Starting phenix.real_space_refine on Sat Jul 27 02:47:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r65_18947/07_2024/8r65_18947.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r65_18947/07_2024/8r65_18947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r65_18947/07_2024/8r65_18947.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r65_18947/07_2024/8r65_18947.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r65_18947/07_2024/8r65_18947.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r65_18947/07_2024/8r65_18947.cif" } resolution = 4.23 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= 0.003 sd= 0.034 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 26 5.49 5 S 124 5.16 5 C 11292 2.51 5 N 3161 2.21 5 O 3476 1.98 5 H 17462 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 493": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 558": "OE1" <-> "OE2" Residue "C GLU 578": "OE1" <-> "OE2" Residue "C ARG 650": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 720": "OE1" <-> "OE2" Residue "C ARG 737": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 35541 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 11519 Classifications: {'peptide': 716} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 31, 'TRANS': 684} Chain: "C" Number of atoms: 11651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 11651 Classifications: {'peptide': 737} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 29, 'TRANS': 707} Chain: "D" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 491 Classifications: {'RNA': 15} Modifications used: {'3*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 3} Link IDs: {'rna2p': 3, 'rna3p': 11} Chain: "E" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 255 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 6} Chain: "X" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 197 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 7, 'TRANS': 17} Chain: "B" Number of atoms: 11428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 11428 Classifications: {'peptide': 718} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 30, 'TRANS': 687} Chain breaks: 2 Time building chain proxies: 15.93, per 1000 atoms: 0.45 Number of scatterers: 35541 At special positions: 0 Unit cell: (133.35, 114.45, 143.85, 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 124 16.00 P 26 15.00 O 3476 8.00 N 3161 7.00 C 11292 6.00 H 17462 1.00 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: 27.86 Conformation dependent library (CDL) restraints added in 3.4 seconds 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4134 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 24 sheets defined 47.3% alpha, 10.7% beta 2 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 15.01 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 removed outlier: 3.641A pdb=" N VAL A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 25 Processing helix chain 'A' and resid 31 through 50 Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 126 through 138 Processing helix chain 'A' and resid 164 through 186 Processing helix chain 'A' and resid 187 through 194 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.880A pdb=" N SER A 247 " --> pdb=" O GLU A 243 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 312 Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 405 through 414 removed outlier: 3.685A pdb=" N SER A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 452 removed outlier: 3.962A pdb=" N HIS A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 476 removed outlier: 3.766A pdb=" N GLU A 457 " --> pdb=" O CYS A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 580 removed outlier: 3.658A pdb=" N LYS A 576 " --> pdb=" O LYS A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 603 removed outlier: 4.061A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 613 Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 3.771A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 694 removed outlier: 3.657A pdb=" N LEU A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N CYS A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A 694 " --> pdb=" O ILE A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 714 Processing helix chain 'C' and resid 2 through 13 removed outlier: 4.272A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 62 through 67 Processing helix chain 'C' and resid 92 through 103 removed outlier: 3.803A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 removed outlier: 3.501A pdb=" N PHE C 119 " --> pdb=" O TYR C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 168 Processing helix chain 'C' and resid 169 through 173 removed outlier: 3.704A pdb=" N VAL C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY C 173 " --> pdb=" O ASN C 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 173' Processing helix chain 'C' and resid 179 through 193 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 231 removed outlier: 4.121A pdb=" N VAL C 231 " --> pdb=" O VAL C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 273 removed outlier: 3.877A pdb=" N VAL C 272 " --> pdb=" O ARG C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 285 Processing helix chain 'C' and resid 294 through 301 Processing helix chain 'C' and resid 305 through 315 Processing helix chain 'C' and resid 390 through 406 removed outlier: 3.652A pdb=" N GLN C 406 " --> pdb=" O MET C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 412 Processing helix chain 'C' and resid 429 through 438 Processing helix chain 'C' and resid 442 through 450 removed outlier: 4.789A pdb=" N GLY C 450 " --> pdb=" O PHE C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 460 removed outlier: 3.959A pdb=" N GLY C 459 " --> pdb=" O ASN C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 556 Processing helix chain 'C' and