 (mmm) REVERT: E 254 CYS cc_start: 0.8305 (m) cc_final: 0.7902 (t) REVERT: E 412 HIS cc_start: 0.8419 (OUTLIER) cc_final: 0.8206 (m-70) REVERT: E 417 SER cc_start: 0.8824 (t) cc_final: 0.8269 (p) REVERT: E 455 TYR cc_start: 0.8856 (m-80) cc_final: 0.8616 (m-80) REVERT: A 775 LYS cc_start: 0.9128 (mttt) cc_final: 0.8860 (mptt) REVERT: G 345 GLN cc_start: 0.9017 (mp10) cc_final: 0.8640 (mp10) outliers start: 31 outliers final: 19 residues processed: 189 average time/residue: 0.3401 time to fit residues: 101.0137 Evaluate side-chains 172 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 152 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 429 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 291 LEU Chi-restraints excluded: chain E residue 75 TYR Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 412 HIS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 464 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 7.9990 chunk 140 optimal weight: 0.5980 chunk 3 optimal weight: 0.0060 chunk 184 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 211 optimal weight: 0.6980 chunk 171 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 222 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 overall best weight: 1.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 580 HIS D 82 ASN ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22264 Z= 0.202 Angle : 0.525 12.339 30400 Z= 0.275 Chirality : 0.038 0.153 3508 Planarity : 0.003 0.047 3607 Dihedral : 17.170 81.498 3714 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.40 % Allowed : 12.76 % Favored : 85.84 % 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: 1.39 (0.18), residues: 2478 helix: 1.83 (0.14), residues: 1472 sheet: -0.82 (0.33), residues: 238 loop : -0.16 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 276 HIS 0.004 0.001 HIS G 284 PHE 0.010 0.001 PHE C 400 TYR 0.014 0.001 TYR C 384 ARG 0.006 0.000 ARG F 231 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 157 time to evaluate : 2.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9222 (tpp) cc_final: 0.8968 (mmm) REVERT: B 391 LYS cc_start: 0.8960 (tptt) cc_final: 0.8754 (tptt) REVERT: B 519 MET cc_start: 0.8159 (tmm) cc_final: 0.7905 (tmm) REVERT: B 540 TYR cc_start: 0.7531 (t80) cc_final: 0.7260 (t80) REVERT: B 584 HIS cc_start: 0.7985 (m90) cc_final: 0.7634 (m-70) REVERT: C 323 MET cc_start: 0.8893 (ttp) cc_final: 0.8678 (ttp) REVERT: C 443 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8016 (mm-30) REVERT: C 457 ASP cc_start: 0.8278 (p0) cc_final: 0.8025 (p0) REVERT: D 347 GLU cc_start: 0.9073 (mp0) cc_final: 0.8725 (mp0) REVERT: D 426 MET cc_start: 0.8750 (mmm) cc_final: 0.8351 (mmm) REVERT: E 254 CYS cc_start: 0.8295 (m) cc_final: 0.7915 (t) REVERT: E 412 HIS cc_start: 0.8473 (OUTLIER) cc_final: 0.8263 (m-70) REVERT: E 417 SER cc_start: 0.8808 (t) cc_final: 0.8249 (p) REVERT: E 455 TYR cc_start: 0.8897 (m-80) cc_final: 0.8652 (m-80) REVERT: A 618 MET cc_start: 0.8999 (mtm) cc_final: 0.8770 (mtm) REVERT: A 775 LYS cc_start: 0.9158 (mttt) cc_final: 0.8886 (mptt) REVERT: G 345 GLN cc_start: 0.8999 (mp10) cc_final: 0.8671 (mp10) REVERT: G 621 MET cc_start: 0.7836 (mtt) cc_final: 0.7540 (mtt) outliers start: 31 outliers final: 21 residues processed: 180 average time/residue: 0.3410 time to fit residues: 96.9649 Evaluate side-chains 173 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 151 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 429 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 227 THR Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain E residue 75 TYR Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 412 HIS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 738 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 464 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 7.9990 chunk 222 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 247 optimal weight: 7.9990 chunk 205 optimal weight: 0.9990 chunk 114 optimal weight: 0.5980 chunk 20 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 chunk 130 optimal weight: 0.4980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 348 ASN ** B 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 HIS ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 260 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 22264 Z= 0.156 Angle : 0.508 13.359 30400 Z= 0.264 Chirality : 0.037 0.152 3508 Planarity : 0.003 0.046 3607 Dihedral : 17.078 82.662 3714 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.31 % Allowed : 13.21 % Favored : 85.48 % 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: 1.61 (0.18), residues: 2478 helix: 2.00 (0.14), residues: 1466 sheet: -0.59 (0.34), residues: 229 loop : -0.12 (0.23), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 191 HIS 0.004 0.001 HIS G 284 PHE 0.009 0.001 PHE C 459 TYR 0.013 0.001 TYR C 384 ARG 0.006 0.000 ARG F 231 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 167 time to evaluate : 2.