Starting phenix.real_space_refine on Thu Feb 15 01:55:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm6_4589/02_2024/6qm6_4589.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm6_4589/02_2024/6qm6_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_4589/02_2024/6qm6_4589.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm6_4589/02_2024/6qm6_4589.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm6_4589/02_2024/6qm6_4589.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm6_4589/02_2024/6qm6_4589.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 5.52, per 1000 atoms: 0.51 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: 3.83 Conformation dependent library (CDL) restraints added in 1.9 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: 0.94 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: 2.98 Time building geometry restraints manager: 4.18 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: 0.760 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: 3.650 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 29.880 Find NCS groups from input model: 0.520 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.750 ------------------------------------------------------------------------------- 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 % Allowed : 5.03 % Favored : 94.97 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 235 HIS 0.005 0.001 HIS A 479 PHE 0.021 0.001 PHE A 205 TYR 0.015 0.001 TYR B 26 ARG 0.002 0.000 ARG B 33 *********************** 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 : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 TYR cc_start: 0.9496 (t80) cc_final: 0.9094 (t80) REVERT: A 211 LEU cc_start: 0.9046 (tp) cc_final: 0.8834 (tt) REVERT: A 286 LYS cc_start: 0.7578 (mttt) cc_final: 0.6672 (mmtt) REVERT: A 507 MET cc_start: 0.8684 (mmp) cc_final: 0.8173 (mmt) REVERT: B 211 LEU cc_start: 0.9074 (tp) cc_final: 0.8835 (tt) REVERT: B 286 LYS cc_start: 0.7415 (mttt) cc_final: 0.6536 (mmtt) REVERT: B 357 MET cc_start: 0.8451 (mtp) cc_final: 0.8234 (ttm) REVERT: B 507 MET cc_start: 0.8816 (mmp) cc_final: 0.8361 (mmt) REVERT: B 693 MET cc_start: 0.7774 (ppp) cc_final: 0.7475 (tmm) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.2377 time to fit residues: 73.5502 Evaluate side-chains 151 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.326 ------------------------------------------------------------------------------- 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: 5.9990 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: 0.8379 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11132 Z= 0.278 Angle : 0.616 7.196 15096 Z= 0.321 Chirality : 0.041 0.181 1656 Planarity : 0.005 0.042 1916 Dihedral : 4.446 16.217 1444 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.04 % Allowed : 13.69 % Favored : 85.27 % 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: -2.81 (0.19), residues: 1320 helix: -1.80 (0.14), residues: 898 sheet: -1.16 (0.59), residues: 58 loop : -1.56 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 141 HIS 0.005 0.001 HIS B 58 PHE 0.025 0.002 PHE A 315 TYR 0.012 0.001 TYR B 360 ARG 0.005 0.001 ARG A 82 *********************** 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 195 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 183 time to evaluate : 1.383 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: A 197 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.8449 (mtt-85) REVERT: A 211 LEU cc_start: 0.9142 (tp) cc_final: 0.8869 (tt) REVERT: A 268 GLU cc_start: 0.7729 (tp30) cc_final: 0.7315 (tp30) REVERT: A 274 GLU cc_start: 0.8277 (tt0) cc_final: 0.7557 (tm-30) REVERT: A 286 LYS cc_start: 0.7515 (mttt) cc_final: 0.6662 (tttt) REVERT: B 211 LEU cc_start: 0.9152 (tp) cc_final: 0.8888 (tt) REVERT: B 268 GLU cc_start: 0.7686 (tp30) cc_final: 0.7263 (tp30) REVERT: B 274 GLU cc_start: 0.8254 (tt0) cc_final: 0.7688 (tm-30) REVERT: B 286 LYS cc_start: 0.7470 (mttt) cc_final: 0.6601 (tttt) REVERT: B 298 CYS cc_start: 0.8428 (m) cc_final: 0.8189 (m) outliers start: 12 outliers final: 6 residues processed: 189 average time/residue: 0.2053 time to fit residues: 57.4847 Evaluate side-chains 169 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 162 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 626 LYS 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: 0.9980 chunk 101 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 