resid 556 through 564 removed outlier: 4.355A pdb=" N ILE C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 573 Processing helix chain 'C' and resid 577 through 582 Processing helix chain 'C' and resid 588 through 606 removed outlier: 3.658A pdb=" N TYR C 592 " --> pdb=" O ALA C 588 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 606 " --> pdb=" O GLN C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 619 Processing helix chain 'C' and resid 620 through 622 No H-bonds generated for 'chain 'C' and resid 620 through 622' Processing helix chain 'C' and resid 709 through 713 removed outlier: 4.029A pdb=" N LEU C 713 " --> pdb=" O ILE C 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 11 Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.592A pdb=" N PHE B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 removed outlier: 3.785A pdb=" N MET B 40 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 124 Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 175 removed outlier: 3.507A pdb=" N MET B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP B 175 " --> pdb=" O MET B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 248 through 265 removed outlier: 3.801A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 293 removed outlier: 3.519A pdb=" N ASN B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 313 removed outlier: 3.549A pdb=" N ASN B 312 " --> pdb=" O TRP B 309 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN B 313 " --> pdb=" O ASN B 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 309 through 313' Processing helix chain 'B' and resid 314 through 326 removed outlier: 3.600A pdb=" N PHE B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 345 removed outlier: 4.761A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.827A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 393 Processing helix chain 'B' and resid 412 through 426 Processing helix chain 'B' and resid 455 through 473 Processing helix chain 'B' and resid 508 through 512 Processing helix chain 'B' and resid 518 through 536 Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 589 removed outlier: 3.860A pdb=" N LEU B 589 " --> pdb=" O LYS B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 662 through 666 removed outlier: 3.912A pdb=" N TRP B 666 " --> pdb=" O THR B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 677 removed outlier: 3.787A pdb=" N LEU B 675 " --> pdb=" O ARG B 672 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN B 676 " --> pdb=" O SER B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 700 removed outlier: 4.229A pdb=" N GLU B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 704 removed outlier: 4.034A pdb=" N SER B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 701 through 704' Processing helix chain 'B' and resid 713 through 732 Processing helix chain 'B' and resid 736 through 756 Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.312A pdb=" N PHE A 117 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N HIS A 146 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N GLU A 119 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N PHE A 148 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLY A 121 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET A 155 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA3, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 322 removed outlier: 5.862A pdb=" N ILE A 545 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N LEU A 543 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 524 " --> pdb=" O TYR A 564 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 521 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 317 through 322 removed outlier: 5.862A pdb=" N ILE A 545 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N LEU A 543 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 524 " --> pdb=" O TYR A 564 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 570 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 379 removed outlier: 4.024A pdb=" N GLN B 367 " --> pdb=" O VAL A 379 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 619 through 624 removed outlier: 4.476A pdb=" N GLU A 629 " --> pdb=" O ILE A 621 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLU A 623 " --> pdb=" O GLY A 627 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLY A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 78 through 82 removed outlier: 3.767A pdb=" N MET C 90 " --> pdb=" O SER C 79 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE B 667 " --> pdb=" O THR C 58 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 129 through 135 removed outlier: 6.052A pdb=" N PHE C 130 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR C 245 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N MET C 243 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 143 through 146 Processing sheet with id=AB2, first strand: chain 'C' and resid 292 through 293 Processing sheet with id=AB3, first strand: chain 'C' and resid 324 through 325 Processing sheet with id=AB4, first strand: chain 'C' and resid 331 through 334 removed outlier: 6.143A pdb=" N GLU C 362 " --> pdb=" O THR C 333 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR C 371 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N VAL C 386 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE C 373 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU C 384 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ARG C 375 " --> pdb=" O ILE C 382 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 342 through 345 Processing sheet with id=AB6, first strand: chain 'C' and resid 452 through 453 removed outlier: 3.737A pdb=" N SER C 474 " --> pdb=" O GLU C 452 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 504 through 505 removed outlier: 6.497A pdb=" N VAL C 504 " --> pdb=" O