Starting phenix.real_space_refine on Tue Mar 19 21:30:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7u_24305/03_2024/7r7u_24305.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7u_24305/03_2024/7r7u_24305.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7u_24305/03_2024/7r7u_24305.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7u_24305/03_2024/7r7u_24305.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7u_24305/03_2024/7r7u_24305.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7u_24305/03_2024/7r7u_24305.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 15976 2.51 5 N 4506 2.21 5 O 4748 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A ARG 358": "NH1" <-> "NH2" Residue "A ARG 424": "NH1" <-> "NH2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A GLU 488": "OE1" <-> "OE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 577": "OD1" <-> "OD2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A GLU 607": "OE1" <-> "OE2" Residue "A ASP 627": "OD1" <-> "OD2" Residue "A ASP 630": "OD1" <-> "OD2" Residue "A GLU 650": "OE1" <-> "OE2" Residue "A ASP 686": "OD1" <-> "OD2" Residue "A ARG 708": "NH1" <-> "NH2" Residue "A GLU 730": "OE1" <-> "OE2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "A ARG 741": "NH1" <-> "NH2" Residue "A PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 753": "NH1" <-> "NH2" Residue "B PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "B ASP 304": "OD1" <-> "OD2" Residue "B ARG 358": "NH1" <-> "NH2" Residue "B ASP 368": "OD1" <-> "OD2" Residue "B ARG 424": "NH1" <-> "NH2" Residue "B PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 478": "OD1" <-> "OD2" Residue "B GLU 483": "OE1" <-> "OE2" Residue "B GLU 488": "OE1" <-> "OE2" Residue "B PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 534": "OE1" <-> "OE2" Residue "B PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 577": "OD1" <-> "OD2" Residue "B ARG 599": "NH1" <-> "NH2" Residue "B ASP 609": "OD1" <-> "OD2" Residue "B ASP 627": "OD1" <-> "OD2" Residue "B ASP 640": "OD1" <-> "OD2" Residue "B ARG 708": "NH1" <-> "NH2" Residue "B GLU 730": "OE1" <-> "OE2" Residue "B ARG 733": "NH1" <-> "NH2" Residue "B ARG 741": "NH1" <-> "NH2" Residue "B ARG 753": "NH1" <-> "NH2" Residue "C GLU 200": "OE1" <-> "OE2" Residue "C PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 273": "OE1" <-> "OE2" Residue "C ASP 307": "OD1" <-> "OD2" Residue "C ARG 358": "NH1" <-> "NH2" Residue "C GLU 402": "OE1" <-> "OE2" Residue "C ARG 424": "NH1" <-> "NH2" Residue "C PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 478": "OD1" <-> "OD2" Residue "C GLU 483": "OE1" <-> "OE2" Residue "C ASP 484": "OD1" <-> "OD2" Residue "C GLU 488": "OE1" <-> "OE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 501": "OD1" <-> "OD2" Residue "C ARG 708": "NH1" <-> "NH2" Residue "C ARG 733": "NH1" <-> "NH2" Residue "C ARG 741": "NH1" <-> "NH2" Residue "C ARG 753": "NH1" <-> "NH2" Residue "D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 358": "NH1" <-> "NH2" Residue "D ASP 368": "OD1" <-> "OD2" Residue "D ARG 424": "NH1" <-> "NH2" Residue "D GLU 466": "OE1" <-> "OE2" Residue "D ASP 478": "OD1" <-> "OD2" Residue "D GLU 483": "OE1" <-> "OE2" Residue "D ASP 501": "OD1" <-> "OD2" Residue "D PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 577": "OD1" <-> "OD2" Residue "D GLU 578": "OE1" <-> "OE2" Residue "D ARG 599": "NH1" <-> "NH2" Residue "D ASP 609": "OD1" <-> "OD2" Residue "D ASP 627": "OD1" <-> "OD2" Residue "D ASP 640": "OD1" <-> "OD2" Residue "D ARG 708": "NH1" <-> "NH2" Residue "D GLU 730": "OE1" <-> "OE2" Residue "D ARG 733": "NH1" <-> "NH2" Residue "D PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 741": "NH1" <-> "NH2" Residue "D PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 753": "NH1" <-> "NH2" Residue "E ASP 205": "OD1" <-> "OD2" Residue "E TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 304": "OD1" <-> "OD2" Residue "E ARG 358": "NH1" <-> "NH2" Residue "E PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 366": "OE1" <-> "OE2" Residue "E ASP 373": "OD1" <-> "OD2" Residue "E ARG 424": "NH1" <-> "NH2" Residue "E ASP 428": "OD1" <-> "OD2" Residue "E PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 