Starting phenix.real_space_refine on Sun Feb 18 10:41:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgr_22329/02_2024/7jgr_22329_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgr_22329/02_2024/7jgr_22329.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgr_22329/02_2024/7jgr_22329.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgr_22329/02_2024/7jgr_22329.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgr_22329/02_2024/7jgr_22329_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgr_22329/02_2024/7jgr_22329_updated.pdb" } resolution = 3.9 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 80 5.49 5 Mg 4 5.21 5 S 111 5.16 5 C 13572 2.51 5 N 3813 2.21 5 O 4137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 279": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 419": "OE1" <-> "OE2" Residue "B GLU 421": "OE1" <-> "OE2" Residue "B ARG 591": "NH1" <-> "NH2" Residue "B GLU 613": "OE1" <-> "OE2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C GLU 153": "OE1" <-> "OE2" Residue "C ARG 179": "NH1" <-> "NH2" Residue "C GLU 354": "OE1" <-> "OE2" Residue "C PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 428": "OE1" <-> "OE2" Residue "C GLU 443": "OE1" <-> "OE2" Residue "C ARG 469": "NH1" <-> "NH2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C GLU 476": "OE1" <-> "OE2" Residue "C GLU 485": "OE1" <-> "OE2" Residue "C GLU 496": "OE1" <-> "OE2" Residue "C GLU 592": "OE1" <-> "OE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 699": "OE1" <-> "OE2" Residue "D GLU 7": "OE1" <-> "OE2" Residue "D ARG 27": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D GLU 45": "OE1" <-> "OE2" Residue "D PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D GLU 191": "OE1" <-> "OE2" Residue "D GLU 213": "OE1" <-> "OE2" Residue "D GLU 236": "OE1" <-> "OE2" Residue "D GLU 298": "OE1" <-> "OE2" Residue "D PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 398": "OE1" <-> "OE2" Residue "D GLU 404": "OE1" <-> "OE2" Residue "D GLU 425": "OE1" <-> "OE2" Residue "E GLU 2": "OE1" <-> "OE2" Residue "E GLU 20": "OE1" <-> "OE2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 144": "NH1" <-> "NH2" Residue "E GLU 223": "OE1" <-> "OE2" Residue "E TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 293": "NH1" <-> "NH2" Residue "E GLU 320": "OE1" <-> "OE2" Residue "E ARG 345": "NH1" <-> "NH2" Residue "E GLU 395": "OE1" <-> "OE2" Residue "E ARG 431": "NH1" <-> "NH2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A GLU 551": "OE1" <-> "OE2" Residue "A GLU 557": "OE1" <-> "OE2" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A GLU 631": "OE1" <-> "OE2" Residue "A GLU 639": "OE1" <-> "OE2" Residue "A ARG 676": "NH1" <-> "NH2" Residue "A ARG 725": "NH1" <-> "NH2" Residue "A GLU 762": "OE1" <-> "OE2" Residue "A GLU 767": "OE1" <-> "OE2" Residue "A ARG 785": "NH1" <-> "NH2" Residue "A ARG 880": "NH1" <-> "NH2" Residue "A GLU 894": "OE1" <-> "OE2" Residue "G GLU 279": "OE1" <-> "OE2" Residue "G GLU 286": "OE1" <-> "OE2" Residue "G GLU 343": "OE1" <-> "OE2" Residue "G GLU 358": "OE1" <-> "OE2" Residue "G ARG 385": "NH1" <-> "NH2" Residue "G GLU 455": "OE1" <-> "OE2" Residue "G ARG 498": "NH1" <-> "NH2" Residue "G GLU 574": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21717 Number of models: 1 Model: "" Number of chains: 13 Chain: "B" Number of atoms: 2321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2321 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 11, 'TRANS': 278} Chain breaks: 3 Chain: "C" Number of atoms: 4918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4918 Classifications: {'peptide': 612} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 588} Chain breaks: 7 Chain: "D" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3549 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 11, 'TRANS': 429} Chain breaks: 2 Chain: "E" Number of atoms: 3161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3161 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 386} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 143 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "A" Number of atoms: 3129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3129 Classifications: {'peptide': 401} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 383} Chain: "G" Number of atoms: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2974 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 13, 'TRANS': 358} Chain breaks: 2 Chain: "H" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 693 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "I" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 701 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.86, per 1000 atoms: 0.55 Number of scatterers: 21717 At special positions: 0 Unit cell: (122.98, 159.1, 123.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 111 16.00 P 80 15.00 Mg 4 11.99 O 4137 8.00 N 3813 7.00 C 13572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.07 Conformation dependent library (CDL) restraints added in 3.7 seconds 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4844 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 13 sheets defined 55.9% alpha, 6.8% beta 28 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 10.30 Creating SS restraints... Processing helix chain 'B' and resid 280 through 284 Processing helix chain 'B' and resid 324 through 338 Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'B' and resid 362 through 371 Processing helix chain 'B' and resid 390 through 400 Processing helix chain 'B' and resid 411 through 423 Processing helix chain 'B' and resid 445 through 455 Processing helix chain 'B' and resid 471 through 473 No H-bonds generated for 'chain 'B' and resid 471 through 473' Processing helix chain 'B' and resid 477 through 482 Processing helix chain 'B' and resid 516 through 523 Processing helix chain 'B' and resid 528 through 544 Processing helix chain 'B' and resid 555 through 564 Processing helix chain 'B' and resid 571 through 583 Processing helix chain 'B' and resid 605 through 614 Processing helix chain 'C' and resid 42 through 45 No H-bonds generated for 'chain 'C' and resid 42 through 45' Processing helix chain 'C' and resid 48 through 88 removed outlier: 5.136A pdb=" N ARG C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N THR C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 123 removed outlier: 3.571A pdb=" N LEU C 111 " --> pdb=" O PRO C 108 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER C 112 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 121 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS C 122 " --> pdb=" O GLN C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 136 No H-bonds generated for 'chain 'C' and resid 134 through 136' Processing helix chain 'C' and resid 140 through 158 Processing helix chain 'C' and resid 185 through 198 removed outlier: 3.995A pdb=" N ASP C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N SER C 198 " --> pdb=" O ASN C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 214 No H-bonds generated for 'chain 'C' and resid 212 through 214' Processing helix chain 'C' and resid 217 through 229 Processing helix chain 'C' and resid 246 through 252 Processing helix chain 'C' and resid 255 through 260 removed outlier: 4.118A pdb=" N LYS C 260 " --> pdb=" O HIS C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 281 Processing helix chain 'C' and resid 294 through 306 Processing helix chain 'C' and resid 311 through 328 removed outlier: 4.563A pdb=" N GLY C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 333 No H-bonds generated for 'chain 'C' and resid 330 through 333' Processing helix chain 'C' and resid 338 through 347 Processing helix chain 'C' and resid 351 through 357 Processing helix chain 'C' and resid 360 through 367 Proline residue: C 364 - end of helix Processing helix chain 'C' and resid 373 through 379 Processing helix chain 'C' and resid 383 through 415 Proline residue: C 390 - end of helix removed outlier: 4.666A pdb=" N GLU C 412 " --> pdb=" O GLU C 408 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU C 413 " --> pdb=" O PHE C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 435 Processing helix chain 'C' and resid 442 through 452 Processing helix chain 'C' and resid 456 through 476 Processing helix chain 'C' and resid 485 through 507 Proline residue: C 493 - end of helix Processing helix chain 'C' and resid 564 through 575 Processing helix chain 'C' and resid 584 through 586 No H-bonds generated for 'chain 'C' and resid 584 through 586' Processing helix chain 'C' and resid 591 