LEU C 512 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 635 through 639 Processing sheet with id=AB9, first strand: chain 'C' and resid 656 through 658 removed outlier: 5.762A pdb=" N LEU C 665 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 694 through 699 removed outlier: 6.913A pdb=" N LEU C 733 " --> pdb=" O LEU C 697 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LYS C 699 " --> pdb=" O VAL C 731 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N VAL C 731 " --> pdb=" O LYS C 699 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AC3, first strand: chain 'B' and resid 128 through 129 Processing sheet with id=AC4, first strand: chain 'B' and resid 178 through 181 Processing sheet with id=AC5, first strand: chain 'B' and resid 240 through 244 removed outlier: 6.388A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 437 through 443 removed outlier: 3.615A pdb=" N ALA B 453 " --> pdb=" O LEU B 298 " (cutoff:3.500A) 796 hydrogen bonds defined for protein. 2214 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 5 hydrogen bonds 10 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 13.41 Time building geometry restraints manager: 29.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.00: 17432 1.00 - 1.21: 31 1.21 - 1.41: 7434 1.41 - 1.61: 10824 1.61 - 1.81: 221 Bond restraints: 35942 Sorted by residual: bond pdb=" C ILE C 319 " pdb=" O ILE C 319 " ideal model delta sigma weight residual 1.235 1.164 0.072 1.05e-02 9.07e+03 4.67e+01 bond pdb=" N ILE C 319 " pdb=" CA ILE C 319 " ideal model delta sigma weight residual 1.457 1.503 -0.046 1.15e-02 7.56e+03 1.63e+01 bond pdb=" N SER C 320 " pdb=" CA SER C 320 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.14e-02 7.69e+03 1.05e+01 bond pdb=" N VAL C 494 " pdb=" CA VAL C 494 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.94e+00 bond pdb=" NE2 GLN C 426 " pdb="HE22 GLN C 426 " ideal model delta sigma weight residual 0.860 0.803 0.057 2.00e-02 2.50e+03 8.02e+00 ... (remaining 35937 not shown) Histogram of bond angle deviations from ideal: 83.71 - 95.16: 3 95.16 - 106.60: 744 106.60 - 118.04: 47533 118.04 - 129.48: 16385 129.48 - 140.93: 118 Bond angle restraints: 64783 Sorted by residual: angle pdb=" N MET C 536 " pdb=" CA MET C 536 " pdb=" C MET C 536 " ideal model delta sigma weight residual 108.07 121.75 -13.68 1.38e+00 5.25e-01 9.83e+01 angle pdb=" C MET C 536 " pdb=" CA MET C 536 " pdb=" HA MET C 536 " ideal model delta sigma weight residual 110.00 83.71 26.29 3.00e+00 1.11e-01 7.68e+01 angle pdb=" N MET C 536 " pdb=" CA MET C 536 " pdb=" HA MET C 536 " ideal model delta sigma weight residual 110.00 83.87 26.13 3.00e+00 1.11e-01 7.59e+01 angle pdb=" N PRO C 542 " pdb=" CA PRO C 542 " pdb=" C PRO C 542 " ideal model delta sigma weight residual 113.53 102.89 10.64 1.39e+00 5.18e-01 5.86e+01 angle pdb=" CB MET C 536 " pdb=" CA MET C 536 " pdb=" HA MET C 536 " ideal model delta sigma weight residual 109.00 86.32 22.68 3.00e+00 1.11e-01 5.72e+01 ... (remaining 64778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 15281 17.93 - 35.86: 1158 35.86 - 53.79: 336 53.79 - 71.71: 118 71.71 - 89.64: 28 Dihedral angle restraints: 16921 sinusoidal: 9540 harmonic: 7381 Sorted by residual: dihedral pdb=" C MET C 536 " pdb=" N MET C 536 " pdb=" CA MET C 536 " pdb=" CB MET C 536 " ideal model delta harmonic sigma weight residual -122.60 -161.29 38.69 0 2.50e+00 1.60e-01 2.39e+02 dihedral pdb=" N MET C 536 " pdb=" C MET C 536 " pdb=" CA MET C 536 " pdb=" CB MET C 536 " ideal model delta harmonic sigma weight residual 122.80 161.21 -38.41 0 2.50e+00 1.60e-01 2.36e+02 dihedral pdb=" CD ARG C 493 " pdb=" NE ARG C 493 " pdb=" CZ ARG C 493 " pdb=" NH1 ARG C 493 " ideal model delta sinusoidal sigma weight residual 0.00 -39.85 39.85 1 1.00e+01 1.00e-02 2.23e+01 ... (remaining 16918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.332: 2769 0.332 - 0.663: 0 0.663 - 0.995: 0 0.995 - 1.327: 0 1.327 - 1.658: 1 Chirality restraints: 2770 Sorted by residual: chirality pdb=" CA MET C 536 " pdb=" N MET C 536 " pdb=" C MET C 536 " pdb=" CB MET C 536 " both_signs ideal model delta sigma weight residual False 2.51 0.85 1.66 2.00e-01 2.50e+01 6.87e+01 chirality pdb=" CA ILE C 319 " pdb=" N ILE C 319 " pdb=" C ILE C 319 " pdb=" CB ILE C 319 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA VAL C 495 " pdb=" N VAL C 495 " pdb=" C VAL C 495 " pdb=" CB VAL C 495 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 2767 not shown) Planarity restraints: 5236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 641 " 0.413 9.50e-02 1.11e+02 4.66e-01 4.48e+03 pdb=" NE ARG C 641 " 0.117 2.00e-02 2.50e+03 pdb=" CZ ARG C 641 " 0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG C 641 " 0.027 2.00e-02 2.50e+03 pdb=" NH2 ARG C 641 " -0.061 2.00e-02 2.50e+03 pdb="HH11 ARG C 641 " -0.543 2.00e-02 2.50e+03 pdb="HH12 ARG C 641 " 0.592 2.00e-02 2.50e+03 pdb="HH21 ARG C 641 " -0.834 2.00e-02 2.50e+03 pdb="HH22 ARG C 641 " 0.652 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 548 " 0.048 2.00e-02 2.50e+03 4.40e-01 2.91e+03 pdb=" CG ASN C 548 " -0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN C 548 " -0.046 2.00e-02 2.50e+03 pdb=" ND2 ASN C 548 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN C 548 " 0.764 2.00e-02 2.50e+03 pdb="HD22 ASN C 548 " -0.759 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 493 " -0.676 9.50e-02 1.11e+02 2.60e-01 4.31e+02 pdb=" NE ARG C 493 " 0.069 2.00e-02 2.50e+03 pdb=" CZ ARG C 493 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG C 493 " -0.029 2.00e-02 2.50e+03 pdb=" NH2 ARG C 493 " 0.018 2.00e-02 2.50e+03 pdb="HH11 ARG C 493 " -0.200 2.00e-02 2.50e+03 pdb="HH12 ARG C 493 " 0.113 2.00e-02 2.50e+03 pdb="HH21 ARG C 493 " 0.237 2.00e-02 2.50e+03 pdb="HH22 ARG C 493 " -0.194 2.00e-02 2.50e+03 ... (remaining 5233 not shown) Histogram of nonbonded