483": "OE1" <-> "OE2" Residue "E GLU 534": "OE1" <-> "OE2" Residue "E PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 577": "OD1" <-> "OD2" Residue "E ASP 598": "OD1" <-> "OD2" Residue "E ARG 599": "NH1" <-> "NH2" Residue "E ASP 640": "OD1" <-> "OD2" Residue "E TYR 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 706": "OE1" <-> "OE2" Residue "E ARG 708": "NH1" <-> "NH2" Residue "E ARG 733": "NH1" <-> "NH2" Residue "E ARG 741": "NH1" <-> "NH2" Residue "E ARG 753": "NH1" <-> "NH2" Residue "F ASP 205": "OD1" <-> "OD2" Residue "F PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 294": "OE1" <-> "OE2" Residue "F GLU 314": "OE1" <-> "OE2" Residue "F GLU 321": "OE1" <-> "OE2" Residue "F ARG 323": "NH1" <-> "NH2" Residue "F ARG 358": "NH1" <-> "NH2" Residue "F ASP 368": "OD1" <-> "OD2" Residue "F GLU 379": "OE1" <-> "OE2" Residue "F ARG 424": "NH1" <-> "NH2" Residue "F PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 478": "OD1" <-> "OD2" Residue "F ASP 501": "OD1" <-> "OD2" Residue "F PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 546": "OE1" <-> "OE2" Residue "F PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 599": "NH1" <-> "NH2" Residue "F GLU 607": "OE1" <-> "OE2" Residue "F ASP 627": "OD1" <-> "OD2" Residue "F ASP 630": "OD1" <-> "OD2" Residue "F ASP 640": "OD1" <-> "OD2" Residue "F ARG 708": "NH1" <-> "NH2" Residue "F ARG 733": "NH1" <-> "NH2" Residue "F ARG 741": "NH1" <-> "NH2" Residue "F ARG 753": "NH1" <-> "NH2" Residue "F PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25362 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4215 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 508} Chain breaks: 3 Chain: "B" Number of atoms: 4233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4233 Classifications: {'peptide': 541} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 511} Chain breaks: 3 Chain: "C" Number of atoms: 4215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4215 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 508} Chain breaks: 3 Chain: "D" Number of atoms: 4233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4233 Classifications: {'peptide': 541} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 511} Chain breaks: 3 Chain: "E" Number of atoms: 4233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4233 Classifications: {'peptide': 541} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 511} Chain breaks: 2 Chain: "F" Number of atoms: 4233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4233 Classifications: {'peptide': 541} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 511} Chain breaks: 3 Time building chain proxies: 12.99, per 1000 atoms: 0.51 Number of scatterers: 25362 At special positions: 0 Unit cell: (160.68, 146.64, 95.16, 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 132 16.00 O 4748 8.00 N 4506 7.00 C 15976 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: 10.06 Conformation dependent library (CDL) restraints added in 4.6 seconds 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6072 Finding SS restraints... Secondary structure from input PDB file: 157 helices and 14 sheets defined 53.1% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 209 through 221 Processing helix chain 'A' and resid 226 through 228 No H-bonds generated for 'chain 'A' and resid 226 through 228' Processing helix chain 'A' and resid 229 through 234 Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 271 through 276 removed outlier: 3.540A pdb=" N MET A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.743A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 319 through 335 Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 407 through 426 removed outlier: 3.792A pdb=" N ALA A 419 " --> pdb=" O CYS A 415 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 444 removed outlier: 3.520A pdb=" N SER A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 440 through 444' Processing helix chain 'A' and resid 448 through 458 Processing helix chain 'A' and resid 482 through 499 Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 522 through 535 removed outlier: 3.656A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 