through 593 No H-bonds generated for 'chain 'C' and resid 591 through 593' Processing helix chain 'C' and resid 599 through 606 Processing helix chain 'C' and resid 610 through 619 Processing helix chain 'C' and resid 621 through 625 removed outlier: 4.093A pdb=" N MET C 625 " --> pdb=" O HIS C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 653 removed outlier: 3.522A pdb=" N VAL C 648 " --> pdb=" O ASP C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 671 Processing helix chain 'C' and resid 688 through 702 Processing helix chain 'D' and resid 4 through 20 removed outlier: 3.742A pdb=" N LEU D 8 " --> pdb=" O ALA D 4 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL D 9 " --> pdb=" O ASP D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 45 Processing helix chain 'D' and resid 63 through 76 Proline residue: D 75 - end of helix Processing helix chain 'D' and resid 96 through 106 Processing helix chain 'D' and resid 121 through 133 Processing helix chain 'D' and resid 149 through 154 removed outlier: 3.772A pdb=" N ALA D 154 " --> pdb=" O ASP D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 168 removed outlier: 5.984A pdb=" N LEU D 160 " --> pdb=" O ASN D 157 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE D 165 " --> pdb=" O TYR D 162 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL D 167 " --> pdb=" O LEU D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 212 through 223 removed outlier: 3.532A pdb=" N LEU D 223 " --> pdb=" O CYS D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 243 Processing helix chain 'D' and resid 251 through 254 Processing helix chain 'D' and resid 258 through 260 No H-bonds generated for 'chain 'D' and resid 258 through 260' Processing helix chain 'D' and resid 265 through 279 Processing helix chain 'D' and resid 282 through 294 Processing helix chain 'D' and resid 298 through 311 removed outlier: 4.071A pdb=" N HIS D 311 " --> pdb=" O ARG D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 332 Processing helix chain 'D' and resid 337 through 340 No H-bonds generated for 'chain 'D' and resid 337 through 340' Processing helix chain 'D' and resid 345 through 361 Processing helix chain 'D' and resid 368 through 379 removed outlier: 3.723A pdb=" N PHE D 378 " --> pdb=" O ARG D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 402 Processing helix chain 'D' and resid 433 through 442 removed outlier: 3.569A pdb=" N GLN D 441 " --> pdb=" O HIS D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 455 removed outlier: 3.819A pdb=" N GLN D 455 " --> pdb=" O ALA D 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 9 Processing helix chain 'E' and resid 16 through 25 Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 77 through 88 Processing helix chain 'E' and resid 93 through 95 No H-bonds generated for 'chain 'E' and resid 93 through 95' Processing helix chain 'E' and resid 101 through 111 removed outlier: 3.722A pdb=" N GLN E 111 " --> pdb=" O GLN E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 133 removed outlier: 3.754A pdb=" N ARG E 132 " --> pdb=" O GLU E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 149 removed outlier: 3.536A pdb=" N ARG E 144 " --> pdb=" O PRO E 140 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLN E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLU E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 165 No H-bonds generated for 'chain 'E' and resid 163 through 165' Processing helix chain 'E' and resid 185 through 204 removed outlier: 4.302A pdb=" N ASP E 195 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N PHE E 196 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLN E 197 " --> pdb=" O GLY E 193 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLN E 198 " --> pdb=" O SER E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 218 Processing helix chain 'E' and resid 223 through 237 removed outlier: 4.106A pdb=" N VAL E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 258 removed outlier: 4.300A pdb=" N LYS E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 263 No H-bonds generated for 'chain 'E' and resid 260 through 263' Processing helix chain 'E' and resid 276 through 289 Proline residue: E 282 - end of helix removed outlier: 3.584A pdb=" N SER E 285 " --> pdb=" O GLY E 281 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR E 288 " --> pdb=" O ARG E 284 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN E 289 " --> pdb=" O SER E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 337 Processing helix chain 'E' and resid 343 through 347 Processing helix chain 'E' and resid 382 through 393 Processing helix chain 'E' and resid 401 through 412 Processing helix chain 'E' and resid 438 through 448 Processing helix chain 'E' and resid 452 through 455 Processing helix chain 'F' and resid 225 through 237 Processing helix chain 'A' and resid 520 through 528 Processing helix chain 'A' and resid 546 through 548 No H-bonds generated for 'chain 'A' and resid 546 through 548' Processing helix chain 'A' and resid 551 through 558 Processing helix chain 'A' and resid 572 through 587 Processing helix chain 'A' and resid 604 through 620 Processing helix chain 'A' and resid 640 through 651 removed outlier: 3.525A pdb=" N ALA A 643 " --> pdb=" O PRO A 640 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE A 647 " --> pdb=" O TYR A 644 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR A 648 " --> pdb=" O VAL A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 669 Processing helix chain 'A' and resid 686 through 689 Processing helix chain 'A' and resid 695 through 702 Processing helix chain 'A' and resid 722 through 725 No H-bonds generated for 'chain 'A' and resid 722 through 725' Processing helix chain 'A' and resid 729 through 735 Processing helix chain 'A' and resid 747 through 757 removed outlier: 3.861A pdb=" N GLN A 751 " --> pdb=" O HIS A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 777 Processing helix chain 'A' and resid 783 through 799 removed outlier: 3.618A pdb=" N ARG A 791 " --> pdb=" O LEU A 787 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 799 " --> pdb=" O GLU A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 817 Processing helix chain 'A' and resid 823 through 827 Processing helix chain 'A' and resid 831 through 847 removed outlier: 3.652A pdb=" N ALA A 841 " --> pdb=" O LEU A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 868 Processing helix chain 'A' and resid 875 through 887 removed outlier: 3.823A pdb=" N ARG A 880 " --> pdb=" O GLY A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 917 removed outlier: 3.734A pdb=" N HIS A 914 " --> pdb=" O ALA A 910 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 259 Processing helix chain 'G' and resid 272 through 286 Processing helix chain 'G' and resid 303 through 310 Processing helix chain 'G' and resid 314 through 319 Processing helix chain 'G' and resid 333 through 344 removed outlier: 3.850A pdb=" N VAL G 336 " --> pdb=" O VAL G 333 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N TYR G 337 " --> pdb=" O GLY G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 365 Processing helix chain 'G' and resid 378 through 381 Processing helix chain 'G' and resid 387 through 393 Processing helix chain 'G' and resid 414 through 418 Processing helix chain 'G' and resid 420 through 424 removed outlier: 3.631A pdb=" N ALA G 424 " --> pdb=" O ARG G 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 440 through 453 removed outlier: 3.616A pdb=" N ALA G 452 " --> pdb=" O LYS G 448 " (cutoff:3.500A) Processing helix chain 'G' and resid 457 through 459 No H-bonds generated for 'chain 'G' and resid 457 through 459' Processing helix chain 'G' and resid 462 through 475 removed outlier: 3.670A pdb=" N ALA G 470 " --> pdb=" O GLN G 466 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA G 474 " --> pdb=" O ALA G 470 " (cutoff:3.500A) Processing helix chain 'G' and resid 479 through 497 removed outlier: 3.797A pdb=" N VAL G 490 " --> pdb=" O GLY G 486 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN G 495 " --> pdb=" O GLU G 491 " (cutoff:3.500A) Processing helix chain 'G' and resid 531 through 541 Processing helix chain 'G' and resid 558 through 573 Processing helix chain 'G' and resid 581 through 594 removed outlier: 3.795A pdb=" N VAL G 587 " --> pdb=" O ARG G 583 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG G 590 " --> pdb=" O GLU G 586 " (cutoff:3.500A) Processing helix chain 'G' and resid 602 through 615 removed outlier: 4.033A pdb=" N GLY G 607 " --> pdb=" O ALA G 603 