108 optimal weight: 0.5980 chunk 120 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 532 ASN 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11132 Z= 0.220 Angle : 0.561 7.589 15096 Z= 0.286 Chirality : 0.040 0.190 1656 Planarity : 0.004 0.033 1916 Dihedral : 4.083 15.024 1444 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.47 % Allowed : 15.68 % Favored : 82.84 % 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: -0.90 (0.22), residues: 1320 helix: -0.21 (0.17), residues: 900 sheet: -0.28 (0.62), residues: 58 loop : -1.31 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 235 HIS 0.005 0.001 HIS A 58 PHE 0.026 0.001 PHE B 315 TYR 0.010 0.001 TYR A 220 ARG 0.002 0.000 ARG B 45 *********************** 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 190 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 173 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8351 (mtt-85) REVERT: A 211 LEU cc_start: 0.9156 (tp) cc_final: 0.8862 (tt) REVERT: A 256 GLN cc_start: 0.8310 (pm20) cc_final: 0.7996 (mm110) REVERT: A 268 GLU cc_start: 0.7680 (tp30) cc_final: 0.7294 (tp30) REVERT: A 298 CYS cc_start: 0.8299 (m) cc_final: 0.8018 (m) REVERT: A 457 TYR cc_start: 0.6061 (t80) cc_final: 0.5834 (t80) REVERT: B 211 LEU cc_start: 0.9170 (tp) cc_final: 0.8874 (tt) REVERT: B 268 GLU cc_start: 0.7635 (tp30) cc_final: 0.7233 (tp30) REVERT: B 298 CYS cc_start: 0.8446 (m) cc_final: 0.8220 (m) REVERT: B 457 TYR cc_start: 0.6130 (t80) cc_final: 0.5863 (t80) REVERT: B 693 MET cc_start: 0.7705 (ppp) cc_final: 0.7433 (ppp) outliers start: 17 outliers final: 8 residues processed: 183 average time/residue: 0.1707 time to fit residues: 47.5574 Evaluate side-chains 170 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 161 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 626 LYS Chi-restraints excluded: chain B residue 701 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 3.9990 chunk 91 optimal weight: 0.2980 chunk 63 optimal weight: 9.9990 chunk 13 optimal weight: 0.1980 chunk 58 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 115 optimal weight: 0.4980 chunk 34 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3043 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= 0.198 Angle : 0.554 11.605 15096 Z= 0.275 Chirality : 0.040 0.191 1656 Planarity : 0.004 0.031 1916 Dihedral : 3.933 13.682 1444 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.65 % Allowed : 17.07 % Favored : 81.28 % 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: -0.04 (0.23), residues: 1320 helix: 0.52 (0.18), residues: 904 sheet: -0.23 (0.65), residues: 58 loop : -1.21 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 227 HIS 0.005 0.001 HIS B 58 PHE 0.025 0.001 PHE A 315 TYR 0.011 0.001 TYR B 26 ARG 0.005 0.000 ARG B 45 *********************** 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 185 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 166 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8326 (mtt-85) REVERT: A 211 LEU cc_start: 0.9161 (tp) cc_final: 0.8838 (tt) REVERT: A 241 ASP cc_start: 0.8185 (t0) cc_final: 0.7944 (t0) REVERT: A 268 GLU cc_start: 0.7668 (tp30) cc_final: 0.7306 (tp30) REVERT: A 298 CYS cc_start: 0.8283 (m) cc_final: 0.7986 (m) REVERT: A 677 GLU cc_start: 0.7062 (mm-30) cc_final: 0.6840 (mm-30) REVERT: B 211 LEU cc_start: 0.9121 (tp) cc_final: 0.8826 (tt) REVERT: B 268 GLU cc_start: 0.7649 (tp30) cc_final: 0.7277 (tp30) REVERT: B 274 GLU cc_start: 0.8126 (tt0) cc_final: 0.7756 (tm-30) REVERT: B 298 CYS cc_start: 0.8364 (m) cc_final: 0.8092 (m) REVERT: B 445 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8169 (mm-40) outliers start: 19 outliers final: 12 residues processed: 178 average time/residue: 0.1822 time to fit residues: 49.7442 Evaluate side-chains 169 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 156 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 626 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 3.9990 chunk 1 optimal weight: 0.3980 chunk 96 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 43 optimal weight: 0.0670 overall best weight: 1.0922 ------------------------------------------------------------------------------- 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: 0.8350 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11132 Z= 0.189 Angle : 0.554 9.884 15096 Z= 0.272 Chirality : 0.040 0.185 1656 Planarity : 0.004 0.031 1916 Dihedral : 3.821 