interaction distances: 1.01 - 1.73: 58 1.73 - 2.45: 21426 2.45 - 3.17: 108856 3.17 - 3.88: 141016 3.88 - 4.60: 227413 Nonbonded interactions: 498769 Sorted by model distance: nonbonded pdb=" H GLY C 223 " pdb=" OE2 GLU C 525 " model vdw 1.014 1.850 nonbonded pdb=" HE1 HIS A 437 " pdb="HH12 ARG C 646 " model vdw 1.085 2.100 nonbonded pdb="HH12 ARG C 143 " pdb=" OG1 THR C 524 " model vdw 1.216 1.850 nonbonded pdb=" HB3 PRO C 276 " pdb="HD11 LEU C 502 " model vdw 1.338 2.440 nonbonded pdb="HH22 ARG C 143 " pdb="HG21 THR C 524 " model vdw 1.354 2.270 ... (remaining 498764 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.500 Extract box with map and model: 1.300 Check model and map are aligned: 0.240 Set scattering table: 0.310 Process input model: 119.340 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 18480 Z= 0.313 Angle : 0.621 13.679 25043 Z= 0.359 Chirality : 0.053 1.658 2770 Planarity : 0.007 0.307 3147 Dihedral : 14.382 89.080 7214 Min Nonbonded Distance : 1.637 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.71 % Favored : 92.78 % Rotamer: Outliers : 1.85 % Allowed : 6.85 % Favored : 91.29 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.18), residues: 2175 helix: 1.04 (0.17), residues: 944 sheet: -2.50 (0.32), residues: 221 loop : -1.99 (0.18), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 537 HIS 0.005 0.001 HIS C 437 PHE 0.020 0.001 PHE C 323 TYR 0.011 0.001 TYR B 555 ARG 0.010 0.000 ARG C 505 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 485 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 449 time to evaluate : 2.668 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8901 (ptm) cc_final: 0.8505 (tpt) REVERT: A 540 TYR cc_start: 0.8608 (m-80) cc_final: 0.8062 (m-80) REVERT: A 570 THR cc_start: 0.7711 (t) cc_final: 0.7382 (t) REVERT: A 584 CYS cc_start: 0.9378 (m) cc_final: 0.9129 (m) REVERT: A 587 GLN cc_start: 0.9419 (tt0) cc_final: 0.9057 (tp-100) REVERT: A 594 SER cc_start: 0.9898 (t) cc_final: 0.9680 (p) REVERT: A 649 LEU cc_start: 0.9086 (mt) cc_final: 0.8877 (mt) REVERT: C 26 ASP cc_start: 0.8215 (m-30) cc_final: 0.7844 (m-30) REVERT: C 69 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8594 (tp30) REVERT: C 90 MET cc_start: 0.9378 (mmm) cc_final: 0.9157 (mmm) REVERT: C 153 ASP cc_start: 0.8865 (t70) cc_final: 0.7975 (m-30) REVERT: C 164 MET cc_start: 0.9138 (mtp) cc_final: 0.8821 (tpp) REVERT: C 483 MET cc_start: 0.6425 (mmp) cc_final: 0.6138 (ptp) REVERT: B 131 TRP cc_start: 0.8706 (p-90) cc_final: 0.7716 (p-90) REVERT: B 137 GLN cc_start: 0.9525 (mm-40) cc_final: 0.9291 (mp10) REVERT: B 303 THR cc_start: 0.7790 (OUTLIER) cc_final: 0.7491 (p) REVERT: B 508 GLU cc_start: 0.9253 (mp0) cc_final: 0.8910 (mp0) REVERT: B 519 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8624 (mt-10) REVERT: B 538 ASP cc_start: 0.9650 (m-30) cc_final: 0.9295 (p0) REVERT: B 599 TYR cc_start: 0.9272 (m-80) cc_final: 0.8622 (m-80) REVERT: B 606 ILE cc_start: 0.8709 (mt) cc_final: 0.8198 (mp) REVERT: B 657 TYR cc_start: 0.8920 (p90) cc_final: 0.8046 (p90) REVERT: B 687 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8934 (mm-40) outliers start: 36 outliers final: 16 residues processed: 478 average time/residue: 0.8375 time to fit residues: 565.9253 Evaluate side-chains 347 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 328 time to evaluate : 2.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 4.9990 chunk 165 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 111 optimal weight: 30.0000 chunk 88 optimal weight: 10.0000 chunk 170 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 197 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 ASN C 27 HIS C 75 GLN C 100 ASN ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 ASN B 532 ASN B 567 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.144 18480 Z= 0.330 Angle : 0.644 7.165 25043 Z= 0.360 Chirality : 0.041 0.615 2770 Planarity : 0.005 0.062 3147 Dihedral : 10.112 86.423 2762 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.20 % Favored : 94.57 % Rotamer: Outliers : 0.10 % Allowed : 2.47 % Favored : 97.42 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.17), residues: 2175 helix: 0.74 (0.16), residues: 964 sheet: -2.26 (0.31), residues: 230 loop : -1.85 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 537 HIS 0.007 0.001 HIS C 27 PHE 0.033 0.002 PHE C 330 TYR 0.021 0.002 TYR C 228 ARG 0.006 0.001 ARG C 641 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 344 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 342 time to evaluate : 2.733 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: 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: 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: 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: 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: 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: A 311 MET cc_start: 0.9570 (mmp) cc_final: 0.9300 (mmm) REVERT: A 460 MET cc_start: 0.9131 (ttp) cc_final: 0.8806 (tmm) REVERT: A 575 MET cc_start: 0.9251 (mtp) cc_final: 0.8984 (mtm) REVERT: A 584 CYS cc_start: 0.9469 (m) cc_final: 0.9220 (m) REVERT: A 587 GLN cc_start: 0.9509 (tt0) cc_final: 0.8937 (mm110) REVERT: A 607 MET cc_start: 0.9018 (mmt) cc_final: 0.8456 (mmm) REVERT: A 649 LEU cc_start: 0.9086 (mt) cc_final: 0.8858 (mt) REVERT: C 283 MET cc_start: 0.9370 (mmm) cc_final: 0.9052 (tpp) REVERT: C 483 MET cc_start: 0.6617 (mmp) cc_final: 0.6180 (mtp) REVERT: B 111 MET cc_start: 0.7379 (mtp) cc_final: 0.7022 (mtt) REVERT: B 131 TRP cc_start: 0.8911 (p-90) cc_final: 0.8390 (p-90) REVERT: B 137 GLN cc_start: 0.9513 (mm-40) cc_final: 0.9052 (mp10) REVERT: B 321 MET cc_start: 0.9586 (mtt) cc_final: 0.9095 (mtt) REVERT: B 348 MET cc_start: 0.9002 (mmt) cc_final: 0.8660 (mmt) REVERT: B 408 MET cc_start: 0.7956 (tpt) cc_final: 0.7278 (tpt) REVERT: B 415 LEU cc_start: 0.9472 (tp) cc_final: 0.9204 (tp) REVERT: B 508 GLU cc_start: 0.8729 (mp0) cc_final: 0.8368 (mp0) REVERT: B 519 GLU cc_start: 0.9146 (mt-10) cc_final: 0.8868 (mt-10) REVERT: B 599 TYR cc_start: 0.9294 (m-80) cc_final: 0.8763 (m-10) REVERT: B 606 ILE cc_start: 0.8954 (mt) cc_final: 0.8522 (mp) REVERT: B 696 PHE cc_start: 0.9279 (t80) cc_final: 0.8989 (t80) outliers start: 2 outliers final: 1 residues processed: 343 average time/residue: 0.7957 time to fit residues: 396.3546 Evaluate side-chains 280 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 279 time to evaluate : 2.