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR G 614 " --> pdb=" O ASP G 610 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG G 615 " --> pdb=" O LEU G 611 " (cutoff:3.500A) Processing helix chain 'G' and resid 626 through 628 No H-bonds generated for 'chain 'G' and resid 626 through 628' Processing helix chain 'G' and resid 637 through 644 removed outlier: 3.767A pdb=" N ALA G 642 " --> pdb=" O GLU G 638 " (cutoff:3.500A) Processing helix chain 'G' and resid 647 through 654 removed outlier: 3.647A pdb=" N SER G 652 " --> pdb=" O GLN G 648 " (cutoff:3.500A) Processing helix chain 'G' and resid 657 through 659 No H-bonds generated for 'chain 'G' and resid 657 through 659' Processing sheet with id= A, first strand: chain 'B' and resid 485 through 488 removed outlier: 6.265A pdb=" N ASN B 352 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N TRP B 488 " --> pdb=" O ASN B 352 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU B 354 " --> pdb=" O TRP B 488 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU B 430 " --> pdb=" O HIS B 461 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU B 463 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU B 432 " --> pdb=" O LEU B 463 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N SER B 465 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL B 434 " --> pdb=" O SER B 465 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR B 377 " --> pdb=" O PHE B 431 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ILE B 433 " --> pdb=" O THR B 377 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU B 379 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N HIS B 435 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL B 381 " --> pdb=" O HIS B 435 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 588 through 591 Processing sheet with id= C, first strand: chain 'C' and resid 261 through 267 removed outlier: 7.321A pdb=" N LEU C 96 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ARG C 264 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N THR C 98 " --> pdb=" O ARG C 264 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N PHE C 266 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA C 100 " --> pdb=" O PHE C 266 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 127 through 131 removed outlier: 6.072A pdb=" N GLN C 204 " --> pdb=" O MET C 128 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N CYS C 130 " --> pdb=" O GLN C 204 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL C 206 " --> pdb=" O CYS C 130 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 658 through 660 Processing sheet with id= F, first strand: chain 'D' and resid 50 through 55 Processing sheet with id= G, first strand: chain 'D' and resid 83 through 89 removed outlier: 6.255A pdb=" N SER D 141 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL D 86 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE D 143 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LEU D 88 " --> pdb=" O ILE D 143 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ILE D 145 " --> pdb=" O LEU D 88 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'D' and resid 406 through 408 Processing sheet with id= I, first strand: chain 'E' and resid 176 through 180 removed outlier: 8.009A pdb=" N ILE E 37 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL E 155 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU E 39 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU E 157 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLY E 41 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N SER E 159 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE E 121 " --> pdb=" O CYS E 154 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE E 156 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE E 123 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU E 158 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL E 125 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ARG E 65 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ALA E 124 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA E 67 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ASP E 126 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU E 69 " --> pdb=" O ASP E 126 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 739 through 742 removed outlier: 8.963A pdb=" N LEU A 740 " --> pdb=" O CYS A 593 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR A 595 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N PHE A 742 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N SER A 597 " --> pdb=" O PHE A 742 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR A 679 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N VAL A 714 " --> pdb=" O THR A 679 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU A 681 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ILE A 716 " --> pdb=" O LEU A 681 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL A 683 " --> pdb=" O ILE A 716 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 851 through 853 removed outlier: 3.531A pdb=" N THR A 852 " --> pdb=" O ILE A 904 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 431 through 435 removed outlier: 6.031A pdb=" N LEU G 371 " --> pdb=" O LEU G 404 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N VAL G 406 " --> pdb=" O LEU G 371 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU G 373 " --> pdb=" O VAL G 406 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE G 408 " --> pdb=" O LEU G 373 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU G 375 " --> pdb=" O ILE G 408 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 618 through 621 895 hydrogen bonds defined for protein. 2544 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 120 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 8.29 Time building geometry restraints manager: 9.72 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: 5636 1.33 - 1.46: 4757 1.46 - 1.58: 11524 1.58 - 1.70: 153 1.70 - 1.82: 163 Bond restraints: 22233 Sorted by residual: bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.20e+01 bond pdb=" C4 ATP E 901 " pdb=" C5 ATP E 901 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.80e+01 bond pdb=" C4 ATP A1001 " pdb=" C5 ATP A1001 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.73e+01 bond pdb=" C4 ATP G 901 " pdb=" C5 ATP G 901 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.51e+01 bond pdb=" C5 ATP E 901 " pdb=" C6 ATP E 901 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.31e+01 ... (remaining 22228 not shown) Histogram of bond angle deviations from ideal: 98.15 - 105.68: 717 105.68 - 113.21: 12256 113.21 - 120.75: 10651 120.75 - 128.28: 6515 128.28 - 135.81: 210 Bond angle restraints: 30349 Sorted by residual: angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 118.67 21.20 1.00e+00 1.00e+00 4.49e+02 angle pdb=" PB ATP E 901 " pdb=" O3B ATP E 901 " pdb=" PG ATP E 901 " ideal model delta sigma weight residual 139.87 121.08 18.79 1.00e+00 1.00e+00 3.53e+02 angle pdb=" PB ATP G 901 " pdb=" O3B ATP G 901 " pdb=" PG ATP G 901 " ideal model delta sigma weight residual 139.87 121.41 18.46 1.00e+00 1.00e+00 3.41e+02 angle pdb=" PA ATP D 901 " pdb=" O3A ATP D 901 " pdb=" PB ATP D 901 " ideal model delta sigma weight residual 136.83 119.69 17.14 1.00e+00 1.00e+00 2.94e+02 angle pdb=" PB ATP A1001 " pdb=" O3B ATP A1001 " pdb=" PG ATP A1001 " ideal model delta sigma weight residual 139.87 122.91 16.96 1.00e+00 1.00e+00 2.88e+02 ... (remaining 30344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 11566 17.93 - 35.86: 1278 35.86 - 53.79: 492 53.79 - 71.72: 116 71.72 - 89.64: 26 Dihedral angle restraints: 13478 sinusoidal: 6058 harmonic: 7420 Sorted by residual: dihedral pdb=" CA LEU G 259 " pdb=" C LEU G 259 " pdb=" N ASN G 260 " pdb=" CA ASN G 260 " ideal model delta harmonic sigma weight residual 180.00 150.60 29.40 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA GLN C 347 " pdb=" C GLN C 347 " pdb=" N LEU C 348 " pdb=" CA LEU C 348 " ideal model delta harmonic sigma weight residual -180.00 -156.10 -23.90 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA SER G 349 " pdb=" C SER G 349 " pdb=" N GLY G 350 " pdb=" CA GLY G 350 " ideal model delta harmonic sigma weight residual 180.00 156.50 23.50 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 13475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2834 0.063 - 0.126: 566 0.126 - 0.189: 97 0.189 - 0.252: 4 0.252 - 0.315: 2 Chirality restraints: 3503 Sorted by residual: chirality pdb=" CG LEU C 275 " pdb=" CB LEU C 275 " pdb=" CD1 LEU C 275 " pdb=" CD2 LEU C 275 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.31 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" C4' DA I 42 " pdb=" C5' DA I 42 " pdb=" O4' DA I 42 " pdb=" C3' DA I 42 " both_signs ideal model delta sigma weight residual False -2.53 -2.27 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB VAL E 221 " pdb=" CA VAL E 221 " pdb=" CG1 VAL E 221 " pdb=" CG2 VAL E 221 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 3500 not shown) Planarity restraints: 3607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 872 " -0.057 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO A 873 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 873 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 873 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 150 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.98e+00 pdb=" CG ASN E 150 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN E 150 " 0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN E 150 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY E 281 " -0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO E 282 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO E 282 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 282 " -0.032 5.00e-02 4.00e+02 ... (remaining 3604 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 53 2.42 - 3.04: 11046 3.04 - 3.66: 33618 3.66 - 4.28: 50376 4.28 - 4.90: 82648 Nonbonded interactions: 177741 Sorted by model distance: nonbonded pdb=" O2 DC H 18 " pdb=" N2 DG I 51 " model vdw 1.799 2.496 nonbonded pdb=" N3 DC H 18 " pdb=" N1 DG I 51 " model vdw 2.066 2.560 nonbonded pdb=" OG1 THR G 304 " pdb="MG MG G 902 " model vdw 2.089 2.170 nonbonded pdb=" OG1 THR D 63 " pdb="MG MG D 902 " model vdw 2.114 2.170 nonbonded pdb=" O2B ATP G 901 " pdb="MG MG G 902 " model vdw 2.128 2.170 ... (remaining 177736 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 7.010 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 65.800 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 22233 Z= 0.370 Angle : 0.952 21.197 30349 Z= 0.589 Chirality : 0.053 0.315 3503 Planarity : 0.006 0.087 3607 Dihedral : 17.946 89.644 8634 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.36 % Allowed : 5.00 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.14), residues: 2481 helix: -2.59 (0.08), residues: 1479 sheet: -2.73 (0.28), residues: 233 loop : 0.54 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 191 HIS 0.006 0.001 HIS E 278 PHE 0.026 0.003 PHE C 215 TYR 0.028 0.002 TYR E 258 ARG 0.009 0.001 ARG G 480 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 587 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9591 (mmm) cc_final: 0.9170 (tpt) REVERT: B 342 LYS cc_start: 0.9470 (tttt) cc_final: 0.9168 (tptp) REVERT: B 388 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.9059 (tp) REVERT: B 417 MET cc_start: 0.9355 (ttt) cc_final: 0.9125 (tmm) REVERT: B 488 TRP cc_start: 0.9074 (m100) cc_final: 0.8700 (m100) REVERT: B 585 LYS cc_start: 0.9423 (mttt) cc_final: 0.9179 (tmtt) REVERT: C 45 VAL cc_start: 0.8843 (t) cc_final: 0.8336 (t) REVERT: C 223 LEU cc_start: 0.9720 (tp) cc_final: 0.9445 (pp) REVERT: C 227 LEU cc_start: 0.9514 (mt) cc_final: 0.9299 (mt) REVERT: C 323 MET cc_start: 0.9154 (ttp) cc_final: 0.8884 (tmm) REVERT: C 353 MET cc_start: 0.8390 (mmt) cc_final: 0.7659 (mmt) REVERT: C 362 PHE cc_start: 0.9052 (t80) cc_final: 0.8839 (t80) REVERT: C 383 ASP cc_start: 0.9328 (m-30) cc_final: 0.8975 (p0) REVERT: C 389 LEU cc_start: 0.9132 (mt) cc_final: 0.8754 (mt) REVERT: C 411 THR cc_start: 0.9031 (p) cc_final: 0.8775 (t) REVERT: C 429 LEU cc_start: 0.9659 (OUTLIER) cc_final: 0.9390 (mt) REVERT: C 433 CYS cc_start: 0.9222 (m) cc_final: 0.8992 (m) REVERT: C 450 MET cc_start: 0.8880 (mtt) cc_final: 0.7766 (mtt) REVERT: C 467 LEU cc_start: 0.9208 (mm) cc_final: 0.8822 (tt) REVERT: C 475 VAL cc_start: 0.9336 (t) cc_final: 0.9007 (p) REVERT: C 491 LEU cc_start: 0.9542 (tp) cc_final: 0.9342 (tt) REVERT: C 571 LEU cc_start: 0.9502 (mm) cc_final: 0.9200 (tp) REVERT: C 594 PHE cc_start: 0.9122 (m-80) cc_final: 0.8746 (m-80) REVERT: C 699 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8716 (mt-10) REVERT: C 707 LYS cc_start: 0.8757 (pttp) cc_final: 0.8200 (pptt) REVERT: D 48 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7574 (mt-10) REVERT: D 151 LEU cc_start: 0.9642 (mt) cc_final: 0.9417 (mp) REVERT: D 188 GLU cc_start: 0.8104 (pt0) cc_final: 0.7474 (pt0) REVERT: D 217 ASP cc_start: 0.9118 (m-30) cc_final: 0.8816 (m-30) REVERT: E 11 LEU cc_start: 0.9589 (mt) cc_final: 0.9345 (tt) REVERT: E 26 ILE cc_start: 0.9532 (pt) cc_final: 0.9322 (pt) REVERT: E 82 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8703 (mt-10) REVERT: E 94 ASP cc_start: 0.8350 (t70) cc_final: 0.7965 (t0) REVERT: E 159 SER cc_start: 0.7990 (t) cc_final: 0.7263 (m) REVERT: E 337 HIS cc_start: 0.8141 (t-90) cc_final: 0.7683 (t-90) REVERT: E 414 ASN cc_start: 0.9368 (m110) cc_final: 0.9086 (t0) REVERT: F 232 MET cc_start: 0.9399 (tpp) cc_final: 0.9141 (mmm) REVERT: A 524 MET cc_start: 0.9451 (mmm) cc_final: 0.9217 (mmp) REVERT: A 526 LYS cc_start: 0.9525 (mttt) cc_final: 0.9273 (mtmt) REVERT: A 648 TYR cc_start: 0.9116 (t80) cc_final: 0.8864 (t80) REVERT: A 695 ASP cc_start: 0.8879 (p0) cc_final: 0.8610 (p0) REVERT: A 737 LEU cc_start: 0.8754 (mt) cc_final: 0.8513 (mt) REVERT: A 788 ASP cc_start: 0.9129 (m-30) cc_final: 0.8656 (m-30) REVERT: A 894 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8303 (mt-10) REVERT: A 911 ASP cc_start: 0.8373 (p0) cc_final: 0.7991 (p0) REVERT: G 327 CYS cc_start: 0.8742 (m) cc_final: 0.8081 (m) REVERT: G 368 LYS cc_start: 0.8870 (mptt) cc_final: 0.8607 (tppt) REVERT: G 376 ASP cc_start: 0.8676 (t0) cc_final: 0.8336 (t0) REVERT: G 414 LEU cc_start: 0.9560 (tt) cc_final: 0.9178 (tt) REVERT: G 471 LYS cc_start: 0.9568 (tptt) cc_final: 0.9360 (tppt) REVERT: G 563 MET cc_start: 0.8728 (tmm) cc_final: 0.8438 (tmm) REVERT: G 565 CYS cc_start: 0.9281 (m) cc_final: 0.8895 (p) REVERT: G 570 MET cc_start: 0.8568 (mtp) cc_final: 0.8254 (mtm) REVERT: G 588 TYR cc_start: 0.9111 (t80) cc_final: 0.8232 (t80) outliers start: 8 outliers final: 0 residues processed: 593 average time/residue: 0.3951 time to fit residues: 339.8653 Evaluate side-chains 271 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 269 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain C residue 429 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 217 optimal weight: 9.9990 chunk 194 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 66 optimal weight: 0.0570 chunk 131 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 201 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 149 optimal weight: 0.9990 chunk 233 optimal weight: 0.7980 overall best weight: 1.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 352 ASN B 435 HIS B 436 ASN B 498 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 GLN C 194 ASN C 250 HIS C 391 GLN C 435 ASN C 605 ASN D 35 ASN D 202 GLN D 421 GLN E 70 ASN E 127 ASN ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 414 ASN E 433 GLN E 451 ASN A 749 GLN A 828 ASN A 838 GLN G 284 HIS G 585 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 22233 Z= 0.210 Angle : 0.632 10.454 30349 Z= 0.328 Chirality : 0.040 0.196 3503 Planarity : 0.005 0.109 3607 Dihedral : 17.768 80.841 3665 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.58 % Allowed : 13.24 % Favored : 85.18 % 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: -0.79 (0.16), residues: 2481 helix: -0.32 (0.12), residues: 1478 sheet: -2.32 (0.29), residues: 224 loop : 0.09 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 276 HIS 0.007 0.001 HIS G 641 PHE 0.026 0.001 PHE C 662 TYR 0.017 0.001 TYR C 72 ARG 0.009 0.001 ARG D 220 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 279 time to evaluate : 2.