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9222 (tpp) cc_final: 0.8963 (mmm) REVERT: B 391 LYS cc_start: 0.8943 (tptt) cc_final: 0.8697 (tptt) REVERT: B 519 MET cc_start: 0.8211 (tmm) cc_final: 0.7937 (tmm) REVERT: B 540 TYR cc_start: 0.7664 (t80) cc_final: 0.7359 (t80) REVERT: B 584 HIS cc_start: 0.7996 (m90) cc_final: 0.7635 (m-70) REVERT: C 72 TYR cc_start: 0.8251 (t80) cc_final: 0.8026 (t80) REVERT: C 185 MET cc_start: 0.8680 (mmm) cc_final: 0.8193 (mmm) REVERT: C 298 LYS cc_start: 0.9153 (tttt) cc_final: 0.8898 (tptp) REVERT: C 323 MET cc_start: 0.8904 (ttp) cc_final: 0.8696 (ttp) REVERT: C 443 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8032 (mm-30) REVERT: C 457 ASP cc_start: 0.8323 (p0) cc_final: 0.8081 (p0) REVERT: C 699 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7102 (mm-30) REVERT: D 253 ARG cc_start: 0.8433 (tpt90) cc_final: 0.8231 (tpt90) REVERT: D 347 GLU cc_start: 0.9021 (mp0) cc_final: 0.8704 (mp0) REVERT: D 426 MET cc_start: 0.8783 (mmm) cc_final: 0.8410 (mmm) REVERT: E 254 CYS cc_start: 0.8246 (m) cc_final: 0.7922 (t) REVERT: E 412 HIS cc_start: 0.8458 (OUTLIER) cc_final: 0.8230 (m-70) REVERT: E 417 SER cc_start: 0.8803 (t) cc_final: 0.8282 (m) REVERT: E 455 TYR cc_start: 0.8885 (m-80) cc_final: 0.8617 (m-80) REVERT: A 775 LYS cc_start: 0.9158 (mttt) cc_final: 0.8880 (mptt) REVERT: G 345 GLN cc_start: 0.8984 (mp10) cc_final: 0.8774 (mp10) REVERT: G 621 MET cc_start: 0.7885 (mtt) cc_final: 0.7633 (mtt) outliers start: 29 outliers final: 21 residues processed: 188 average time/residue: 0.3304 time to fit residues: 98.7810 Evaluate side-chains 176 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 154 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain C residue 658 MET Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain E residue 75 TYR Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 412 HIS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain G residue 464 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 141 optimal weight: 2.9990 chunk 180 optimal weight: 0.3980 chunk 140 optimal weight: 0.6980 chunk 208 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 246 optimal weight: 4.9990 chunk 154 optimal weight: 9.9990 chunk 150 optimal weight: 8.9990 chunk 113 optimal weight: 10.0000 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22264 Z= 0.212 Angle : 0.538 13.259 30400 Z= 0.278 Chirality : 0.038 0.166 3508 Planarity : 0.003 0.047 3607 Dihedral : 17.022 82.452 3714 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.40 % Allowed : 13.66 % Favored : 84.94 % 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: 1.74 (0.18), residues: 2478 helix: 2.04 (0.14), residues: 1476 sheet: -0.46 (0.35), residues: 226 loop : -0.00 (0.24), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 664 HIS 0.005 0.001 HIS C 230 PHE 0.010 0.001 PHE D 368 TYR 0.011 0.001 TYR B 496 ARG 0.006 0.000 ARG F 231 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 154 time to evaluate : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9228 (tpp) cc_final: 0.8964 (mmm) REVERT: B 503 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7687 (pm20) REVERT: B 540 TYR cc_start: 0.7628 (t80) cc_final: 0.7358 (t80) REVERT: B 584 HIS cc_start: 0.8052 (m90) cc_final: 0.7699 (m-70) REVERT: C 185 MET cc_start: 0.8903 (mmm) cc_final: 0.8304 (mmm) REVERT: C 298 LYS cc_start: 0.9140 (tttt) cc_final: 0.8895 (tptp) REVERT: C 443 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8040 (mm-30) REVERT: C 457 ASP cc_start: 0.8371 (p0) cc_final: 0.8127 (p0) REVERT: D 347 GLU cc_start: 0.9037 (mp0) cc_final: 0.8705 (mp0) REVERT: D 426 MET cc_start: 0.8778 (mmm) cc_final: 0.8348 (mmm) REVERT: E 254 CYS cc_start: 0.8266 (m) cc_final: 0.7953 (t) REVERT: E 412 HIS cc_start: 0.8469 (OUTLIER) cc_final: 0.8248 (m-70) REVERT: E 417 SER cc_start: 0.8813 (t) cc_final: 0.8314 (m) REVERT: A 775 LYS cc_start: 0.9183 (mttt) cc_final: 0.8909 (mptt) REVERT: G 345 GLN cc_start: 0.9005 (mp10) cc_final: 0.8790 (mp10) REVERT: G 621 MET cc_start: 0.7872 (mtt) cc_final: 0.7608 (mtt) outliers start: 31 outliers final: 23 residues processed: 176 average time/residue: 0.3292 time to fit residues: 91.3760 Evaluate side-chains 173 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain C residue 658 MET Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain E residue 75 TYR Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 412 HIS 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 464 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 147 optimal weight: 0.8980 chunk 74 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 156 optimal weight: 7.9990 chunk 168 optimal weight: 0.9990 chunk 121 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 193 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22264 Z= 0.140 Angle : 0.518 13.309 30400 Z= 0.267 Chirality : 0.037 0.153 3508 Planarity : 0.003 0.045 3607 Dihedral : 16.929 83.598 3714 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.22 % Allowed : 13.84 % Favored : 84.94 % 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: 1.85 (0.18), residues: 2478 helix: 2.16 (0.14), residues: 1466 sheet: -0.43 (0.34), residues: 234 loop : 0.03 (0.24), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 276 HIS 0.004 0.000 HIS G 284 PHE 0.021 0.001 PHE B 611 TYR 0.020 0.001 TYR C 72 ARG 0.008 0.000 ARG G 575 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 156 time to evaluate : 2.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9223 (tpp) cc_final: 0.8954 (mmm) REVERT: B 417 MET cc_start: 0.8571 (tmm) cc_final: 0.8221 (tmm) REVERT: B 503 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7696 (pm20) REVERT: B 540 TYR cc_start: 0.7632 (t80) cc_final: 0.7382 (t80) REVERT: B 584 HIS cc_start: 0.8063 (m90) cc_final: 0.7712 (m-70) REVERT: C 72 TYR cc_start: 0.8175 (t80) cc_final: 0.7879 (t80) REVERT: C 185 MET cc_start: 0.8834 (mmm) cc_final: 0.8214 (mmm) REVERT: C 298 LYS cc_start: 0.9117 (tttt) cc_final: 0.8895 (tptp) REVERT: C 443 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8047 (mm-30) REVERT: C 457 ASP cc_start: 0.8361 (p0) cc_final: 0.8116 (p0) REVERT: D 253 ARG cc_start: 0.8355 (tpt90) cc_final: 0.7685 (tpt-90) REVERT: D 347 GLU cc_start: 0.9002 (mp0) cc_final: 0.8690 (mp0) REVERT: D 426 MET cc_start: 0.8801 (mmm) cc_final: 0.8406 (mmm) REVERT: E 254 CYS cc_start: 0.8217 (m) cc_final: 0.7929 (t) REVERT: A 618 MET cc_start: 0.8961 (mtm) cc_final: 0.8755 (mtt) REVERT: A 775 LYS cc_start: 0.9154 (mttt) cc_final: 0.8888 (mptt) REVERT: G 345 GLN cc_start: 0.8987 (mp10) cc_final: 0.8785 (mp10) REVERT: G 621 MET cc_start: 0.7806 (mtt) cc_final: 0.7548 (mtt) outliers start: 27 outliers final: 22 residues processed: 174 average time/residue: 0.3260 time to fit residues: 90.4479 Evaluate side-chains 171 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain C residue 658 MET Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain E residue 75 TYR Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 464 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 3.9990 chunk 236 optimal weight: 9.9990 chunk 215 optimal weight: 6.9990 chunk 229 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 180 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 207 optimal weight: 0.9990 chunk 217 optimal weight: 0.9990 chunk 150 optimal weight: 8.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22264 Z= 0.225 Angle : 0.548 14.112 30400 Z= 0.281 Chirality : 0.038 0.155 3508 Planarity : 0.003 0.047 3607 Dihedral : 16.916 83.154 3714 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.31 % Allowed : 14.16 % Favored : 84.54 % 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: 1.90 (0.18), residues: 2478 helix: 2.16 (0.14), residues: 1471 sheet: -0.32 (0.35), residues: 226 loop : 0.10 (0.24), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 664 HIS 0.005 0.001 HIS C 230 PHE 0.016 0.001 PHE B 611 TYR 0.017 0.001 TYR C 72 ARG 0.008 0.000 ARG F 231 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 149 time to evaluate : 2.