Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 22:48:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm6_4589/04_2023/6qm6_4589.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm6_4589/04_2023/6qm6_4589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm6_4589/04_2023/6qm6_4589.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm6_4589/04_2023/6qm6_4589.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm6_4589/04_2023/6qm6_4589.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm6_4589/04_2023/6qm6_4589.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 7056 2.51 5 N 1814 2.21 5 O 1942 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 34": "OD1" <-> "OD2" Residue "A GLU 35": "OE1" <-> "OE2" Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A ASP 179": "OD1" <-> "OD2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 425": "OE1" <-> "OE2" Residue "A ASP 478": "OD1" <-> "OD2" Residue "A GLU 480": "OE1" <-> "OE2" Residue "A ASP 499": "OD1" <-> "OD2" Residue "A ASP 556": "OD1" <-> "OD2" Residue "A ASP 628": "OD1" <-> "OD2" Residue "A GLU 635": "OE1" <-> "OE2" Residue "A GLU 649": "OE1" <-> "OE2" Residue "A ARG 672": "NH1" <-> "NH2" Residue "A GLU 677": "OE1" <-> "OE2" Residue "A GLU 691": "OE1" <-> "OE2" Residue "A ARG 699": "NH1" <-> "NH2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 34": "OD1" <-> "OD2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B ASP 179": "OD1" <-> "OD2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "B PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 239": "OE1" <-> "OE2" Residue "B ASP 241": "OD1" <-> "OD2" Residue "B GLU 264": "OE1" <-> "OE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 352": "OE1" <-> "OE2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 425": "OE1" <-> "OE2" Residue "B ASP 478": "OD1" <-> "OD2" Residue "B GLU 480": "OE1" <-> "OE2" Residue "B ASP 499": "OD1" <-> "OD2" Residue "B ASP 556": "OD1" <-> "OD2" Residue "B ASP 628": "OD1" <-> "OD2" Residue "B GLU 635": "OE1" <-> "OE2" Residue "B GLU 649": "OE1" <-> "OE2" Residue "B ARG 672": "NH1" <-> "NH2" Residue "B GLU 677": "OE1" <-> "OE2" Residue "B GLU 691": "OE1" <-> "OE2" Residue "B ARG 699": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 10852 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 672, 5426 Classifications: {'peptide': 672} Link IDs: {'PTRANS': 29, 'TRANS': 642} Chain breaks: 5 Chain: "B" Number of atoms: 5426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 672, 5426 Classifications: {'peptide': 672} Link IDs: {'PTRANS': 29, 'TRANS': 642} Chain breaks: 5 Time building chain proxies: 6.07, per 1000 atoms: 0.56 Number of scatterers: 10852 At special positions: 0 Unit cell: (88.044, 141.68, 107.272, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1942 8.00 N 1814 7.00 C 7056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.42 Conformation dependent library (CDL) restraints added in 1.6 seconds 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2544 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 4 sheets defined 70.5% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 32 through 50 removed outlier: 3.753A pdb=" N THR A 48 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 90 removed outlier: 3.776A pdb=" N LYS A 78 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS A 90 " --> pdb=" O GLY A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 111 through 123 Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.540A pdb=" N ASN A 138 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 139 " --> pdb=" O PRO A 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 135 through 139' Processing helix chain 'A' and resid 152 through 166 removed outlier: 3.573A pdb=" N SER A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 199 removed outlier: 3.779A pdb=" N ILE A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS A 180 " --> pdb=" O ASN A 176 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N GLU A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N SER A 184 " --> pdb=" O LYS A 180 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL A 185 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TYR A 188 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 212 Processing helix chain 'A' and resid 217 through 244 removed outlier: 3.513A pdb=" N ALA A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 229 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 244 " --> pdb=" O VAL A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 290 through 318 removed outlier: 3.554A pdb=" N LEU A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 338 removed outlier: 3.519A pdb=" N PHE A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 359 removed outlier: 3.644A pdb=" N SER A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN A 359 " --> pdb=" O ASN A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 392 removed outlier: 4.252A pdb=" N VAL A 376 " --> pdb=" O GLN A 372 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER A 382 " --> pdb=" O ASN A 378 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ALA