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 417 MET cc_start: 0.9361 (ttt) cc_final: 0.9123 (tmm) REVERT: B 441 MET cc_start: 0.8912 (mmm) cc_final: 0.8649 (mmm) REVERT: B 585 LYS cc_start: 0.9521 (mttt) cc_final: 0.9180 (tmtt) REVERT: C 145 GLU cc_start: 0.9224 (OUTLIER) cc_final: 0.8823 (pp20) REVERT: C 227 LEU cc_start: 0.9437 (mt) cc_final: 0.9234 (mt) REVERT: C 353 MET cc_start: 0.7976 (mmt) cc_final: 0.7732 (mmt) REVERT: C 389 LEU cc_start: 0.9148 (mt) cc_final: 0.8747 (mt) REVERT: C 410 LEU cc_start: 0.9356 (mp) cc_final: 0.9096 (mp) REVERT: C 625 MET cc_start: 0.8812 (mtp) cc_final: 0.8240 (ttm) REVERT: C 699 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8538 (mt-10) REVERT: D 151 LEU cc_start: 0.9610 (mt) cc_final: 0.9409 (mp) REVERT: E 11 LEU cc_start: 0.9595 (mt) cc_final: 0.9388 (tt) REVERT: E 82 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8767 (mt-10) REVERT: E 94 ASP cc_start: 0.8406 (t70) cc_final: 0.7968 (t0) REVERT: E 164 GLU cc_start: 0.8344 (mp0) cc_final: 0.7992 (mp0) REVERT: E 287 LEU cc_start: 0.9292 (tp) cc_final: 0.9060 (tt) REVERT: E 289 GLN cc_start: 0.9322 (tp40) cc_final: 0.8546 (tp-100) REVERT: E 292 MET cc_start: 0.8521 (mpp) cc_final: 0.7130 (mpp) REVERT: E 337 HIS cc_start: 0.8183 (t-90) cc_final: 0.7700 (t-90) REVERT: E 395 GLU cc_start: 0.9182 (tp30) cc_final: 0.8771 (mp0) REVERT: E 414 ASN cc_start: 0.9357 (m-40) cc_final: 0.9071 (t0) REVERT: F 232 MET cc_start: 0.9487 (tpp) cc_final: 0.9085 (mmm) REVERT: A 524 MET cc_start: 0.9474 (mmm) cc_final: 0.9144 (mmm) REVERT: A 648 TYR cc_start: 0.9176 (t80) cc_final: 0.8953 (t80) REVERT: A 788 ASP cc_start: 0.9268 (m-30) cc_final: 0.8751 (m-30) REVERT: A 832 MET cc_start: 0.9337 (mmt) cc_final: 0.8871 (mmm) REVERT: A 894 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8349 (mt-10) REVERT: G 327 CYS cc_start: 0.7829 (m) cc_final: 0.7430 (m) REVERT: G 333 VAL cc_start: 0.9020 (t) cc_final: 0.8811 (p) REVERT: G 368 LYS cc_start: 0.8801 (mptt) cc_final: 0.8554 (tppt) REVERT: G 370 MET cc_start: 0.8865 (tpp) cc_final: 0.8634 (mmt) REVERT: G 376 ASP cc_start: 0.8278 (t0) cc_final: 0.8012 (t70) REVERT: G 429 LYS cc_start: 0.9417 (pttt) cc_final: 0.9189 (ptpp) REVERT: G 563 MET cc_start: 0.8727 (tmm) cc_final: 0.8495 (tmm) REVERT: G 588 TYR cc_start: 0.8911 (t80) cc_final: 0.8608 (t80) REVERT: G 610 ASP cc_start: 0.9217 (m-30) cc_final: 0.8935 (m-30) outliers start: 35 outliers final: 18 residues processed: 301 average time/residue: 0.3209 time to fit residues: 150.7301 Evaluate side-chains 238 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 219 time to evaluate : 2.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 882 CYS Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 568 VAL Chi-restraints excluded: chain G residue 644 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 129 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 194 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 233 optimal weight: 2.9990 chunk 252 optimal weight: 10.0000 chunk 208 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 187 optimal weight: 0.5980 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 435 HIS B 544 ASN B 577 GLN B 609 GLN ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 HIS E 289 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22233 Z= 0.188 Angle : 0.584 12.599 30349 Z= 0.299 Chirality : 0.039 0.310 3503 Planarity : 0.004 0.065 3607 Dihedral : 17.521 79.126 3661 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.98 % Allowed : 14.10 % Favored : 83.92 % 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: 0.12 (0.17), residues: 2481 helix: 0.62 (0.13), residues: 1497 sheet: -2.03 (0.30), residues: 237 loop : -0.00 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 276 HIS 0.004 0.001 HIS G 434 PHE 0.017 0.001 PHE C 594 TYR 0.016 0.001 TYR B 356 ARG 0.007 0.000 ARG D 266 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 221 time to evaluate : 2.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 342 LYS cc_start: 0.9493 (tttt) cc_final: 0.9266 (tptp) REVERT: B 585 LYS cc_start: 0.9512 (mttt) cc_final: 0.9178 (tmtt) REVERT: C 145 GLU cc_start: 0.9238 (OUTLIER) cc_final: 0.8839 (pp20) REVERT: C 281 LYS cc_start: 0.9643 (mttm) cc_final: 0.9410 (mtmm) REVERT: C 389 LEU cc_start: 0.9155 (mt) cc_final: 0.8754 (mt) REVERT: C 495 LEU cc_start: 0.9477 (mm) cc_final: 0.9024 (tt) REVERT: C 699 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8550 (mt-10) REVERT: E 11 LEU cc_start: 0.9610 (mt) cc_final: 0.9381 (tt) REVERT: E 82 GLU cc_start: 0.9069 (mt-10) cc_final: 0.8795 (mt-10) REVERT: E 94 ASP cc_start: 0.8406 (t70) cc_final: 0.7947 (t0) REVERT: E 164 GLU cc_start: 0.8355 (mp0) cc_final: 0.8047 (mp0) REVERT: E 292 MET cc_start: 0.8587 (mpp) cc_final: 0.8176 (mpp) REVERT: E 337 HIS cc_start: 0.8221 (t-90) cc_final: 0.7805 (t-90) REVERT: E 395 GLU cc_start: 0.9175 (tp30) cc_final: 0.8761 (mp0) REVERT: E 414 ASN cc_start: 0.9305 (m-40) cc_final: 0.9093 (t0) REVERT: F 232 MET cc_start: 0.9542 (tpp) cc_final: 0.9114 (tpt) REVERT: A 524 MET cc_start: 0.9467 (mmm) cc_final: 0.8996 (mmp) REVERT: A 536 MET cc_start: 0.8996 (tpp) cc_final: 0.8423 (tpp) REVERT: A 788 ASP cc_start: 0.9254 (m-30) cc_final: 0.8911 (t0) REVERT: A 832 MET cc_start: 0.9375 (mmt) cc_final: 0.8890 (mmm) REVERT: A 855 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8786 (mtp) REVERT: A 894 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8459 (mt-10) REVERT: G 327 CYS cc_start: 0.7771 (m) cc_final: 0.7351 (m) REVERT: G 333 VAL cc_start: 0.9058 (t) cc_final: 0.8838 (p) REVERT: G 370 MET cc_start: 0.8849 (tpp) cc_final: 0.8514 (mmt) REVERT: G 378 ILE cc_start: 0.9254 (tt) cc_final: 0.9036 (tp) REVERT: G 420 MET cc_start: 0.9230 (pmm) cc_final: 0.8924 (pmm) REVERT: G 429 LYS cc_start: 0.9402 (pttt) cc_final: 0.9172 (ptpp) REVERT: G 563 MET cc_start: 0.8787 (tmm) cc_final: 0.8570 (tmm) REVERT: G 565 CYS cc_start: 0.9255 (m) cc_final: 0.8969 (p) REVERT: G 588 TYR cc_start: 0.8930 (t80) cc_final: 0.8674 (t80) REVERT: G 610 ASP cc_start: 0.9254 (m-30) cc_final: 0.8933 (m-30) outliers start: 44 outliers final: 25 residues processed: 254 average time/residue: 0.3193 time to fit residues: 130.2125 Evaluate side-chains 213 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 186 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 338 LYS Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 644 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 231 optimal weight: 0.0570 chunk 175 optimal weight: 0.3980 chunk 121 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 234 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 overall best weight: 0.8904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 HIS B 577 GLN C 68 GLN C 113 GLN ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22233 Z= 0.152 Angle : 0.546 11.114 30349 Z= 0.280 Chirality : 0.038 0.279 3503 Planarity : 0.003 0.052 3607 Dihedral : 17.313 76.228 3661 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.71 % Allowed : 15.59 % Favored : 82.70 % 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: 0.57 (0.17), residues: 2481 helix: 0.99 (0.14), residues: 1492 sheet: -1.64 (0.31), residues: 233 loop : 0.07 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 276 HIS 0.003 0.001 HIS G 641 PHE 0.013 0.001 PHE G 280 TYR 0.022 0.001 TYR A 648 ARG 0.006 0.000 ARG G 575 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 210 time to evaluate : 2.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 391 LYS cc_start: 0.8953 (tptt) cc_final: 0.8161 (tptt) REVERT: B 395 ASP cc_start: 0.9096 (m-30) cc_final: 0.8720 (m-30) REVERT: B 585 LYS cc_start: 0.9503 (mttt) cc_final: 0.9224 (tmtt) REVERT: B 588 LYS cc_start: 0.8261 (mtmm) cc_final: 0.8051 (mtmm) REVERT: C 145 GLU cc_start: 0.9254 (OUTLIER) cc_final: 0.8824 (pp20) REVERT: C 281 LYS cc_start: 0.9634 (mttm) cc_final: 0.9401 (mtmm) REVERT: C 389 LEU cc_start: 0.9195 (mt) cc_final: 0.8758 (mt) REVERT: C 495 LEU cc_start: 0.9491 (mm) cc_final: 0.8993 (tt) REVERT: C 604 ARG cc_start: 0.8723 (mmp80) cc_final: 0.8275 (mmm160) REVERT: C 699 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8543 (mt-10) REVERT: E 11 LEU cc_start: 0.9605 (mt) cc_final: 0.9378 (tt) REVERT: E 82 GLU cc_start: 0.9084 (mt-10) cc_final: 0.8797 (mt-10) REVERT: E 94 ASP cc_start: 0.8395 (t70) cc_final: 0.7922 (t0) REVERT: E 292 MET cc_start: 0.8529 (mpp) cc_final: 0.8012 (mpp) REVERT: E 337 HIS cc_start: 0.8262 (t-90) cc_final: 0.7761 (t70) REVERT: E 395 GLU cc_start: 0.9158 (tp30) cc_final: 0.8775 (mp0) REVERT: F 232 MET cc_start: 0.9486 (tpp) cc_final: 0.9062 (tpp) REVERT: A 524 MET cc_start: 0.9472 (mmm) cc_final: 0.8932 (mmp) REVERT: A 536 MET cc_start: 0.8986 (tpp) cc_final: 0.8393 (tpp) REVERT: A 728 MET cc_start: 0.8197 (mtt) cc_final: 0.7881 (mmm) REVERT: A 788 ASP cc_start: 0.9234 (m-30) cc_final: 0.8893 (t0) REVERT: A 832 MET cc_start: 0.9372 (mmt) cc_final: 0.8882 (mmm) REVERT: A 855 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8735 (mtp) REVERT: A 894 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8466 (mt-10) REVERT: G 327 CYS cc_start: 0.7666 (m) cc_final: 0.7291 (m) REVERT: G 333 VAL cc_start: 0.9068 (t) cc_final: 0.8861 (p) REVERT: G 370 MET cc_start: 0.8923 (tpp) cc_final: 0.8492 (mmt) REVERT: G 376 ASP cc_start: 0.8401 (t0) cc_final: 0.8026 (t0) REVERT: G 378 