552 removed outlier: 3.826A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 557 No H-bonds generated for 'chain 'A' and resid 555 through 557' Processing helix chain 'A' and resid 558 through 569 Processing helix chain 'A' and resid 579 through 585 removed outlier: 3.920A pdb=" N ALA A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 608 removed outlier: 3.659A pdb=" N THR A 606 " --> pdb=" O ASN A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 662 Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'A' and resid 684 through 702 Processing helix chain 'A' and resid 703 through 712 removed outlier: 4.045A pdb=" N ARG A 708 " --> pdb=" O GLU A 704 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ARG A 709 " --> pdb=" O SER A 705 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 740 Processing helix chain 'A' and resid 748 through 757 Processing helix chain 'A' and resid 758 through 760 No H-bonds generated for 'chain 'A' and resid 758 through 760' Processing helix chain 'B' and resid 209 through 221 removed outlier: 3.835A pdb=" N GLU B 221 " --> pdb=" O LYS B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 234 Processing helix chain 'B' and resid 250 through 263 Processing helix chain 'B' and resid 272 through 277 Processing helix chain 'B' and resid 286 through 296 Processing helix chain 'B' and resid 305 through 310 Processing helix chain 'B' and resid 319 through 335 Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 396 through 403 Processing helix chain 'B' and resid 407 through 426 Processing helix chain 'B' and resid 448 through 458 Processing helix chain 'B' and resid 483 through 499 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 500 through 505 Processing helix chain 'B' and resid 522 through 535 removed outlier: 3.618A pdb=" N LEU B 526 " --> pdb=" O CYS B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 552 removed outlier: 3.671A pdb=" N MET B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TRP B 551 " --> pdb=" O LEU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 557 No H-bonds generated for 'chain 'B' and resid 555 through 557' Processing helix chain 'B' and resid 558 through 569 Processing helix chain 'B' and resid 579 through 588 removed outlier: 4.517A pdb=" N ALA B 583 " --> pdb=" O LEU B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 610 removed outlier: 3.558A pdb=" N ASP B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 660 removed outlier: 3.894A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE B 656 " --> pdb=" O SER B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 679 Processing helix chain 'B' and resid 683 through 712 removed outlier: 4.189A pdb=" N GLU B 704 " --> pdb=" O ARG B 700 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE B 707 " --> pdb=" O ILE B 703 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ARG B 709 " --> pdb=" O SER B 705 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLU B 710 " --> pdb=" O GLU B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 742 Processing helix chain 'B' and resid 748 through 756 removed outlier: 3.624A pdb=" N ILE B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS B 754 " --> pdb=" O ASN B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 761 removed outlier: 4.011A pdb=" N GLN B 760 " --> pdb=" O MET B 757 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 761 " --> pdb=" O PHE B 758 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 757 through 761' Processing helix chain 'C' and resid 209 through 221 removed outlier: 3.605A pdb=" N GLU C 221 " --> pdb=" O LYS C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 234 Processing helix chain 'C' and resid 250 through 262 Processing helix chain 'C' and resid 272 through 277 Processing helix chain 'C' and resid 280 through 284 removed outlier: 3.882A pdb=" N GLU C 283 " --> pdb=" O GLY C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 296 Processing helix chain 'C' and resid 318 through 335 removed outlier: 3.595A pdb=" N ARG C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 387 removed outlier: 4.100A pdb=" N ASN C 387 " --> pdb=" O ILE C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 