A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 415 removed outlier: 4.154A pdb=" N PHE A 403 " --> pdb=" O ILE A 399 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TRP A 407 " --> pdb=" O PHE A 403 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN A 412 " --> pdb=" O ARG A 408 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 442 Processing helix chain 'A' and resid 442 through 453 removed outlier: 3.630A pdb=" N VAL A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 467 removed outlier: 3.504A pdb=" N GLN A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A 467 " --> pdb=" O PHE A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 494 removed outlier: 3.919A pdb=" N THR A 494 " --> pdb=" O ARG A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 516 removed outlier: 4.085A pdb=" N ASP A 503 " --> pdb=" O ASP A 499 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR A 513 " --> pdb=" O MET A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 546 removed outlier: 3.623A pdb=" N ASN A 531 " --> pdb=" O CYS A 527 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 534 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG A 537 " --> pdb=" O TRP A 533 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA A 544 " --> pdb=" O ALA A 540 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 546 " --> pdb=" O LYS A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 585 removed outlier: 3.680A pdb=" N SER A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A 581 " --> pdb=" O SER A 577 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER A 584 " --> pdb=" O VAL A 580 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASN A 585 " --> pdb=" O TYR A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 627 removed outlier: 3.584A pdb=" N LEU A 602 " --> pdb=" O LYS A 598 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 649 removed outlier: 3.540A pdb=" N GLN A 633 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS A 634 " --> pdb=" O PRO A 630 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS A 643 " --> pdb=" O ARG A 639 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 649 " --> pdb=" O ARG A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 678 removed outlier: 3.637A pdb=" N ILE A 670 " --> pdb=" O HIS A 666 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR A 671 " --> pdb=" O SER A 667 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 673 " --> pdb=" O LYS A 669 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 676 " --> pdb=" O ARG A 672 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU A 678 " --> pdb=" O ALA A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 693 Processing helix chain 'A' and resid 700 through 718 removed outlier: 3.914A pdb=" N THR A 704 " --> pdb=" O GLY A 700 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET A 711 " --> pdb=" O ILE A 707 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE A 712 " --> pdb=" O GLY A 708 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU A 713 " --> pdb=" O ARG A 709 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN A 714 " --> pdb=" O ARG A 710 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA A 718 " --> pdb=" O GLN A 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 50 removed outlier: 3.753A pdb=" N THR B 48 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR B 49 " --> pdb=" O ARG B 45 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL B 50 " --> pdb=" O ALA B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 90 removed outlier: 3.776A pdb=" N LYS B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS B 90 " --> pdb=" O GLY B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 111 through 123 Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.539A pdb=" N ASN B 138 " --> pdb=" O THR B 135 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 139 " --> pdb=" O PRO B 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 135 through 139' Processing helix chain 'B' and resid 152 through 166 removed outlier: 3.573A pdb=" N SER B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS B 166 " --> pdb=" O LYS B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 199 removed outlier: 3.779A pdb=" N ILE B 174 " --> pdb=" O GLU B 170 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS B 180 " --> pdb=" O ASN B 176 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N GLU B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N SER B 184 " --> pdb=" O LYS B 180 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL B 185 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 186 " --> pdb=" O GLY B 182 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TYR B 188 " --> pdb=" O SER B 184 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 212 Processing helix chain 'B' and resid 217 through 244 removed outlier: 3.513A pdb=" N ALA B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL B 229 " --> pdb=" O GLY B 225 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 240 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B 