ILE cc_start: 0.9282 (tt) cc_final: 0.9023 (tp) REVERT: G 420 MET cc_start: 0.9235 (pmm) cc_final: 0.8968 (pmm) REVERT: G 429 LYS cc_start: 0.9384 (pttt) cc_final: 0.9154 (ptpp) REVERT: G 563 MET cc_start: 0.8787 (tmm) cc_final: 0.8546 (tmm) REVERT: G 565 CYS cc_start: 0.9242 (m) cc_final: 0.8959 (p) REVERT: G 588 TYR cc_start: 0.8919 (t80) cc_final: 0.8636 (t80) REVERT: G 610 ASP cc_start: 0.9251 (m-30) cc_final: 0.8922 (m-30) outliers start: 38 outliers final: 19 residues processed: 237 average time/residue: 0.3219 time to fit residues: 121.6011 Evaluate side-chains 204 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 183 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 644 LEU Chi-restraints excluded: chain G residue 655 SER Chi-restraints excluded: chain G residue 657 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 206 optimal weight: 0.7980 chunk 141 optimal weight: 0.3980 chunk 3 optimal weight: 0.8980 chunk 184 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 chunk 211 optimal weight: 7.9990 chunk 171 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 126 optimal weight: 0.9990 chunk 222 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22233 Z= 0.141 Angle : 0.539 13.682 30349 Z= 0.273 Chirality : 0.038 0.274 3503 Planarity : 0.003 0.044 3607 Dihedral : 17.115 76.927 3661 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.98 % Allowed : 16.17 % Favored : 81.85 % 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: 0.80 (0.17), residues: 2481 helix: 1.22 (0.14), residues: 1486 sheet: -1.46 (0.32), residues: 234 loop : 0.04 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 276 HIS 0.003 0.001 HIS C 230 PHE 0.019 0.001 PHE C 318 TYR 0.025 0.001 TYR A 648 ARG 0.005 0.000 ARG G 575 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 206 time to evaluate : 2.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 395 ASP cc_start: 0.9109 (m-30) cc_final: 0.8908 (m-30) REVERT: B 535 MET cc_start: 0.8623 (ppp) cc_final: 0.8401 (ppp) REVERT: B 585 LYS cc_start: 0.9490 (mttt) cc_final: 0.9195 (tmtt) REVERT: C 128 MET cc_start: 0.8825 (mpp) cc_final: 0.8558 (mmm) REVERT: C 145 GLU cc_start: 0.9276 (OUTLIER) cc_final: 0.8846 (pp20) REVERT: C 281 LYS cc_start: 0.9642 (mttm) cc_final: 0.9410 (mtmm) REVERT: C 389 LEU cc_start: 0.9197 (mt) cc_final: 0.8756 (mt) REVERT: C 446 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8344 (tm-30) REVERT: C 495 LEU cc_start: 0.9481 (mm) cc_final: 0.9008 (tt) REVERT: C 575 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.7829 (tp-100) REVERT: C 604 ARG cc_start: 0.8709 (mmp80) cc_final: 0.8288 (mmm160) REVERT: C 699 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8545 (mt-10) REVERT: D 389 GLU cc_start: 0.8222 (tt0) cc_final: 0.7968 (tt0) REVERT: E 11 LEU cc_start: 0.9609 (mt) cc_final: 0.9388 (tt) REVERT: E 82 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8592 (mt-10) REVERT: E 94 ASP cc_start: 0.8407 (t70) cc_final: 0.7918 (t0) REVERT: E 292 MET cc_start: 0.8490 (mpp) cc_final: 0.7938 (mpp) REVERT: E 337 HIS cc_start: 0.8262 (t-90) cc_final: 0.7764 (t70) REVERT: E 395 GLU cc_start: 0.9138 (tp30) cc_final: 0.8740 (mp0) REVERT: F 232 MET cc_start: 0.9557 (tpp) cc_final: 0.9172 (tpt) REVERT: A 524 MET cc_start: 0.9469 (mmm) cc_final: 0.8897 (mmp) REVERT: A 536 MET cc_start: 0.9001 (tpp) cc_final: 0.8373 (tpp) REVERT: A 788 ASP cc_start: 0.9231 (m-30) cc_final: 0.8890 (t0) REVERT: A 817 MET cc_start: 0.7975 (mtm) cc_final: 0.6387 (mtm) REVERT: A 832 MET cc_start: 0.9355 (mmt) cc_final: 0.8863 (mmm) REVERT: A 894 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8478 (mt-10) REVERT: G 327 CYS cc_start: 0.7694 (m) cc_final: 0.7344 (m) REVERT: G 333 VAL cc_start: 0.9082 (t) cc_final: 0.8880 (p) REVERT: G 376 ASP cc_start: 0.8331 (t0) cc_final: 0.7947 (t0) REVERT: G 378 ILE cc_start: 0.9289 (tt) cc_final: 0.9048 (tp) REVERT: G 420 MET cc_start: 0.9251 (pmm) cc_final: 0.8962 (pmm) REVERT: G 429 LYS cc_start: 0.9359 (pttt) cc_final: 0.9141 (ptpp) REVERT: G 563 MET cc_start: 0.8806 (tmm) cc_final: 0.8586 (tmm) REVERT: G 565 CYS cc_start: 0.9235 (m) cc_final: 0.8963 (p) REVERT: G 588 TYR cc_start: 0.8917 (t80) cc_final: 0.8650 (t80) outliers start: 44 outliers final: 25 residues processed: 243 average time/residue: 0.3250 time to fit residues: 125.2096 Evaluate side-chains 211 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 183 time to evaluate : 2.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain C residue 575 GLN Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 644 LEU Chi-restraints excluded: chain G residue 657 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 83 optimal weight: 8.9990 chunk 223 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 145 optimal weight: 0.0970 chunk 61 optimal weight: 0.0060 chunk 248 optimal weight: 0.9990 chunk 206 optimal weight: 0.0370 chunk 115 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 overall best weight: 0.3874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN ** D 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22233 Z= 0.139 Angle : 0.540 12.470 30349 Z= 0.272 Chirality : 0.038 0.243 3503 Planarity : 0.003 0.042 3607 Dihedral : 17.008 84.758 3661 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.03 % Allowed : 16.85 % Favored : 81.13 % 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: 0.90 (0.17), residues: 2481 helix: 1.31 (0.14), residues: 1484 sheet: -1.31 (0.32), residues: 236 loop : 0.01 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 276 HIS 0.012 0.001 HIS B 362 PHE 0.016 0.001 PHE C 318 TYR 0.034 0.001 TYR C 72 ARG 0.007 0.000 ARG G 575 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 203 time to evaluate : 2.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 391 LYS cc_start: 0.8960 (tptt) cc_final: 0.8200 (tptt) REVERT: B 395 ASP cc_start: 0.9142 (m-30) cc_final: 0.8850 (m-30) REVERT: B 451 LEU cc_start: 0.9648 (mp) cc_final: 0.9447 (tt) REVERT: B 568 VAL cc_start: 0.8620 (OUTLIER) cc_final: 0.8381 (p) REVERT: B 585 LYS cc_start: 0.9486 (mttt) cc_final: 0.9228 (tmtt) REVERT: B 588 LYS cc_start: 0.8446 (mtmm) cc_final: 0.8177 (mtmm) REVERT: C 1 MET cc_start: 0.6616 (ttm) cc_final: 0.6330 (ttm) REVERT: C 128 MET cc_start: 0.8823 (mpp) cc_final: 0.8618 (mmm) REVERT: C 145 GLU cc_start: 0.9258 (OUTLIER) cc_final: 0.8857 (pp20) REVERT: C 281 LYS cc_start: 0.9633 (mttm) cc_final: 0.9409 (mtmm) REVERT: C 389 LEU cc_start: 0.9209 (mt) cc_final: 0.8780 (mt) REVERT: C 446 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8387 (tm-30) REVERT: C 604 ARG cc_start: 0.8699 (mmp80) cc_final: 0.8349 (mmm160) REVERT: C 699 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8548 (mt-10) REVERT: D 22 ASP cc_start: 0.8484 (t0) cc_final: 0.8273 (t0) REVERT: D 389 GLU cc_start: 0.8199 (tt0) cc_final: 0.7943 (tt0) REVERT: E 11 LEU cc_start: 0.9606 (mt) cc_final: 0.9379 (tt) REVERT: E 80 MET cc_start: 0.9183 (ptp) cc_final: 0.8696 (ptp) REVERT: E 82 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8785 (mt-10) REVERT: E 94 ASP cc_start: 0.8409 (t70) cc_final: 0.7926 (t0) REVERT: E 291 TYR cc_start: 0.7534 (m-10) cc_final: 0.7141 (m-10) REVERT: E 292 MET cc_start: 0.8442 (mpp) cc_final: 0.7932 (mpp) REVERT: E 337 HIS cc_start: 0.8256 (t-90) cc_final: 0.7770 (t70) REVERT: E 395 GLU cc_start: 0.9148 (tp30) cc_final: 0.8706 (mp0) REVERT: F 232 MET cc_start: 0.9561 (tpp) cc_final: 0.9172 (tpp) REVERT: A 524 MET cc_start: 0.9450 (mmm) cc_final: 0.8858 (mmp) REVERT: A 536 MET cc_start: 0.8998 (tpp) cc_final: 0.8313 (tpp) REVERT: A 594 MET cc_start: 0.8113 (tpp) cc_final: 0.7831 (tpp) REVERT: A 788 ASP cc_start: 0.9239 (m-30) cc_final: 0.8865 (t0) REVERT: A 817 MET cc_start: 0.8097 (mtm) cc_final: 0.6381 (mtm) REVERT: A 832 MET cc_start: 0.9341 (mmt) cc_final: 0.8836 (mmm) REVERT: A 894 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8497 (mt-10) REVERT: G 327 CYS cc_start: 0.7735 (m) cc_final: 0.7423 (m) REVERT: G 333 VAL cc_start: 0.9087 (t) cc_final: 0.8881 (p) REVERT: G 370 MET cc_start: 0.8866 (tpp) cc_final: 0.8394 (mmt) REVERT: G 376 ASP cc_start: 0.8359 (t0) cc_final: 0.8107 (t0) REVERT: G 378 ILE cc_start: 0.9306 (tt) cc_final: 0.9069 (tp) REVERT: G 420 MET cc_start: 0.9281 (pmm) cc_final: 0.8968 (pmm) REVERT: G 429 LYS cc_start: 0.9341 (pttt) cc_final: 0.9126 (ptpp) REVERT: G 563 MET cc_start: 0.8813 (tmm) cc_final: 0.8574 (tmm) REVERT: G 565 CYS cc_start: 0.9233 (m) cc_final: 0.8963 (p) REVERT: G 588 TYR cc_start: 0.8919 (t80) cc_final: 0.8654 (t80) outliers start: 45 outliers final: 28 residues processed: 239 average time/residue: 0.3230 time to fit residues: 122.6199 Evaluate side-chains 215 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 184 time to evaluate : 2.