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 110 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 chunk 134 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 198 optimal weight: 0.7980 chunk 214 optimal weight: 10.0000 chunk 176 optimal weight: 3.9990 chunk 196 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 chunk 159 optimal weight: 10.0000 overall best weight: 4.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 ASN ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18480 Z= 0.262 Angle : 0.581 7.560 25043 Z= 0.318 Chirality : 0.039 0.390 2770 Planarity : 0.004 0.061 3147 Dihedral : 10.100 82.626 2762 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.29 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.17), residues: 2175 helix: 0.74 (0.16), residues: 962 sheet: -2.00 (0.31), residues: 240 loop : -1.82 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 537 HIS 0.014 0.001 HIS A 146 PHE 0.030 0.002 PHE A 446 TYR 0.019 0.001 TYR A 393 ARG 0.005 0.000 ARG C 264 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 314 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 2.717 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: 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: 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: 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: 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: 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: A 311 MET cc_start: 0.9582 (mmp) cc_final: 0.9208 (mmp) REVERT: A 360 MET cc_start: 0.6886 (mmm) cc_final: 0.6284 (mmm) REVERT: A 431 ASP cc_start: 0.8835 (p0) cc_final: 0.8490 (m-30) REVERT: A 446 PHE cc_start: 0.9475 (m-80) cc_final: 0.9003 (m-80) REVERT: A 460 MET cc_start: 0.9104 (ttp) cc_final: 0.8790 (tmm) REVERT: A 584 CYS cc_start: 0.9462 (m) cc_final: 0.9246 (m) REVERT: A 587 GLN cc_start: 0.9517 (tt0) cc_final: 0.8940 (tp40) REVERT: A 607 MET cc_start: 0.9046 (mmt) cc_final: 0.8540 (mmm) REVERT: A 612 PHE cc_start: 0.8843 (m-80) cc_final: 0.8579 (m-10) REVERT: C 146 ASP cc_start: 0.8443 (m-30) cc_final: 0.8044 (t70) REVERT: C 164 MET cc_start: 0.9256 (mtp) cc_final: 0.8964 (ptt) REVERT: C 297 ILE cc_start: 0.8528 (tp) cc_final: 0.8286 (pt) REVERT: C 315 MET cc_start: -0.2736 (tpt) cc_final: -0.2938 (tpt) REVERT: C 317 LEU cc_start: 0.8560 (mm) cc_final: 0.8024 (pp) REVERT: C 429 ASN cc_start: 0.6408 (m-40) cc_final: 0.6024 (m-40) REVERT: C 460 MET cc_start: -0.2258 (ptt) cc_final: -0.2644 (ptt) REVERT: C 483 MET cc_start: 0.6545 (mmp) cc_final: 0.6326 (mtp) REVERT: B 131 TRP cc_start: 0.8897 (p-90) cc_final: 0.8273 (p-90) REVERT: B 137 GLN cc_start: 0.9470 (mm-40) cc_final: 0.9028 (mp10) REVERT: B 348 MET cc_start: 0.8925 (mmt) cc_final: 0.8624 (mmt) REVERT: B 519 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8824 (mt-10) REVERT: B 546 MET cc_start: 0.9487 (mmp) cc_final: 0.9124 (mmm) REVERT: B 606 ILE cc_start: 0.8947 (mt) cc_final: 0.8707 (mp) REVERT: B 690 GLN cc_start: 0.9162 (tp-100) cc_final: 0.8953 (tp-100) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.7401 time to fit residues: 342.0149 Evaluate side-chains 272 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 195 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 133 optimal weight: 20.0000 chunk 199 optimal weight: 10.0000 chunk 210 optimal weight: 9.9990 chunk 103 optimal weight: 20.0000 chunk 188 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS C 236 GLN ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 HIS ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18480 Z= 0.299 Angle : 0.616 8.845 25043 Z= 0.344 Chirality : 0.039 0.398 2770 Planarity : 0.005 0.080 3147 Dihedral : 10.159 79.734 2762 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.16 % Favored : 93.70 % Rotamer: Outliers : 0.05 % Allowed : 1.70 % Favored : 98.25 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.17), residues: 2175 helix: 0.50 (0.16), residues: 962 sheet: -1.94 (0.32), residues: 220 loop : -1.78 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 55 HIS 0.011 0.001 HIS A 437 PHE 0.017 0.002 PHE B 696 TYR 0.016 0.002 TYR A 393 ARG 0.005 0.001 ARG C 476 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 303 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 302 time to evaluate : 2.982 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 MET cc_start: 0.9329 (ttp) cc_final: 0.9096 (ttp) REVERT: A 360 MET cc_start: 0.7158 (mmm) cc_final: 0.6624 (mmm) REVERT: A 431 ASP cc_start: 0.8889 (p0) cc_final: 0.8503 (m-30) REVERT: A 460 MET cc_start: 0.9115 (ttp) cc_final: 0.8793 (tmm) REVERT: A 584 CYS cc_start: 0.9532 (m) cc_final: 0.9282 (m) REVERT: A 587 GLN cc_start: 0.9500 (tt0) cc_final: 0.8950 (tp40) REVERT: A 607 MET cc_start: 0.8995 (mmt) cc_final: 0.8538 (mmm) REVERT: C 50 MET cc_start: 0.9508 (tpp) cc_final: 0.9293 (tpp) REVERT: C 146 ASP cc_start: 0.8700 (m-30) cc_final: 0.8299 (t70) REVERT: C 164 MET cc_start: 0.9247 (mtp) cc_final: 0.8952 (ptt) REVERT: C 283 MET cc_start: 0.9543 (mmp) cc_final: 0.9276 (tpp) REVERT: C 297 ILE cc_start: 0.8556 (tp) cc_final: 0.8311 (pt) REVERT: C 317 LEU cc_start: 0.8623 (mm) cc_final: 0.8083 (pp) REVERT: C 483 MET cc_start: 0.6896 (mmp) cc_final: 0.6583 (mtp) REVERT: B 131 TRP cc_start: 0.8833 (p-90) cc_final: 0.8120 (p-90) REVERT: B 137 GLN cc_start: 0.9486 (mm-40) cc_final: 0.9280 (mp10) REVERT: B 251 PHE cc_start: 0.9717 (m-10) cc_final: 0.9363 (m-80) REVERT: B 348 MET cc_start: 0.8813 (mmt) cc_final: 0.8589 (mmt) REVERT: B 414 MET cc_start: 0.7999 (mmm) cc_final: 0.7633 (tpp) REVERT: B 546 MET cc_start: 0.9534 (mmp) cc_final: 0.9032 (mmp) REVERT: B 606 ILE cc_start: 0.8974 (mt) cc_final: 0.8745 (mp) REVERT: B 690 GLN cc_start: 0.9127 (tp-100) cc_final: 0.8896 (tp-100) outliers start: 1 outliers final: 1 residues processed: 303 average time/residue: 0.8033 time to fit residues: 352.7084 Evaluate side-chains 264 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 263 time to evaluate : 2.