13.852 1444 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.08 % Allowed : 18.11 % Favored : 79.81 % 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: 0.52 (0.24), residues: 1320 helix: 1.00 (0.18), residues: 904 sheet: -0.19 (0.66), residues: 58 loop : -1.13 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 227 HIS 0.004 0.001 HIS B 58 PHE 0.045 0.001 PHE A 205 TYR 0.016 0.001 TYR B 457 ARG 0.004 0.000 ARG B 45 *********************** 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 190 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 166 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8333 (mtt-85) REVERT: A 211 LEU cc_start: 0.9096 (tp) cc_final: 0.8801 (tt) REVERT: A 268 GLU cc_start: 0.7655 (tp30) cc_final: 0.7304 (tp30) REVERT: A 298 CYS cc_start: 0.8236 (m) cc_final: 0.7955 (m) REVERT: A 353 LYS cc_start: 0.7643 (mttp) cc_final: 0.6961 (mtpt) REVERT: B 211 LEU cc_start: 0.9161 (tp) cc_final: 0.8845 (tt) REVERT: B 268 GLU cc_start: 0.7629 (tp30) cc_final: 0.7254 (tp30) REVERT: B 298 CYS cc_start: 0.8317 (m) cc_final: 0.8013 (m) REVERT: B 445 GLN cc_start: 0.8496 (mm-40) cc_final: 0.7983 (mm110) REVERT: B 693 MET cc_start: 0.7429 (ppp) cc_final: 0.7063 (tmm) outliers start: 24 outliers final: 17 residues processed: 184 average time/residue: 0.1779 time to fit residues: 49.7429 Evaluate side-chains 177 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 159 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 626 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 31 optimal weight: 0.1980 chunk 129 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- 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 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11132 Z= 0.183 Angle : 0.556 9.261 15096 Z= 0.273 Chirality : 0.039 0.172 1656 Planarity : 0.003 0.031 1916 Dihedral : 3.756 12.713 1444 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.34 % Allowed : 18.46 % Favored : 79.20 % 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: 0.83 (0.24), residues: 1320 helix: 1.25 (0.18), residues: 904 sheet: -0.14 (0.67), residues: 58 loop : -1.04 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 600 HIS 0.003 0.001 HIS B 58 PHE 0.052 0.001 PHE A 205 TYR 0.012 0.001 TYR B 457 ARG 0.005 0.000 ARG A 33 *********************** 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 191 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 164 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8358 (mtt-85) REVERT: A 211 LEU cc_start: 0.9088 (tp) cc_final: 0.8783 (tt) REVERT: A 268 GLU cc_start: 0.7661 (tp30) cc_final: 0.7297 (tp30) REVERT: A 298 CYS cc_start: 0.8245 (m) cc_final: 0.7955 (m) REVERT: A 353 LYS cc_start: 0.7613 (mttp) cc_final: 0.7086 (ttpt) REVERT: A 693 MET cc_start: 0.7475 (ppp) cc_final: 0.7040 (tmm) REVERT: B 211 LEU cc_start: 0.9097 (tp) cc_final: 0.8797 (tt) REVERT: B 268 GLU cc_start: 0.7619 (tp30) cc_final: 0.7248 (tp30) REVERT: B 298 CYS cc_start: 0.8319 (m) cc_final: 0.8011 (m) REVERT: B 445 GLN cc_start: 0.8508 (mm-40) cc_final: 0.8016 (mm110) REVERT: B 693 MET cc_start: 0.7529 (ppp) cc_final: 0.7143 (tmm) outliers start: 27 outliers final: 21 residues processed: 182 average time/residue: 0.1636 time to fit residues: 45.4189 Evaluate side-chains 183 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 161 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 626 LYS Chi-restraints excluded: chain B residue 701 MET 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: 3.9990 chunk 94 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 72 optimal weight: 0.0020 chunk 129 optimal weight: 0.3980 chunk 80 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.8590 ------------------------------------------------------------------------------- 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 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: 0.8333 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11132 Z= 0.171 Angle : 0.574 10.962 15096 Z= 0.279 Chirality : 0.039 0.178 1656 Planarity : 0.003 0.031 1916 Dihedral : 3.717 12.487 1444 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.51 % Allowed : 18.54 % Favored : 78.94 % 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: 1.06 (0.24), residues: 1320 helix: 1.43 (0.18), residues: 904 sheet: -0.06 (0.68), residues: 58 loop : -0.99 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 600 HIS 0.003 0.000 HIS B 58 PHE 0.057 0.001 