403 Processing helix chain 'C' and resid 407 through 426 removed outlier: 3.659A pdb=" N SER C 416 " --> pdb=" O ALA C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 482 through 495 Processing helix chain 'C' and resid 501 through 506 Processing helix chain 'C' and resid 522 through 536 Processing helix chain 'C' and resid 543 through 549 Processing helix chain 'C' and resid 557 through 569 Processing helix chain 'C' and resid 579 through 585 removed outlier: 4.125A pdb=" N ALA C 583 " --> pdb=" O LEU C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 609 removed outlier: 3.682A pdb=" N GLU C 607 " --> pdb=" O GLN C 603 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP C 609 " --> pdb=" O LEU C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 661 Processing helix chain 'C' and resid 671 through 679 Processing helix chain 'C' and resid 684 through 703 removed outlier: 3.988A pdb=" N GLU C 701 " --> pdb=" O LEU C 697 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE C 703 " --> pdb=" O ILE C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 713 removed outlier: 4.581A pdb=" N ARG C 709 " --> pdb=" O SER C 705 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU C 710 " --> pdb=" O GLU C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 741 removed outlier: 3.565A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 757 Processing helix chain 'D' and resid 209 through 221 removed outlier: 3.826A pdb=" N GLU D 221 " --> pdb=" O LYS D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 233 removed outlier: 4.216A pdb=" N ALA D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 263 Processing helix chain 'D' and resid 286 through 296 removed outlier: 3.711A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 Processing helix chain 'D' and resid 319 through 334 removed outlier: 3.706A pdb=" N GLY D 334 " --> pdb=" O THR D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 336 No H-bonds generated for 'chain 'D' and resid 335 through 336' Processing helix chain 'D' and resid 337 through 341 removed outlier: 3.617A pdb=" N HIS D 340 " --> pdb=" O GLN D 337 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL D 341 " --> pdb=" O ARG D 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 337 through 341' Processing helix chain 'D' and resid 373 through 385 removed outlier: 3.625A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 426 removed outlier: 3.773A pdb=" N ALA D 419 " --> pdb=" O CYS D 415 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 444 Processing helix chain 'D' and resid 448 through 458 Processing helix chain 'D' and resid 482 through 499 Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 501 through 506 removed outlier: 3.675A pdb=" N PHE D 506 " --> pdb=" O LYS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 536 removed outlier: 3.673A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 552 removed outlier: 3.766A pdb=" N THR D 549 " --> pdb=" O PRO D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 569 removed outlier: 4.017A pdb=" N GLU D 561 " --> pdb=" O ALA D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 588 removed outlier: 4.342A pdb=" N GLY D 587 " --> pdb=" O ALA D 583 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY D 588 " --> pdb=" O LYS D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 611 removed outlier: 4.289A pdb=" N GLU D 607 " --> pdb=" O GLN D 603 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET D 608 " --> pdb=" O ILE D 604 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP D 609 " --> pdb=" O LEU D 605 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY D 610 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 662 removed outlier: 3.603A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 679 Processing helix chain 'D' and resid 683 through 713 removed outlier: 4.101A pdb=" N GLU D 704 " --> pdb=" O ARG D 700 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU D 706 " --> pdb=" O SER D 702 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG D 708 " --> pdb=" O GLU D 704 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ARG D 709 " --> pdb=" O SER D 705 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU D 710 " --> pdb=" O GLU D 706 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 740 Processing helix chain 'D' and resid 748 through 757 Processing helix chain 'D' and resid 758 through 761 removed outlier: 3.591A pdb=" N THR D 761 " --> pdb=" O PHE D 758 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 758 through 761' Processing helix chain 'E' and resid 209 through 220 Processing helix chain 'E' and resid 229 through 234 Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 271 through 277 removed outlier: 4.147A pdb=" N MET E 275 " --> pdb=" O GLY E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 295 Processing helix chain 'E' and resid 305 through 310 Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 318 through 335 removed outlier: 4.045A pdb=" N ARG E 322 " --> pdb=" O GLY E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 387 removed outlier: 4.086A pdb=" N ASN E 387 " --> pdb=" O ILE E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 403 Processing helix chain 'E' and resid 407 through 426 removed outlier: 3.970A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 457 Processing helix chain 'E' and resid 482 through 499 Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 506 removed outlier: 4.118A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 536 Processing helix chain 'E' and resid 543 through 552 Processing helix chain 'E' and resid 556 through 569 removed outlier: 3.647A pdb=" N ARG E 560 " --> pdb=" O GLU E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 588 removed outlier: 4.038A pdb=" N ALA E 583 " --> pdb=" O LEU E 579 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 608 Processing helix chain 'E' and resid 649 through 661 Processing helix chain 'E' and resid 671 through 679 removed outlier: 3.681A pdb=" N LEU E 675 " --> pdb=" O ASP E 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 684 through 703 removed outlier: 3.665A pdb=" N GLU E 701 " --> pdb=" O LEU E 697 " (cutoff:3.500A) Processing helix chain 'E' and resid 703 through 713 removed outlier: 3.705A pdb=" N ARG E 708 " --> pdb=" O GLU E 704 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG E 709 " --> pdb=" O SER E 705 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU E 710 " --> pdb=" O GLU E 706 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 740 removed outlier: 3.537A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 741 through 743 No H-bonds generated for 'chain 'E' and resid 741 through 743' Processing helix chain 'E' and resid 748 through 756 Processing helix chain 'E' and resid 757 through 761 removed outlier: 4.013A pdb=" N GLN E 760 " --> pdb=" O MET E 757 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR E 761 " --> pdb=" O PHE E 758 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 757 through 761' Processing helix chain 'F' and resid 209 through 221 Processing helix chain 'F' and resid 229 through 234 Processing helix chain 'F' and resid 250 through 263 Processing helix chain 'F' and resid 271 through 277 removed outlier: 3.903A pdb=" N MET F 275 " --> pdb=" O GLY F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.665A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 316 Processing helix chain 'F' and resid 319 through 335 Processing helix chain 'F' and resid 349 through 353 removed outlier: 3.642A pdb=" N ILE F 353 " --> pdb=" O PRO F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 396 through 403 Processing helix chain 'F' and resid 407 through 426 removed outlier: 3.897A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 459 Processing helix chain 'F' and resid 482 through 499 removed outlier: 4.112A pdb=" N VAL F 493 " --> pdb=" O LEU F 489 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 501 through 506 removed outlier: 3.581A pdb=" N PHE F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 536 Processing helix chain 'F' and resid 543 through 552 removed outlier: 3.839A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TRP F 551 " --> pdb=" O LEU F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 556 through 569 removed outlier: 4.239A pdb=" N ARG F 560 " --> pdb=" O GLU F 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 