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 175 optimal weight: 5.9990 chunk 119 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 179 optimal weight: 6.9990 chunk 145 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 189 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18480 Z= 0.246 Angle : 0.566 6.338 25043 Z= 0.313 Chirality : 0.038 0.386 2770 Planarity : 0.004 0.060 3147 Dihedral : 10.106 78.296 2762 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.89 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.17), residues: 2175 helix: 0.55 (0.16), residues: 963 sheet: -1.84 (0.31), residues: 220 loop : -1.75 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 55 HIS 0.011 0.001 HIS A 437 PHE 0.029 0.002 PHE A 35 TYR 0.018 0.001 TYR A 393 ARG 0.005 0.000 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 291 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 2.808 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: 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: 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: 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: 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: A 311 MET cc_start: 0.9647 (mmp) cc_final: 0.9235 (mmp) REVERT: A 360 MET cc_start: 0.7276 (mmm) cc_final: 0.6752 (mmm) REVERT: A 431 ASP cc_start: 0.8897 (p0) cc_final: 0.8361 (m-30) REVERT: A 436 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8221 (mt-10) REVERT: A 446 PHE cc_start: 0.9358 (m-80) cc_final: 0.8889 (m-10) REVERT: A 460 MET cc_start: 0.9119 (ttp) cc_final: 0.8752 (tmm) REVERT: A 587 GLN cc_start: 0.9516 (tt0) cc_final: 0.9004 (tp40) REVERT: A 607 MET cc_start: 0.8964 (mmt) cc_final: 0.8433 (mmm) REVERT: A 612 PHE cc_start: 0.8765 (m-80) cc_final: 0.8506 (m-10) REVERT: C 50 MET cc_start: 0.9458 (tpp) cc_final: 0.9172 (tpp) REVERT: C 146 ASP cc_start: 0.8608 (m-30) cc_final: 0.8183 (t70) REVERT: C 164 MET cc_start: 0.9262 (mtp) cc_final: 0.8957 (ptt) REVERT: C 283 MET cc_start: 0.9497 (mmp) cc_final: 0.9247 (tpp) REVERT: C 289 ILE cc_start: 0.8112 (mp) cc_final: 0.7812 (mp) REVERT: C 297 ILE cc_start: 0.8566 (tp) cc_final: 0.8336 (pt) REVERT: C 317 LEU cc_start: 0.8677 (mm) cc_final: 0.8150 (pp) REVERT: C 382 ILE cc_start: 0.8505 (mm) cc_final: 0.8248 (mm) REVERT: C 483 MET cc_start: 0.7063 (mmp) cc_final: 0.6780 (mtp) REVERT: B 171 MET cc_start: 0.9243 (ptt) cc_final: 0.8789 (ptt) REVERT: B 348 MET cc_start: 0.8745 (mmt) cc_final: 0.8475 (mmt) REVERT: B 414 MET cc_start: 0.7911 (mmm) cc_final: 0.7567 (tpp) REVERT: B 534 MET cc_start: 0.9425 (tpt) cc_final: 0.9221 (tpt) REVERT: B 606 ILE cc_start: 0.9005 (mt) cc_final: 0.8789 (mp) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.7878 time to fit residues: 330.7615 Evaluate side-chains 257 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 2.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 70 optimal weight: 4.9990 chunk 189 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 chunk 210 optimal weight: 3.9990 chunk 175 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 110 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 GLN B 136 ASN ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.5973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18480 Z= 0.282 Angle : 0.589 6.520 25043 Z= 0.326 Chirality : 0.039 0.388 2770 Planarity : 0.005 0.073 3147 Dihedral : 10.150 75.884 2762 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.53 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.17), residues: 2175 helix: 0.34 (0.16), residues: 971 sheet: -1.94 (0.31), residues: 217 loop : -1.81 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 55 HIS 0.011 0.001 HIS A 437 PHE 0.018 0.002 PHE B 696 TYR 0.022 0.002 TYR C 205 ARG 0.011 0.001 ARG C 209 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 286 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 2.769 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: 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: 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: 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: 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: symmetry clash REVERT: A 311 MET cc_start: 0.9667 (mmp) cc_final: 0.9238 (mmp) REVERT: A 360 MET cc_start: 0.7508 (mmm) cc_final: 0.6950 (mmm) REVERT: A 431 ASP cc_start: 0.8917 (p0) cc_final: 0.8502 (m-30) REVERT: A 446 PHE cc_start: 0.9298 (m-80) cc_final: 0.8926 (m-10) REVERT: A 460 MET cc_start: 0.9132 (ttp) cc_final: 0.8784 (tmm) REVERT: A 587 GLN cc_start: 0.9527 (tt0) cc_final: 0.9131 (tp40) REVERT: A 607 MET cc_start: 0.8978 (mmt) cc_final: 0.8473 (mmm) REVERT: A 612 PHE cc_start: 0.8755 (m-80) cc_final: 0.8500 (m-80) REVERT: C 50 MET cc_start: 0.9426 (tpp) cc_final: 0.9134 (tpp) REVERT: C 164 MET cc_start: 0.9310 (mtp) cc_final: 0.8979 (ptt) REVERT: C 297 ILE cc_start: 0.8538 (tp) cc_final: 0.8245 (pt) REVERT: C 483 MET cc_start: 0.6914 (mmp) cc_final: 0.6642 (mtp) REVERT: C 512 LEU cc_start: 0.8157 (tt) cc_final: 0.7905 (mt) REVERT: B 174 MET cc_start: 0.8146 (tpp) cc_final: 0.7795 (mmm) REVERT: B 227 MET cc_start: 0.8317 (pmm) cc_final: 0.8093 (pmm) REVERT: B 251 PHE cc_start: 0.9682 (m-10) cc_final: 0.9388 (m-80) REVERT: B 348 MET cc_start: 0.8689 (mmt) cc_final: 0.8451 (mmt) REVERT: B 414 MET cc_start: 0.7829 (mmm) cc_final: 0.7300 (tpp) REVERT: B 599 TYR cc_start: 0.9220 (m-80) cc_final: 0.8739 (m-80) REVERT: B 606 ILE cc_start: 0.9044 (mt) cc_final: 0.8523 (mp) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.8193 time to fit residues: 339.7356 Evaluate side-chains 257 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 2.