244 " --> pdb=" O VAL B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 290 through 318 removed outlier: 3.554A pdb=" N LEU B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU B 318 " --> pdb=" O VAL B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 338 removed outlier: 3.518A pdb=" N PHE B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 359 removed outlier: 3.644A pdb=" N SER B 344 " --> pdb=" O THR B 340 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN B 359 " --> pdb=" O ASN B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 392 removed outlier: 4.252A pdb=" N VAL B 376 " --> pdb=" O GLN B 372 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER B 382 " --> pdb=" O ASN B 378 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ALA B 385 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 415 removed outlier: 4.153A pdb=" N PHE B 403 " --> pdb=" O ILE B 399 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TRP B 407 " --> pdb=" O PHE B 403 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN B 412 " --> pdb=" O ARG B 408 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 442 Processing helix chain 'B' and resid 442 through 453 removed outlier: 3.630A pdb=" N VAL B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 467 removed outlier: 3.504A pdb=" N GLN B 464 " --> pdb=" O GLN B 460 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 467 " --> pdb=" O PHE B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 494 removed outlier: 3.919A pdb=" N THR B 494 " --> pdb=" O ARG B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 516 removed outlier: 4.086A pdb=" N ASP B 503 " --> pdb=" O ASP B 499 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 546 removed outlier: 3.623A pdb=" N ASN B 531 " --> pdb=" O CYS B 527 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP B 533 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 534 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG B 537 " --> pdb=" O TRP B 533 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA B 544 " --> pdb=" O ALA B 540 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 546 " --> pdb=" O LYS B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 585 removed outlier: 3.681A pdb=" N SER B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER B 577 " --> pdb=" O SER B 573 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR B 581 " --> pdb=" O SER B 577 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN B 585 " --> pdb=" O TYR B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 627 removed outlier: 3.585A pdb=" N LEU B 602 " --> pdb=" O LYS B 598 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 649 removed outlier: 3.540A pdb=" N GLN B 633 " --> pdb=" O SER B 629 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS B 634 " --> pdb=" O PRO B 630 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU B 638 " --> pdb=" O LYS B 634 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS B 643 " --> pdb=" O ARG B 639 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU B 649 " --> pdb=" O ARG B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 678 removed outlier: 3.637A pdb=" N ILE B 670 " --> pdb=" O HIS B 666 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR B 671 " --> pdb=" O SER B 667 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU B 673 " --> pdb=" O LYS B 669 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 676 " --> pdb=" O ARG B 672 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU B 678 " --> pdb=" O ALA B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 693 Processing helix chain 'B' and resid 700 through 718 removed outlier: 3.914A pdb=" N THR B 704 " --> pdb=" O GLY B 700 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET B 711 " --> pdb=" O ILE B 707 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE B 712 " --> pdb=" O GLY B 708 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU B 713 " --> pdb=" O ARG B 709 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN B 714 " --> pdb=" O ARG B 710 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA B 718 " --> pdb=" O GLN B 714 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56 removed outlier: 3.576A pdb=" N PHE A 22 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 268 removed outlier: 3.725A pdb=" N HIS A 265 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 267 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 56 removed outlier: 3.576A pdb=" N PHE B 22 " --> pdb=" O VAL B 68 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 265 through 268 removed outlier: 3.724A pdb=" N HIS B 265 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 267 " --> pdb=" O VAL B 276 " (cutoff:3.500A) 601 hydrogen bonds defined for protein. 1797 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.11 Time building geometry restraints manager: 4.