PHE A 205 TYR 0.010 0.001 TYR B 457 ARG 0.004 0.000 ARG A 33 *********************** 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 188 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 159 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8373 (mtt-85) REVERT: A 205 PHE cc_start: 0.8529 (p90) cc_final: 0.8300 (p90) REVERT: A 211 LEU cc_start: 0.9080 (tp) cc_final: 0.8778 (tt) REVERT: A 268 GLU cc_start: 0.7636 (tp30) cc_final: 0.7272 (tp30) REVERT: A 298 CYS cc_start: 0.8233 (m) cc_final: 0.7943 (m) REVERT: A 445 GLN cc_start: 0.8480 (mm-40) cc_final: 0.8059 (mm110) REVERT: A 693 MET cc_start: 0.7550 (ppp) cc_final: 0.7107 (tmm) REVERT: B 211 LEU cc_start: 0.9088 (tp) cc_final: 0.8793 (tt) REVERT: B 268 GLU cc_start: 0.7611 (tp30) cc_final: 0.7233 (tp30) REVERT: B 298 CYS cc_start: 0.8301 (m) cc_final: 0.8042 (m) REVERT: B 693 MET cc_start: 0.7601 (ppp) cc_final: 0.7172 (tmm) outliers start: 29 outliers final: 22 residues processed: 180 average time/residue: 0.1738 time to fit residues: 48.1675 Evaluate side-chains 174 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 151 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 626 LYS Chi-restraints excluded: chain B residue 701 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 12 optimal weight: 0.0670 chunk 101 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.7122 ------------------------------------------------------------------------------- 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 460 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: 0.8319 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11132 Z= 0.162 Angle : 0.562 10.104 15096 Z= 0.274 Chirality : 0.039 0.178 1656 Planarity : 0.003 0.032 1916 Dihedral : 3.675 12.758 1444 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.60 % Allowed : 18.46 % Favored : 78.94 % 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: 1.22 (0.24), residues: 1320 helix: 1.57 (0.18), residues: 904 sheet: 0.00 (0.69), residues: 58 loop : -0.96 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 533 HIS 0.002 0.000 HIS A 58 PHE 0.054 0.001 PHE A 205 TYR 0.010 0.001 TYR B 26 ARG 0.004 0.000 ARG A 33 *********************** 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 185 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 155 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8358 (mtt-85) REVERT: A 205 PHE cc_start: 0.8404 (p90) cc_final: 0.8182 (p90) REVERT: A 211 LEU cc_start: 0.9060 (tp) cc_final: 0.8761 (tt) REVERT: A 268 GLU cc_start: 0.7631 (tp30) cc_final: 0.7267 (tp30) REVERT: A 286 LYS cc_start: 0.7983 (mttt) cc_final: 0.7144 (tttt) REVERT: A 298 CYS cc_start: 0.8266 (m) cc_final: 0.7958 (m) REVERT: A 353 LYS cc_start: 0.7536 (mttp) cc_final: 0.7015 (ttpt) REVERT: A 445 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8039 (mm110) REVERT: A 693 MET cc_start: 0.7598 (ppp) cc_final: 0.7152 (tmm) REVERT: B 211 LEU cc_start: 0.9086 (tp) cc_final: 0.8768 (tt) REVERT: B 268 GLU cc_start: 0.7607 (tp30) cc_final: 0.7227 (tp30) REVERT: B 286 LYS cc_start: 0.7921 (mttt) cc_final: 0.7065 (tttt) REVERT: B 298 CYS cc_start: 0.8299 (m) cc_final: 0.8026 (m) REVERT: B 693 MET cc_start: 0.7644 (ppp) cc_final: 0.7212 (tmm) outliers start: 30 outliers final: 24 residues processed: 179 average time/residue: 0.1834 time to fit residues: 49.8041 Evaluate side-chains 174 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 149 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 626 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 2.9990 chunk 123 optimal weight: 0.2980 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 79 optimal weight: 0.4980 chunk 127 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 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 460 GLN ** 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: 0.8377 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11132 Z= 0.274 Angle : 0.612 10.145 15096 Z= 0.304 Chirality : 0.042 0.173 1656 Planarity : 0.004 0.030 1916 Dihedral : 3.820 13.777 1444 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.51 % Allowed : 18.63 % Favored : 78.86 % 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: 1.13 (0.24), residues: 1320 helix: 1.43 (0.18), residues: 908 sheet: -0.02 (0.69), residues: 58 loop : -0.84 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 533 HIS 0.002 0.001 HIS A 401 PHE 0.050 0.002 PHE B 205 TYR 0.012 0.001 TYR A 220 ARG 