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 203 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 chunk 119 optimal weight: 0.0370 chunk 177 optimal weight: 0.7980 chunk 117 optimal weight: 6.9990 chunk 210 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 128 optimal weight: 0.3980 chunk 97 optimal weight: 9.9990 overall best weight: 2.0462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 GLN ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.6075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18480 Z= 0.173 Angle : 0.518 5.845 25043 Z= 0.280 Chirality : 0.038 0.381 2770 Planarity : 0.004 0.089 3147 Dihedral : 10.052 76.080 2762 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.52 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.18), residues: 2175 helix: 0.91 (0.16), residues: 965 sheet: -1.78 (0.30), residues: 238 loop : -1.60 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 537 HIS 0.005 0.001 HIS A 146 PHE 0.026 0.002 PHE B 696 TYR 0.019 0.001 TYR A 24 ARG 0.011 0.000 ARG A 179 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 288 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 2.825 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 MET cc_start: 0.9643 (mmp) cc_final: 0.9201 (mmp) REVERT: A 360 MET cc_start: 0.7383 (mmm) cc_final: 0.6889 (mmm) REVERT: A 431 ASP cc_start: 0.8959 (p0) cc_final: 0.8437 (m-30) REVERT: A 436 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8287 (mt-10) REVERT: A 460 MET cc_start: 0.9102 (ttp) cc_final: 0.8749 (tmm) REVERT: A 587 GLN cc_start: 0.9500 (tt0) cc_final: 0.9106 (tp40) REVERT: A 607 MET cc_start: 0.8923 (mmt) cc_final: 0.8462 (mmm) REVERT: C 50 MET cc_start: 0.9345 (tpp) cc_final: 0.8986 (tpp) REVERT: C 153 ASP cc_start: 0.8690 (t0) cc_final: 0.8068 (m-30) REVERT: C 297 ILE cc_start: 0.8494 (tp) cc_final: 0.8193 (pt) REVERT: B 251 PHE cc_start: 0.9659 (m-10) cc_final: 0.9422 (m-80) REVERT: B 508 GLU cc_start: 0.8687 (mp0) cc_final: 0.8486 (mp0) REVERT: B 530 ILE cc_start: 0.9749 (mm) cc_final: 0.9528 (tt) REVERT: B 599 TYR cc_start: 0.9199 (m-80) cc_final: 0.8709 (m-80) REVERT: B 605 HIS cc_start: 0.9148 (p-80) cc_final: 0.8885 (p-80) REVERT: B 606 ILE cc_start: 0.9055 (mt) cc_final: 0.8530 (mp) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.7853 time to fit residues: 323.9210 Evaluate side-chains 260 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 3.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 129 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 143 optimal weight: 6.9990 chunk 103 optimal weight: 30.0000 chunk 19 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.6455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18480 Z= 0.245 Angle : 0.561 6.452 25043 Z= 0.309 Chirality : 0.038 0.388 2770 Planarity : 0.004 0.090 3147 Dihedral : 10.067 73.656 2762 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.07 % Favored : 93.89 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.18), residues: 2175 helix: 0.77 (0.17), residues: 965 sheet: -1.94 (0.31), residues: 235 loop : -1.63 (0.19), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 557 HIS 0.004 0.001 HIS A 146 PHE 0.070 0.002 PHE C 330 TYR 0.020 0.002 TYR A 24 ARG 0.005 0.000 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 283 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 283 time to evaluate : 3.070 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: 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: 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: 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: 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: A 47 MET cc_start: 0.1179 (ttm) cc_final: 0.0872 (ttm) REVERT: A 360 MET cc_start: 0.7767 (mmm) cc_final: 0.7225 (mmm) REVERT: A 431 ASP cc_start: 0.8947 (p0) cc_final: 0.8540 (m-30) REVERT: A 460 MET cc_start: 0.9127 (ttp) cc_final: 0.8755 (tmm) REVERT: A 587 GLN cc_start: 0.9466 (tt0) cc_final: 0.8900 (tp40) REVERT: A 607 MET cc_start: 0.8969 (mmt) cc_final: 0.8543 (mmm) REVERT: A 646 PHE cc_start: 0.9238 (m-80) cc_final: 0.8657 (m-80) REVERT: C 50 MET cc_start: 0.9337 (tpp) cc_final: 0.8929 (tpp) REVERT: C 153 ASP cc_start: 0.8692 (t0) cc_final: 0.8017 (m-30) REVERT: C 297 ILE cc_start: 0.8563 (tp) cc_final: 0.8262 (pt) REVERT: B 111 MET cc_start: 0.7446 (mtp) cc_final: 0.6763 (mtt) REVERT: B 174 MET cc_start: 0.8236 (tpp) cc_final: 0.7837 (mmm) REVERT: B 227 MET cc_start: 0.8243 (pmm) cc_final: 0.8012 (pmm) REVERT: B 251 PHE cc_start: 0.9665 (m-10) cc_final: 0.9420 (m-80) REVERT: B 414 MET cc_start: 0.7737 (mmm) cc_final: 0.7214 (tpp) REVERT: B 508 GLU cc_start: 0.8666 (mp0) cc_final: 0.8450 (mp0) REVERT: B 599 TYR cc_start: 0.9224 (m-80) cc_final: 0.8794 (m-80) REVERT: B 605 HIS cc_start: 0.9254 (p-80) cc_final: 0.8972 (p-80) REVERT: B 606 ILE cc_start: 0.9085 (mt) cc_final: 0.8602 (mp) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.7926 time to fit residues: 324.0859 Evaluate side-chains 258 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 191 optimal weight: 10.0000 chunk 201 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 195 optimal weight: 10.0000 chunk 117 optimal weight: 0.0770 chunk 85 optimal weight: 9.9990 chunk 153 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 176 optimal weight: 6.9990 chunk 185 optimal weight: 5.9990 chunk 128 optimal weight: 20.0000 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 591 GLN ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.6740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18480 Z= 0.217 Angle : 0.545 5.956 25043 Z= 0.301 Chirality : 0.039 0.389 2770 Planarity : 0.005 0.085 3147 Dihedral : 10.064 73.491 2762 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.07 % Favored : 93.89 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.18), residues: 2175 helix: 0.85 (0.17), residues: 958 sheet: -1.89 (0.31), residues: 235 loop : -1.58 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 317 HIS 0.007 0.001 HIS A 437 PHE 0.028 0.002 PHE C 330 TYR 0.020 0.001 TYR A 24 ARG 0.011 0.001 ARG C 17 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 282 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 3.368 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash REVERT: A 431 ASP cc_start: 0.8921 (p0) cc_final: 0.8534 (m-30) REVERT: A 460 MET cc_start: 0.9109 (ttp) cc_final: 0.8734 (tmm) REVERT: A 587 GLN cc_start: 0.9481 (tt0) cc_final: 0.8908 (tp40) REVERT: A 607 MET cc_start: 0.8958 (mmt) cc_final: 0.8558 (mmm) REVERT: A 646 PHE cc_start: 0.9237 (m-80) cc_final: 0.8659 (m-80) REVERT: C 50 MET cc_start: 0.9316 (tpp) cc_final: 0.8920 (tpp) REVERT: C 153 ASP cc_start: 0.8669 (t0) cc_final: 0.8037 (m-30) REVERT: C 297 ILE cc_start: 0.8551 (tp) cc_final: 0.8242 (pt) REVERT: B 111 MET cc_start: 0.7857 (mtp) cc_final: 0.7343 (mtt) REVERT: B 227 MET cc_start: 0.8217 (pmm) cc_final: 0.7969 (pmm) REVERT: B 251 PHE cc_start: 0.9656 (m-10) cc_final: 0.9406 (m-80) REVERT: B 414 MET cc_start: 0.7684 (mmm) cc_final: 0.7300 (tpp) REVERT: B 599 TYR cc_start: 0.9207 (m-80) cc_final: 0.8799 (m-80) REVERT: B 605 HIS cc_start: 0.9330 (p-80) cc_final: 0.9085 (p-80) REVERT: B 606 ILE cc_start: 0.9135 (mt) cc_final: 0.8640 (mp) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.7648 time to fit residues: 312.1323 Evaluate side-chains 251 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 2.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 207 optimal weight: 0.9990 chunk 126 optimal weight: 9.9990 chunk 98 optimal weight: 0.6980 chunk 143 optimal weight: 9.9990 chunk 217 optimal weight: 0.9980 chunk 199 optimal weight: 7.9990 chunk 172 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.6787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18480 Z= 0.167 Angle : 0.512 5.992 25043 Z= 0.278 Chirality : 0.038 0.385 2770 Planarity : 0.004 0.072 3147 Dihedral : 9.994 73.357 2762 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.75 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.18), residues: 2175 helix: 1.01 (0.17), residues: 966 sheet: -1.80 (0.30), residues: 246 loop : -1.50 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 55 HIS 0.011 0.001 HIS A 437 PHE 0.035 0.002 PHE C 330 TYR 0.019 0.001 TYR A 24 ARG 0.013 0.000 ARG A 84 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 285 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 2.600 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: 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: 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: 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: 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: A 1 MET cc_start: 0.9051 (ptm) cc_final: 0.8752 (tpt) REVERT: A 47 MET cc_start: 0.1415 (ttm) cc_final: 0.1117 (ttm) REVERT: A 360 MET cc_start: 0.7966 (mmm) cc_final: 0.7411 (mmm) REVERT: A 431 ASP cc_start: 0.8933 (p0) cc_final: 0.8584 (m-30) REVERT: A 460 MET cc_start: 0.9068 (ttp) cc_final: 0.8673 (tmm) REVERT: A 587 GLN cc_start: 0.9457 (tt0) cc_final: 0.8883 (tp40) REVERT: A 646 PHE cc_start: 0.9171 (m-80) cc_final: 0.8597 (m-80) REVERT: C 50 MET cc_start: 0.9306 (tpp) cc_final: 0.8902 (tpp) REVERT: C 153 ASP cc_start: 0.8703 (t0) cc_final: 0.8110 (m-30) REVERT: C 297 ILE cc_start: 0.8522 (tp) cc_final: 0.8130 (pt) REVERT: C 317 LEU cc_start: 0.8760 (mm) cc_final: 0.8295 (pp) REVERT: B 227 MET cc_start: 0.8114 (pmm) cc_final: 0.7847 (pmm) REVERT: B 251 PHE cc_start: 0.9647 (m-10) cc_final: 0.9416 (m-80) REVERT: B 414 MET cc_start: 0.7671 (mmm) cc_final: 0.7161 (tpp) REVERT: B 530 ILE cc_start: 0.9766 (mm) cc_final: 0.9521 (tt) REVERT: B 545 GLN cc_start: 0.9324 (mt0) cc_final: 0.9039 (mt0) REVERT: B 599 TYR cc_start: 0.9193 (m-80) cc_final: 0.8773 (m-80) REVERT: B 605 HIS cc_start: 0.9330 (p-80) cc_final: 0.9043 (p-80) REVERT: B 606 ILE cc_start: 0.9132 (mt) cc_final: 0.8634 (mp) REVERT: B 657 TYR cc_start: 0.8780 (p90) cc_final: 0.8143 (p90) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.7718 time to fit residues: 320.0587 Evaluate side-chains 255 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 177 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 152 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN B 225 ASN ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.092110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.079906 restraints weight = 516838.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.082081 restraints weight = 244913.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.083319 restraints weight = 138211.206| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.7120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 18480 Z= 0.253 Angle : 0.572 7.391 25043 Z= 0.318 Chirality : 0.039 0.384 2770 Planarity : 0.005 0.071 3147 Dihedral : 10.058 73.428 2762 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.71 % Favored : 93.24 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.18), residues: 2175 helix: 0.70 (0.16), residues: 973 sheet: -1.83 (0.31), residues: 237 loop : -1.64 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 55 HIS 0.006 0.001 HIS A 146 PHE 0.032 0.002 PHE C 330 TYR 0.020 0.002 TYR A 24 ARG 0.011 0.001 ARG A 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8078.43 seconds wall clock time: 141 minutes 57.10 seconds (8517.10 seconds total)