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3436 1.34 - 1.46: 2295 1.46 - 1.58: 5335 1.58 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 11132 Sorted by residual: bond pdb=" C SER B 595 " pdb=" N PRO B 596 " ideal model delta sigma weight residual 1.330 1.372 -0.041 1.23e-02 6.61e+03 1.13e+01 bond pdb=" C SER A 595 " pdb=" N PRO A 596 " ideal model delta sigma weight residual 1.330 1.371 -0.041 1.23e-02 6.61e+03 1.12e+01 bond pdb=" C ILE B 394 " pdb=" N PRO B 395 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.09e+00 bond pdb=" C ILE A 394 " pdb=" N PRO A 395 " ideal model delta sigma weight residual 1.334 1.391 -0.057 2.34e-02 1.83e+03 6.01e+00 bond pdb=" N GLU B 32 " pdb=" CA GLU B 32 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.88e+00 ... (remaining 11127 not shown) Histogram of bond angle deviations from ideal: 100.06 - 106.95: 326 106.95 - 113.84: 6145 113.84 - 120.73: 5240 120.73 - 127.62: 3239 127.62 - 134.51: 146 Bond angle restraints: 15096 Sorted by residual: angle pdb=" CA ILE A 394 " pdb=" C ILE A 394 " pdb=" N PRO A 395 " ideal model delta sigma weight residual 118.88 124.52 -5.64 1.54e+00 4.22e-01 1.34e+01 angle pdb=" CA ILE B 394 " pdb=" C ILE B 394 " pdb=" N PRO B 395 " ideal model delta sigma weight residual 118.88 124.49 -5.61 1.54e+00 4.22e-01 1.33e+01 angle pdb=" CA GLU A 32 " pdb=" CB GLU A 32 " pdb=" CG GLU A 32 " ideal model delta sigma weight residual 114.10 120.84 -6.74 2.00e+00 2.50e-01 1.13e+01 angle pdb=" CA GLU B 32 " pdb=" CB GLU B 32 " pdb=" CG GLU B 32 " ideal model delta sigma weight residual 114.10 120.83 -6.73 2.00e+00 2.50e-01 1.13e+01 angle pdb=" CA THR A 340 " pdb=" C THR A 340 " pdb=" N PRO A 341 " ideal model delta sigma weight residual 118.44 123.43 -4.99 1.59e+00 3.96e-01 9.83e+00 ... (remaining 15091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.20: 5737 16.20 - 32.40: 661 32.40 - 48.59: 124 48.59 - 64.79: 20 64.79 - 80.99: 14 Dihedral angle restraints: 6556 sinusoidal: 2636 harmonic: 3920 Sorted by residual: dihedral pdb=" CA HIS B 401 " pdb=" C HIS B 401 " pdb=" N PRO B 402 " pdb=" CA PRO B 402 " ideal model delta harmonic sigma weight residual 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA HIS A 401 " pdb=" C HIS A 401 " pdb=" N PRO A 402 " pdb=" CA PRO A 402 " ideal model delta harmonic sigma weight residual 180.00 162.24 17.76 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA THR A 340 " pdb=" C THR A 340 " pdb=" N PRO A 341 " pdb=" CA PRO A 341 " ideal model delta harmonic sigma weight residual 180.00 163.50 16.50 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 6553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1283 0.047 - 0.094: 271 0.094 - 0.141: 82 0.141 - 0.188: 18 0.188 - 0.235: 2 Chirality restraints: 1656 Sorted by residual: chirality pdb=" CA THR A 340 " pdb=" N THR A 340 " pdb=" C THR A 340 " pdb=" CB THR A 340 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA THR B 340 " pdb=" N THR B 340 " pdb=" C THR B 340 " pdb=" CB THR B 340 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CB VAL A 229 " pdb=" CA VAL A 229 " pdb=" CG1 VAL A 229 " pdb=" CG2 VAL A 229 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.86e-01 ... (remaining 1653 not shown) Planarity restraints: 1916 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 401 " 0.045 5.00e-02 4.00e+02 6.77e-02 7.34e+00 pdb=" N PRO A 402 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 402 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 402 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 401 " 0.045 5.00e-02 4.00e+02 6.76e-02 7.32e+00 pdb=" N PRO B 402 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 402 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 402 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 595 " 0.029 5.00e-02 4.00e+02 4.38e-02 3.08e+00 pdb=" N PRO A 596 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 596 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 596 " 0.025 5.00e-02 4.00e+02 ... (remaining 1913 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 3674 2.85 - 3.36: 10232 3.36 - 3.88: 17348 3.88 - 4.39: 20232 4.39 - 4.90: 34081 Nonbonded interactions: 85567 Sorted by model distance: nonbonded pdb=" OH TYR B 188 " pdb=" OD2 ASP B 539 " model vdw 2.338 2.440 nonbonded pdb=" OH TYR A 188 " pdb=" OD2 ASP A 539 " model vdw 2.338 2.440 nonbonded pdb=" O PHE A 528 " pdb=" ND2 ASN A 532 " model vdw 2.376 2.520 nonbonded pdb=" O PHE B 528 " pdb=" ND2 ASN B 532 " model vdw 2.376 2.520 nonbonded pdb=" O GLN A 374 " pdb=" ND2 ASN A 378 " model vdw 2.382 2.520 ... (remaining 85562 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.600 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: 0.010 Extract box with map and model: 3.850 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 30.280 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 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 : 0.004 0.058 11132 Z= 0.282 Angle : 0.844 9.915 15096 Z= 0.500 Chirality : 0.045 0.235 1656 Planarity : 0.006 0.068 1916 Dihedral : 14.338 80.989 4012 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % 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: -6.02 (0.14), residues: 1320 helix: -4.55 (0.06), residues: 874 sheet: -2.94 (0.54), residues: 