0.003 0.000 ARG A 33 *********************** 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 172 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 143 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8352 (mtt-85) REVERT: A 211 LEU cc_start: 0.9108 (tp) cc_final: 0.8832 (tt) REVERT: A 268 GLU cc_start: 0.7654 (tp30) cc_final: 0.7314 (tp30) REVERT: A 298 CYS cc_start: 0.8299 (m) cc_final: 0.7991 (m) REVERT: A 516 MET cc_start: 0.8507 (mtt) cc_final: 0.8072 (mtt) REVERT: A 693 MET cc_start: 0.7672 (ppp) cc_final: 0.7204 (tmm) REVERT: B 195 TYR cc_start: 0.9422 (t80) cc_final: 0.9007 (t80) REVERT: B 211 LEU cc_start: 0.9112 (tp) cc_final: 0.8841 (tt) REVERT: B 268 GLU cc_start: 0.7659 (tp30) cc_final: 0.7284 (tp30) REVERT: B 298 CYS cc_start: 0.8372 (m) cc_final: 0.8058 (m) REVERT: B 693 MET cc_start: 0.7665 (ppp) cc_final: 0.7177 (tmm) outliers start: 29 outliers final: 28 residues processed: 167 average time/residue: 0.1767 time to fit residues: 45.0587 Evaluate side-chains 167 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 138 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 626 LYS 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: 0.8980 chunk 88 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 84 optimal weight: 0.5980 chunk 113 optimal weight: 0.3980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 460 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: 0.8349 moved from start: 0.3583 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= 0.199 Angle : 0.597 10.895 15096 Z= 0.292 Chirality : 0.041 0.186 1656 Planarity : 0.003 0.032 1916 Dihedral : 3.793 14.911 1444 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.51 % Allowed : 19.15 % Favored : 78.34 % 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: 1.21 (0.24), residues: 1320 helix: 1.55 (0.18), residues: 904 sheet: 0.08 (0.69), residues: 58 loop : -0.94 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 533 HIS 0.002 0.001 HIS A 58 PHE 0.031 0.001 PHE A 315 TYR 0.011 0.001 TYR B 26 ARG 0.004 0.000 ARG A 33 ********************** 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 175 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 146 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8338 (mtt-85) REVERT: A 211 LEU cc_start: 0.9102 (tp) cc_final: 0.8822 (tt) REVERT: A 268 GLU cc_start: 0.7653 (tp30) cc_final: 0.7289 (tp30) REVERT: A 286 LYS cc_start: 0.8004 (mttt) cc_final: 0.7164 (tttt) REVERT: A 298 CYS cc_start: 0.8257 (m) cc_final: 0.7943 (m) REVERT: A 693 MET cc_start: 0.7621 (ppp) cc_final: 0.7131 (tmm) REVERT: B 211 LEU cc_start: 0.9104 (tp) cc_final: 0.8826 (tt) REVERT: B 268 GLU cc_start: 0.7635 (tp30) cc_final: 0.7255 (tp30) REVERT: B 298 CYS cc_start: 0.8340 (m) cc_final: 0.8059 (m) REVERT: B 313 GLU cc_start: 0.7778 (tt0) cc_final: 0.7534 (mt-10) REVERT: B 693 MET cc_start: 0.7695 (ppp) cc_final: 0.7219 (tmm) outliers start: 29 outliers final: 27 residues processed: 171 average time/residue: 0.1740 time to fit residues: 45.5769 Evaluate side-chains 168 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 140 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 626 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 15 optimal weight: 0.2980 chunk 29 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 109 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 412 GLN B 460 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.113142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.085317 restraints weight = 19636.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.087925 restraints weight = 10511.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.089560 restraints weight = 7314.479| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11132 Z= 0.162 Angle : 0.578 12.272 15096 Z= 0.281 Chirality : 0.040 0.185 1656 Planarity : 0.003 0.031 1916 Dihedral : 3.694 14.399 1444 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.51 % Allowed : 19.24 % Favored : 78.25 % 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: 1.39 (0.24), residues: 1320 helix: 1.70 (0.18), residues: 904 sheet: 0.16 (0.70), residues: 58 loop : -0.91 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 533 HIS 0.002 0.000 HIS A 58 PHE 0.053 0.001 PHE A 205 TYR 0.010 0.001 TYR B 26 ARG 0.004 0.000 ARG A 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2053.85 seconds wall clock time: 42 minutes 17.45 seconds (2537.45 seconds total)