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 644 LEU Chi-restraints excluded: chain G residue 657 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 239 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 141 optimal weight: 10.0000 chunk 181 optimal weight: 0.0270 chunk 140 optimal weight: 9.9990 chunk 209 optimal weight: 20.0000 chunk 138 optimal weight: 9.9990 chunk 247 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 151 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 overall best weight: 3.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN B 615 GLN C 68 GLN D 20 GLN D 76 ASN ** D 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN G 273 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22233 Z= 0.278 Angle : 0.591 12.766 30349 Z= 0.303 Chirality : 0.039 0.194 3503 Planarity : 0.004 0.042 3607 Dihedral : 17.090 82.546 3661 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.30 % Allowed : 17.16 % Favored : 80.54 % 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: 1.16 (0.17), residues: 2481 helix: 1.49 (0.14), residues: 1492 sheet: -1.24 (0.31), residues: 250 loop : 0.22 (0.24), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 276 HIS 0.019 0.001 HIS C 230 PHE 0.017 0.001 PHE C 594 TYR 0.044 0.002 TYR C 72 ARG 0.008 0.001 ARG G 575 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 179 time to evaluate : 2.512 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: B 585 LYS cc_start: 0.9475 (mttt) cc_final: 0.9193 (tmtt) REVERT: C 1 MET cc_start: 0.6618 (ttm) cc_final: 0.6280 (ttm) REVERT: C 281 LYS cc_start: 0.9643 (mttm) cc_final: 0.9420 (mtmm) REVERT: C 389 LEU cc_start: 0.9260 (mt) cc_final: 0.8828 (mt) REVERT: C 446 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8434 (tm-30) REVERT: C 604 ARG cc_start: 0.8746 (mmp80) cc_final: 0.8343 (mmm160) REVERT: C 699 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8542 (mt-10) REVERT: C 708 MET cc_start: 0.9088 (mmm) cc_final: 0.8763 (mmm) REVERT: D 389 GLU cc_start: 0.8408 (tt0) cc_final: 0.8043 (tt0) REVERT: E 11 LEU cc_start: 0.9631 (mt) cc_final: 0.9347 (tt) REVERT: E 80 MET cc_start: 0.9266 (ptp) cc_final: 0.8744 (ptp) REVERT: E 82 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8806 (mt-10) REVERT: E 94 ASP cc_start: 0.8493 (t70) cc_final: 0.8015 (t0) REVERT: E 254 CYS cc_start: 0.8763 (m) cc_final: 0.8054 (t) REVERT: E 292 MET cc_start: 0.8509 (mpp) cc_final: 0.7914 (mpp) REVERT: E 337 HIS cc_start: 0.8388 (t-90) cc_final: 0.7920 (t70) REVERT: E 395 GLU cc_start: 0.9145 (tp30) cc_final: 0.8582 (mm-30) REVERT: F 232 MET cc_start: 0.9601 (tpp) cc_final: 0.9245 (tpt) REVERT: A 524 MET cc_start: 0.9453 (mmm) cc_final: 0.8835 (mmp) REVERT: A 536 MET cc_start: 0.9064 (tpp) cc_final: 0.8360 (tpp) REVERT: A 594 MET cc_start: 0.8212 (tpp) cc_final: 0.7774 (tpp) REVERT: A 788 ASP cc_start: 0.9280 (m-30) cc_final: 0.8825 (m-30) REVERT: A 832 MET cc_start: 0.9367 (mmt) cc_final: 0.8913 (mmm) REVERT: A 894 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8407 (mt-10) REVERT: G 327 CYS cc_start: 0.7889 (m) cc_final: 0.7562 (m) REVERT: G 378 ILE cc_start: 0.9317 (tt) cc_final: 0.9082 (tp) REVERT: G 420 MET cc_start: 0.9257 (pmm) cc_final: 0.8918 (pmm) REVERT: G 429 LYS cc_start: 0.9329 (pttt) cc_final: 0.9113 (ptpp) REVERT: G 563 MET cc_start: 0.8867 (tmm) cc_final: 0.8598 (tmm) REVERT: G 581 MET cc_start: 0.9190 (mmm) cc_final: 0.8817 (tpp) REVERT: G 610 ASP cc_start: 0.9223 (m-30) cc_final: 0.8767 (t0) outliers start: 51 outliers final: 35 residues processed: 219 average time/residue: 0.3120 time to fit residues: 110.1334 Evaluate side-chains 204 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 168 time to evaluate : 2.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain G residue 318 LYS Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 578 ASP Chi-restraints excluded: chain G residue 657 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 153 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 147 optimal weight: 0.0370 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 47 optimal weight: 0.9980 chunk 157 optimal weight: 6.9990 chunk 168 optimal weight: 0.0370 chunk 122 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 194 optimal weight: 0.0000 overall best weight: 0.3140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN ** D 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 ASN ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22233 Z= 0.143 Angle : 0.550 13.274 30349 Z= 0.277 Chirality : 0.038 0.228 3503 Planarity : 0.003 0.043 3607 Dihedral : 16.985 80.458 3661 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.71 % Allowed : 17.70 % Favored : 80.59 % 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: 1.26 (0.18), residues: 2481 helix: 1.58 (0.14), residues: 1484 sheet: -1.08 (0.32), residues: 252 loop : 0.21 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 276 HIS 0.008 0.001 HIS B 362 PHE 0.016 0.001 PHE C 318 TYR 0.024 0.001 TYR A 648 ARG 0.007 0.000 ARG G 575 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 180 time to evaluate : 2.629 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: B 585 LYS cc_start: 0.9476 (mttt) cc_final: 0.9180 (tmtt) REVERT: C 1 MET cc_start: 0.6638 (ttm) cc_final: 0.6327 (ttm) REVERT: C 145 GLU cc_start: 0.9282 (OUTLIER) cc_final: 0.8440 (mm-30) REVERT: C 281 LYS cc_start: 0.9645 (mttm) cc_final: 0.9406 (mtmm) REVERT: C 306 TYR cc_start: 0.9156 (m-80) cc_final: 0.8702 (m-80) REVERT: C 389 LEU cc_start: 0.9207 (mt) cc_final: 0.8755 (mt) REVERT: C 446 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8442 (tm-30) REVERT: C 604 ARG cc_start: 0.8698 (mmp80) cc_final: 0.8378 (mmm160) REVERT: C 699 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8510 (mt-10) REVERT: C 708 MET cc_start: 0.9060 (mmm) cc_final: 0.8715 (mmm) REVERT: E 11 LEU cc_start: 0.9616 (mt) cc_final: 0.9338 (tt) REVERT: E 80 MET cc_start: 0.9196 (ptp) cc_final: 0.8704 (ptp) REVERT: E 82 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8772 (mt-10) REVERT: E 94 ASP cc_start: 0.8441 (t70) cc_final: 0.7951 (t0) REVERT: E 292 MET cc_start: 0.8429 (mpp) cc_final: 0.7845 (mpp) REVERT: E 337 HIS cc_start: 0.8320 (t-90) cc_final: 0.7863 (t70) REVERT: E 395 GLU cc_start: 0.9129 (tp30) cc_final: 0.8606 (mm-30) REVERT: F 232 MET cc_start: 0.9563 (tpp) cc_final: 0.9197 (tpp) REVERT: A 524 MET cc_start: 0.9448 (mmm) cc_final: 0.8836 (mmp) REVERT: A 536 MET cc_start: 0.9057 (tpp) cc_final: 0.8351 (tpp) REVERT: A 594 MET cc_start: 0.8206 (tpp) cc_final: 0.7770 (tpp) REVERT: A 728 MET cc_start: 0.8447 (mmp) cc_final: 0.8187 (mmm) REVERT: A 788 ASP cc_start: 0.9256 (m-30) cc_final: 0.8837 (t0) REVERT: A 832 MET cc_start: 0.9354 (mmt) cc_final: 0.8886 (mmm) REVERT: A 894 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8429 (mt-10) REVERT: G 324 TYR cc_start: 0.8507 (t80) cc_final: 0.7993 (t80) REVERT: G 327 CYS cc_start: 0.7692 (m) cc_final: 0.7232 (m) REVERT: G 376 ASP cc_start: 0.8299 (t0) cc_final: 0.7221 (p0) REVERT: G 378 ILE cc_start: 0.9308 (tt) cc_final: 0.9066 (tp) REVERT: G 420 MET cc_start: 0.9275 (pmm) cc_final: 0.8937 (pmm) REVERT: G 429 LYS cc_start: 0.9339 (pttt) cc_final: 0.9127 (ptpp) REVERT: G 563 MET cc_start: 0.8800 (tmm) cc_final: 0.8539 (tmm) REVERT: G 565 CYS cc_start: 0.9227 (m) cc_final: 0.9025 (p) REVERT: G 581 MET cc_start: 0.9189 (mmm) cc_final: 0.8735 (tpp) REVERT: G 588 TYR cc_start: 0.8922 (t80) cc_final: 0.8709 (t80) outliers start: 38 outliers final: 27 residues processed: 207 average time/residue: 0.3309 time to fit residues: 109.5768 Evaluate side-chains 197 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 168 time to evaluate : 2.