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9224 (tpp) cc_final: 0.8951 (mmm) REVERT: B 417 MET cc_start: 0.8588 (tmm) cc_final: 0.8228 (tmm) REVERT: B 503 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7692 (pm20) REVERT: B 540 TYR cc_start: 0.7627 (t80) cc_final: 0.7371 (t80) REVERT: B 584 HIS cc_start: 0.8082 (m90) cc_final: 0.7740 (m-70) REVERT: C 298 LYS cc_start: 0.9130 (tttt) cc_final: 0.8893 (tptp) REVERT: C 443 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8032 (mm-30) REVERT: C 457 ASP cc_start: 0.8384 (p0) cc_final: 0.8119 (p0) REVERT: D 253 ARG cc_start: 0.8376 (tpt90) cc_final: 0.7876 (tpt-90) REVERT: D 347 GLU cc_start: 0.9038 (mp0) cc_final: 0.8696 (mp0) REVERT: D 426 MET cc_start: 0.8809 (mmm) cc_final: 0.8386 (mmm) REVERT: E 254 CYS cc_start: 0.8244 (m) cc_final: 0.7932 (t) REVERT: G 345 GLN cc_start: 0.9020 (mp10) cc_final: 0.8807 (mp10) REVERT: G 621 MET cc_start: 0.7876 (mtt) cc_final: 0.7599 (mtt) outliers start: 29 outliers final: 24 residues processed: 172 average time/residue: 0.3256 time to fit residues: 88.6586 Evaluate side-chains 169 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 144 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain C residue 658 MET Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 464 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 6.9990 chunk 148 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 chunk 255 optimal weight: 10.0000 chunk 234 optimal weight: 3.9990 chunk 203 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 chunk 156 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 161 optimal weight: 9.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 325 HIS ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22264 Z= 0.189 Angle : 0.540 14.490 30400 Z= 0.278 Chirality : 0.037 0.152 3508 Planarity : 0.003 0.046 3607 Dihedral : 16.898 83.247 3714 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.22 % Allowed : 14.25 % Favored : 84.54 % 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: 1.93 (0.18), residues: 2478 helix: 2.16 (0.14), residues: 1478 sheet: -0.30 (0.35), residues: 226 loop : 0.13 (0.24), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 721 HIS 0.004 0.001 HIS C 230 PHE 0.017 0.001 PHE B 611 TYR 0.016 0.001 TYR C 72 ARG 0.009 0.000 ARG G 575 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 150 time to evaluate : 2.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9222 (tpp) cc_final: 0.8947 (mmm) REVERT: B 503 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7660 (pm20) REVERT: B 540 TYR cc_start: 0.7581 (t80) cc_final: 0.7282 (t80) REVERT: B 584 HIS cc_start: 0.8078 (m90) cc_final: 0.7732 (m-70) REVERT: C 185 MET cc_start: 0.8622 (mmm) cc_final: 0.8169 (mmm) REVERT: C 298 LYS cc_start: 0.9123 (tttt) cc_final: 0.8889 (tptp) REVERT: C 443 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8012 (mm-30) REVERT: C 457 ASP cc_start: 0.8337 (p0) cc_final: 0.8074 (p0) REVERT: D 253 ARG cc_start: 0.8394 (tpt90) cc_final: 0.7895 (tpt-90) REVERT: D 347 GLU cc_start: 0.9027 (mp0) cc_final: 0.8690 (mp0) REVERT: D 426 MET cc_start: 0.8816 (mmm) cc_final: 0.8400 (mmm) REVERT: E 254 CYS cc_start: 0.8238 (m) cc_final: 0.7946 (t) REVERT: A 790 CYS cc_start: 0.8867 (m) cc_final: 0.8623 (m) REVERT: G 345 GLN cc_start: 0.9010 (mp10) cc_final: 0.8806 (mp10) REVERT: G 621 MET cc_start: 0.7845 (mtt) cc_final: 0.7585 (mtt) outliers start: 27 outliers final: 23 residues processed: 171 average time/residue: 0.3354 time to fit residues: 89.8092 Evaluate side-chains 167 residues out of total 2219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 143 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain C residue 658 MET Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 439 CYS Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain G residue 464 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 187 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 203 optimal weight: 8.9990 chunk 85 optimal weight: 0.6980 chunk 208 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 325 HIS ** B 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.087423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.062814 restraints weight = 57700.714| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.18 r_work: 0.2972 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22264 Z= 0.178 Angle : 0.542 14.688 30400 Z= 0.278 Chirality : 0.037 0.150 3508 Planarity : 0.003 0.061 3607 Dihedral : 16.854 83.757 3714 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.35 % Allowed : 14.07 % Favored : 84.58 % 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: 1.96 (0.18), residues: 2478 helix: 2.19 (0.14), residues: 1473 sheet: -0.25 (0.35), residues: 226 loop : 0.14 (0.24), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 664 HIS 0.004 0.001 HIS C 230 PHE 0.016 0.001 PHE B 611 TYR 0.021 0.001 TYR B 496 ARG 0.009 0.000 ARG A 675 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3888.24 seconds wall clock time: 70 minutes 37.01 seconds (4237.01 seconds total)