50 loop : -1.98 (0.25), residues: 396 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.2506 time to fit residues: 77.4304 Evaluate side-chains 146 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.333 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 56 optimal weight: 0.0270 chunk 34 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 42 GLN A 98 HIS A 99 ASN A 143 HIS A 359 ASN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS A 412 GLN ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN B 17 ASN B 42 GLN B 98 HIS B 99 ASN B 143 HIS B 359 ASN ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 HIS B 461 GLN B 510 GLN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 11132 Z= 0.276 Angle : 0.620 7.177 15096 Z= 0.324 Chirality : 0.041 0.179 1656 Planarity : 0.005 0.043 1916 Dihedral : 4.446 16.095 1444 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % 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: -2.82 (0.19), residues: 1320 helix: -1.82 (0.14), residues: 898 sheet: -1.22 (0.59), residues: 58 loop : -1.54 (0.30), residues: 364 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 185 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 191 average time/residue: 0.2085 time to fit residues: 59.4436 Evaluate side-chains 161 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 155 time to evaluate : 1.461 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2177 time to fit residues: 3.6966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 GLN A 461 GLN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 HIS ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 11132 Z= 0.210 Angle : 0.567 8.854 15096 Z= 0.287 Chirality : 0.040 0.181 1656 Planarity : 0.004 0.033 1916 Dihedral : 4.133 14.891 1444 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % 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: -1.00 (0.22), residues: 1320 helix: -0.30 (0.16), residues: 906 sheet: -0.33 (0.61), residues: 58 loop : -1.34 (0.32), residues: 356 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 171 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 175 average time/residue: 0.1825 time to fit residues: 49.9930 Evaluate side-chains 160 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 154 time to evaluate : 1.320 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1064 time to fit residues: 2.9094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 4.9990 chunk 91 optimal weight: 0.4980 chunk 63 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 129 optimal weight: 9.9990 chunk 115 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 256 GLN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 GLN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 11132 Z= 0.252 Angle : 0.581 11.110 15096 Z= 0.292 Chirality : 0.041 0.193 1656 Planarity : 0.004 0.046 1916 Dihedral : 4.043 14.608 1444 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % 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: -0.15 (0.23), residues: 1320 helix: 0.41 (0.17), residues: 902 sheet: -0.23 (0.65), residues: 58 loop : -1.13 (0.32), residues: 360 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 161 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 166 average time/residue: 0.1699 time to fit residues: 44.9660 Evaluate side-chains 150 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 147 time to evaluate : 1.356 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0957 time to fit residues: 2.2827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 0.9980 chunk 1 optimal weight: 0.0870 chunk 96 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 116 optimal weight: 0.0870 chunk 32 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 GLN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.051 11132 Z= 0.159 Angle : 0.553 12.586 15096 Z= 0.269 Chirality : 0.039 0.166 1656 Planarity : 0.004 0.033 1916 Dihedral : 3.874 14.014 1444 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % 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: 0.40 (0.23), residues: 1320 helix: 0.90 (0.18), residues: 904 sheet: -0.29 (0.65), residues: 58 loop : -1.12 (0.32), residues: 358 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 169 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 180 average time/residue: 0.1757 time to fit residues: 49.9049 Evaluate side-chains 162 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 157 time to evaluate : 1.374 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1101 time to fit residues: 2.7437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 0.5980 chunk 25 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 31 optimal weight: 0.0060 chunk 129 optimal weight: 5.9990 chunk 107 optimal weight: 0.0770 chunk 60 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.7156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 11132 Z= 0.163 Angle : 0.572 12.001 15096 Z= 0.273 Chirality : 0.039 0.176 1656 Planarity : 0.003 0.032 1916 Dihedral : 3.761 14.200 1444 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % 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: 0.79 (0.24), residues: 1320 helix: 1.22 (0.18), residues: 904 sheet: -0.29 (0.66), residues: 58 loop : -1.03 (0.32), residues: 358 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 162 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 169 average time/residue: 0.1799 time to fit residues: 48.2411 Evaluate side-chains 164 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 157 time to evaluate : 1.352 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1029 time to fit residues: 3.2608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 GLN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 GLN ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 11132 Z= 0.299 Angle : 0.636 9.660 15096 Z= 0.314 Chirality : 0.042 0.181 1656 Planarity : 0.004 0.031 1916 Dihedral : 3.934 14.551 1444 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % 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: 0.76 (0.24), residues: 1320 helix: 1.16 (0.18), residues: 902 sheet: -0.14 (0.65), residues: 58 loop : -0.95 (0.33), residues: 360 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 152 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 158 average time/residue: 0.1850 time to fit residues: 46.6480 Evaluate side-chains 145 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 141 time to evaluate : 1.359 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1080 time to fit residues: 2.6277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 63 optimal weight: 20.0000 chunk 12 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 chunk 123 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 11132 Z= 0.288 Angle : 0.633 10.026 15096 Z= 0.314 Chirality : 0.042 0.169 1656 Planarity : 0.004 0.032 1916 Dihedral : 3.980 14.593 1444 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % 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: 0.71 (0.24), residues: 1320 helix: 1.12 (0.18), residues: 902 sheet: -0.23 (0.64), residues: 58 loop : -0.95 (0.33), residues: 360 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 146 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 151 average time/residue: 0.1715 time to fit residues: 41.2995 Evaluate side-chains 144 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 139 time to evaluate : 1.319 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1073 time to fit residues: 2.8032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 11132 Z= 0.194 Angle : 0.594 10.852 15096 Z= 0.289 Chirality : 0.040 0.176 1656 Planarity : 0.003 0.032 1916 Dihedral : 3.850 14.693 1444 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % 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: 0.93 (0.24), residues: 1320 helix: 1.33 (0.18), residues: 902 sheet: -0.17 (0.65), residues: 58 loop : -0.97 (0.32), residues: 360 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 148 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 153 average time/residue: 0.1726 time to fit residues: 42.0277 Evaluate side-chains 142 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 139 time to evaluate : 1.351 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0946 time to fit residues: 2.2148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 133 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 11 optimal weight: 0.3980 chunk 82 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 11132 Z= 0.243 Angle : 0.621 11.878 15096 Z= 0.304 Chirality : 0.041 0.173 1656 Planarity : 0.003 0.030 1916 Dihedral : 3.883 14.208 1444 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % 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: 0.94 (0.24), residues: 1320 helix: 1.32 (0.18), residues: 902 sheet: -0.22 (0.64), residues: 58 loop : -0.92 (0.33), residues: 360 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1845 time to fit residues: 40.7970 Evaluate side-chains 136 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.322 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 0.0270 chunk 98 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 106 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.0642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.111721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.083729 restraints weight = 19713.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.086363 restraints weight = 10448.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.087987 restraints weight = 7230.692| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 11132 Z= 0.192 Angle : 0.593 11.612 15096 Z= 0.288 Chirality : 0.040 0.164 1656 Planarity : 0.003 0.032 1916 Dihedral : 3.810 14.230 1444 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % 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: 1.10 (0.24), residues: 1320 helix: 1.43 (0.18), residues: 902 sheet: -0.03 (0.66), residues: 58 loop : -0.87 (0.33), residues: 360 =============================================================================== Job complete usr+sys time: 1897.65 seconds wall clock time: 35 minutes 34.69 seconds (2134.69 seconds total)