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 644 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 225 optimal weight: 9.9990 chunk 237 optimal weight: 9.9990 chunk 216 optimal weight: 0.9980 chunk 230 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 181 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 208 optimal weight: 0.9980 chunk 218 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 HIS B 577 GLN ** D 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 HIS ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22233 Z= 0.234 Angle : 0.578 13.094 30349 Z= 0.293 Chirality : 0.039 0.264 3503 Planarity : 0.003 0.041 3607 Dihedral : 16.954 82.684 3661 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.80 % Allowed : 17.75 % Favored : 80.45 % 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: 1.35 (0.18), residues: 2481 helix: 1.64 (0.14), residues: 1490 sheet: -1.10 (0.32), residues: 241 loop : 0.25 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 276 HIS 0.008 0.001 HIS B 362 PHE 0.014 0.001 PHE C 594 TYR 0.033 0.001 TYR C 72 ARG 0.007 0.000 ARG G 575 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 173 time to evaluate : 2.551 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 344 MET cc_start: 0.9654 (mmm) cc_final: 0.9342 (tpp) REVERT: B 585 LYS cc_start: 0.9459 (mttt) cc_final: 0.9182 (tmtt) REVERT: B 588 LYS cc_start: 0.8505 (mtmm) cc_final: 0.8160 (mtmm) REVERT: C 1 MET cc_start: 0.6718 (ttm) cc_final: 0.6518 (ttm) REVERT: C 281 LYS cc_start: 0.9652 (mttm) cc_final: 0.9432 (mtmm) REVERT: C 323 MET cc_start: 0.9120 (ppp) cc_final: 0.8875 (ppp) REVERT: C 389 LEU cc_start: 0.9255 (mt) cc_final: 0.8820 (mt) REVERT: C 446 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8450 (tm-30) REVERT: C 604 ARG cc_start: 0.8743 (mmp80) cc_final: 0.8376 (mmm160) REVERT: C 708 MET cc_start: 0.9053 (mmm) cc_final: 0.8796 (mmm) REVERT: E 11 LEU cc_start: 0.9620 (mt) cc_final: 0.9320 (tt) REVERT: E 80 MET cc_start: 0.9239 (ptp) cc_final: 0.8732 (ptp) REVERT: E 82 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8760 (mt-10) REVERT: E 94 ASP cc_start: 0.8479 (t70) cc_final: 0.7982 (t0) REVERT: E 254 CYS cc_start: 0.8763 (m) cc_final: 0.8077 (t) REVERT: E 292 MET cc_start: 0.8432 (mpp) cc_final: 0.7863 (mpp) REVERT: E 337 HIS cc_start: 0.8388 (t-90) cc_final: 0.7942 (t70) REVERT: E 395 GLU cc_start: 0.9148 (tp30) cc_final: 0.8581 (mm-30) REVERT: F 232 MET cc_start: 0.9627 (tpp) cc_final: 0.9259 (tpp) REVERT: F 233 LEU cc_start: 0.9268 (pt) cc_final: 0.8952 (pt) REVERT: A 524 MET cc_start: 0.9462 (mmm) cc_final: 0.8834 (mmp) REVERT: A 536 MET cc_start: 0.9085 (tpp) cc_final: 0.8683 (tpp) REVERT: A 728 MET cc_start: 0.8524 (mmp) cc_final: 0.8280 (mmm) REVERT: A 788 ASP cc_start: 0.9252 (m-30) cc_final: 0.8842 (t0) REVERT: A 832 MET cc_start: 0.9365 (mmt) cc_final: 0.8899 (mmm) REVERT: A 894 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8391 (mt-10) REVERT: G 324 TYR cc_start: 0.8497 (t80) cc_final: 0.8013 (t80) REVERT: G 327 CYS cc_start: 0.7776 (m) cc_final: 0.7304 (m) REVERT: G 370 MET cc_start: 0.8784 (mmt) cc_final: 0.8416 (tpp) REVERT: G 376 ASP cc_start: 0.8179 (t0) cc_final: 0.7110 (p0) REVERT: G 378 ILE cc_start: 0.9306 (tt) cc_final: 0.9064 (tp) REVERT: G 420 MET cc_start: 0.9267 (pmm) cc_final: 0.8904 (pmm) REVERT: G 429 LYS cc_start: 0.9329 (pttt) cc_final: 0.9108 (ptpp) REVERT: G 563 MET cc_start: 0.8851 (tmm) cc_final: 0.8603 (tmm) REVERT: G 581 MET cc_start: 0.9168 (mmm) cc_final: 0.8803 (tpp) REVERT: G 610 ASP cc_start: 0.9204 (m-30) cc_final: 0.8737 (t0) outliers start: 40 outliers final: 34 residues processed: 201 average time/residue: 0.3034 time to fit residues: 99.2216 Evaluate side-chains 202 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 167 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 644 LEU Chi-restraints excluded: chain G residue 657 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 244 optimal weight: 7.9990 chunk 148 optimal weight: 6.9990 chunk 115 optimal weight: 0.6980 chunk 169 optimal weight: 9.9990 chunk 256 optimal weight: 10.0000 chunk 235 optimal weight: 0.4980 chunk 203 optimal weight: 0.6980 chunk 21 optimal weight: 9.9990 chunk 157 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 161 optimal weight: 0.0670 overall best weight: 1.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN ** D 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22233 Z= 0.173 Angle : 0.562 13.049 30349 Z= 0.282 Chirality : 0.038 0.314 3503 Planarity : 0.003 0.041 3607 Dihedral : 16.929 83.320 3661 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.58 % Allowed : 18.11 % Favored : 80.32 % 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: 1.38 (0.18), residues: 2481 helix: 1.64 (0.14), residues: 1490 sheet: -0.99 (0.33), residues: 241 loop : 0.28 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 276 HIS 0.007 0.001 HIS B 362 PHE 0.014 0.001 PHE C 318 TYR 0.033 0.001 TYR C 72 ARG 0.013 0.000 ARG G 575 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 174 time to evaluate : 2.562 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: B 585 LYS cc_start: 0.9475 (mttt) cc_final: 0.9185 (tmtt) REVERT: B 588 LYS cc_start: 0.8512 (mtmm) cc_final: 0.8185 (mtmm) REVERT: C 1 MET cc_start: 0.6759 (ttm) cc_final: 0.6411 (ttm) REVERT: C 145 GLU cc_start: 0.9288 (OUTLIER) cc_final: 0.8892 (pp20) REVERT: C 281 LYS cc_start: 0.9654 (mttm) cc_final: 0.9429 (mtmm) REVERT: C 323 MET cc_start: 0.9106 (ppp) cc_final: 0.8853 (ppp) REVERT: C 389 LEU cc_start: 0.9251 (mt) cc_final: 0.8819 (mt) REVERT: C 446 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8500 (tm-30) REVERT: C 604 ARG cc_start: 0.8725 (mmp80) cc_final: 0.8401 (mmm160) REVERT: C 699 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8544 (mt-10) REVERT: E 11 LEU cc_start: 0.9619 (mt) cc_final: 0.9330 (tt) REVERT: E 80 MET cc_start: 0.9225 (ptp) cc_final: 0.8717 (ptp) REVERT: E 82 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8733 (mt-10) REVERT: E 94 ASP cc_start: 0.8497 (t70) cc_final: 0.8006 (t0) REVERT: E 254 CYS cc_start: 0.8740 (m) cc_final: 0.8072 (t) REVERT: E 292 MET cc_start: 0.8490 (mpp) cc_final: 0.7914 (mpp) REVERT: E 337 HIS cc_start: 0.8376 (t-90) cc_final: 0.7933 (t70) REVERT: E 395 GLU cc_start: 0.9150 (tp30) cc_final: 0.8592 (mm-30) REVERT: F 232 MET cc_start: 0.9477 (tpp) cc_final: 0.9167 (tpt) REVERT: A 524 MET cc_start: 0.9462 (mmm) cc_final: 0.9254 (mmm) REVERT: A 536 MET cc_start: 0.9100 (tpp) cc_final: 0.8627 (tpp) REVERT: A 594 MET cc_start: 0.8408 (tpp) cc_final: 0.8111 (tpp) REVERT: A 728 MET cc_start: 0.8543 (mmp) cc_final: 0.8314 (mmm) REVERT: A 788 ASP cc_start: 0.9246 (m-30) cc_final: 0.8787 (t0) REVERT: A 832 MET cc_start: 0.9359 (mmt) cc_final: 0.8891 (mmm) REVERT: A 894 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8395 (mt-10) REVERT: G 324 TYR cc_start: 0.8496 (t80) cc_final: 0.8014 (t80) REVERT: G 327 CYS cc_start: 0.7750 (m) cc_final: 0.7290 (m) REVERT: G 370 MET cc_start: 0.8788 (mmt) cc_final: 0.8205 (tpp) REVERT: G 376 ASP cc_start: 0.8174 (t0) cc_final: 0.7073 (p0) REVERT: G 378 ILE cc_start: 0.9297 (tt) cc_final: 0.9053 (tp) REVERT: G 420 MET cc_start: 0.9261 (pmm) cc_final: 0.8897 (pmm) REVERT: G 563 MET cc_start: 0.8816 (tmm) cc_final: 0.8577 (tmm) REVERT: G 576 ASN cc_start: 0.9175 (p0) cc_final: 0.8884 (p0) REVERT: G 581 MET cc_start: 0.9143 (mmm) cc_final: 0.8770 (tpp) REVERT: G 610 ASP cc_start: 0.9190 (m-30) cc_final: 0.8720 (t0) outliers start: 35 outliers final: 33 residues processed: 197 average time/residue: 0.3168 time to fit residues: 101.5242 Evaluate side-chains 204 residues out of total 2221 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 169 time to evaluate : 2.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 HIS Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 577 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 644 LEU Chi-restraints excluded: chain G residue 657 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 217 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 187 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 204 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 209 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 179 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 HIS ** E 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 634 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.054095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.041187 restraints weight = 110270.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.042545 restraints weight = 58969.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.043444 restraints weight = 38363.330| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 22233 Z= 0.445 Angle : 0.729 12.751 30349 Z= 0.372 Chirality : 0.043 0.273 3503 Planarity : 0.004 0.048 3607 Dihedral : 17.204 87.291 3661 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.16 % Allowed : 17.70 % Favored : 80.14 % 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: 0.96 (0.17), residues: 2481 helix: 1.23 (0.14), residues: 1506 sheet: -0.98 (0.33), residues: 234 loop : 0.20 (0.24), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 271 HIS 0.008 0.002 HIS B 362 PHE 0.024 0.002 PHE B 581 TYR 0.032 0.002 TYR C 72 ARG 0.009 0.001 ARG G 575 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3928.09 seconds wall clock time: 73 minutes 4.54 seconds (4384.54 seconds total)