588 removed outlier: 3.852A pdb=" N ARG F 586 " --> pdb=" O ILE F 582 " (cutoff:3.500A) Processing helix chain 'F' and resid 600 through 610 Processing helix chain 'F' and resid 631 through 635 Processing helix chain 'F' and resid 649 through 661 Processing helix chain 'F' and resid 671 through 679 Processing helix chain 'F' and resid 683 through 713 removed outlier: 3.680A pdb=" N GLU F 701 " --> pdb=" O LEU F 697 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ILE F 703 " --> pdb=" O ILE F 699 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU F 704 " --> pdb=" O ARG F 700 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU F 706 " --> pdb=" O SER F 702 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG F 708 " --> pdb=" O GLU F 704 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG F 709 " --> pdb=" O SER F 705 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 743 removed outlier: 3.520A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA F 743 " --> pdb=" O ALA F 739 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 756 removed outlier: 4.097A pdb=" N LYS F 754 " --> pdb=" O ASN F 750 " (cutoff:3.500A) Processing helix chain 'F' and resid 757 through 761 removed outlier: 3.551A pdb=" N GLN F 760 " --> pdb=" O MET F 757 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR F 761 " --> pdb=" O PHE F 758 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 757 through 761' Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 270 removed outlier: 5.801A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 538 through 542 removed outlier: 3.680A pdb=" N ILE A 540 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N ILE A 643 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 268 through 269 removed outlier: 6.326A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 538 through 542 removed outlier: 8.331A pdb=" N ILE B 643 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU B 515 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 268 through 269 removed outlier: 5.848A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 513 through 514 removed outlier: 3.668A pdb=" N GLY C 621 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 268 through 269 removed outlier: 5.905A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 513 through 517 removed outlier: 3.698A pdb=" N GLY D 621 " --> pdb=" O VAL D 514 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 241 through 242 Processing sheet with id=AB1, first strand: chain 'E' and resid 300 through 303 removed outlier: 6.062A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 538 through 542 removed outlier: 6.936A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR E 517 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 241 through 242 Processing sheet with id=AB4, first strand: chain 'F' and resid 268 through 270 removed outlier: 3.869A pdb=" N ASP F 304 " --> pdb=" O ILE F 269 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 513 through 517 removed outlier: 6.700A pdb=" N VAL F 514 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N THR F 623 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE F 516 " --> pdb=" O THR F 623 " (cutoff:3.500A) 1069 hydrogen bonds defined for protein. 3150 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: 7.39 Time building geometry restraints manager: 11.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5390 1.33 - 1.45: 5272 1.45 - 1.58: 14887 1.58 - 1.70: 0 1.70 - 1.83: 222 Bond restraints: 25771 Sorted by residual: bond pdb=" N ASP F 368 " pdb=" CA ASP F 368 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.35e+00 bond pdb=" C GLY D 544 " pdb=" N PRO D 545 " ideal model delta sigma weight residual 1.336 1.362 -0.026 1.08e-02 8.57e+03 5.80e+00 bond pdb=" CA GLU E 534 " pdb=" C GLU E 534 " ideal model delta sigma weight residual 1.523 1.491 0.032 1.35e-02 5.49e+03 5.75e+00 bond pdb=" C GLY F 544 " pdb=" N PRO F 545 " ideal model delta sigma weight residual 1.335 1.368 -0.032 1.36e-02 5.41e+03 5.70e+00 bond pdb=" C PRO D 237 " pdb=" N PRO D 238 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.61e+00 ... (remaining 25766 not shown) Histogram of bond angle deviations from ideal: 97.62 - 105.10: 599 105.10 - 112.59: 12818 112.59 - 120.07: 10373 120.07 - 127.55: 10736 127.55 - 135.04: 227 Bond angle restraints: 34753 Sorted by residual: angle pdb=" N VAL B 441 " pdb=" CA VAL B 441 " pdb=" C VAL B 441 " ideal model delta sigma weight residual 112.96 107.05 5.91 1.00e+00 1.00e+00 3.50e+01 angle pdb=" N VAL D 474 " pdb=" CA VAL D 474 " pdb=" C VAL D 474 " ideal model delta sigma weight residual 113.71 108.25 5.46 9.50e-01 1.11e+00 3.30e+01 angle pdb=" C THR B 679 " pdb=" N ASN B 680 " pdb=" CA ASN B 680 " ideal model delta sigma weight residual 120.82 129.14 -8.32 1.50e+00 4.44e-01 3.07e+01 angle pdb=" CA LEU C 335 " pdb=" CB LEU C 335 " pdb=" CG LEU C 335 " ideal model delta sigma weight residual 116.30 134.34 -18.04 3.50e+00 8.16e-02 2.66e+01 angle pdb=" N PHE A 618 " pdb=" CA PHE A 618 " pdb=" C PHE A 618 " ideal model delta sigma weight residual 110.64 118.23 -7.59 1.48e+00 4.57e-01 2.63e+01 ... (remaining 34748 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.14: 14235 18.14 - 36.27: 1463 36.27 - 54.41: 250 54.41 - 72.55: 51 72.55 - 90.69: 30 Dihedral angle restraints: 16029 sinusoidal: 6704 harmonic: 9325 Sorted by residual: dihedral pdb=" CA PRO E 237 " pdb=" C PRO E 237 " pdb=" N PRO E 238 " pdb=" CA PRO E 238 " ideal model delta harmonic sigma weight residual 180.00 136.59 43.41 0 5.00e+00 4.00e-02 7.54e+01 dihedral pdb=" CA LEU B 482 " pdb=" C LEU B 482 " pdb=" N GLU B 483 " pdb=" CA GLU B 483 " ideal model delta harmonic sigma weight residual -180.00 -147.07 -32.93 0 5.00e+00 4.00e-02 4.34e+01 dihedral pdb=" CA PHE E 360 " pdb=" C PHE E 360 " pdb=" N GLY E 361 " pdb=" CA GLY E 361 " ideal model delta harmonic sigma weight residual 180.00 -147.90 -32.10 0 5.00e+00 4.00e-02 4.12e+01 ... (remaining 16026 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 3644 0.111 - 0.221: 239 0.221 - 0.332: 11 0.332 - 0.443: 6 0.443 - 0.553: 6 Chirality restraints: 3906 Sorted by residual: chirality pdb=" CB ILE D 629 " pdb=" CA ILE D 629 " pdb=" CG1 ILE D 629 " pdb=" CG2 ILE D 629 " both_signs ideal model delta sigma weight residual False 2.64 2.09 0.55 2.00e-01 2.50e+01 7.66e+00 chirality pdb=" CB ILE C 629 " pdb=" CA ILE C 629 " pdb=" CG1 ILE C 629 " pdb=" CG2 ILE C 629 " both_signs ideal model delta sigma weight residual False 2.64 2.10 0.55 2.00e-01 2.50e+01 7.45e+00 chirality pdb=" CB VAL B 407 " pdb=" CA VAL B 407 " pdb=" CG1 VAL B 407 " pdb=" CG2 VAL B 407 " both_signs ideal model delta sigma weight residual False -2.63 -2.10 -0.53 2.00e-01 2.50e+01 7.11e+00 ... (remaining 3903 not shown) Planarity restraints: 4595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 544 " 0.058 5.00e-02 4.00e+02 8.83e-02 1.25e+01 pdb=" N PRO E 545 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO E 545 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO E 545 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 544 " 0.057 5.00e-02 4.00e+02 8.57e-02 1.18e+01 pdb=" N PRO B 545 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 545 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 545 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY F 271 " -0.056 5.00e-02 4.00e+02 8.52e-02 1.16e+01 pdb=" N PRO F 272 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO F 272 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO F 272 " -0.047 5.00e-02 4.00e+02 ... (remaining 4592 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 6610 2.80 - 3.33: 24520 3.33 - 3.85: 43838 3.85 - 4.38: 49642 4.38 - 4.90: 81169 Nonbonded interactions: 205779 Sorted by model distance: nonbonded pdb=" O VAL D 258 " pdb=" OG1 THR D 262 " model vdw 2.278 2.440 nonbonded pdb=" OG1 THR E 613 " pdb=" OE2 GLU F 402 " model vdw 2.280 2.440 nonbonded pdb=" O VAL E 258 " pdb=" OG1 THR E 262 " model vdw 2.283 2.440 nonbonded pdb=" OD1 ASP C 307 " pdb=" OG SER C 352 " model vdw 2.292 2.440 nonbonded pdb=" O PHE E 758 " pdb=" OG1 THR E 761 " model vdw 2.295 2.440 ... (remaining 205774 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' and (resid 199 through 588 or resid 599 through 764)) selection = chain 'C' selection = (chain 'D' and (resid 199 through 588 or resid 599 through 764)) selection = (chain 'E' and (resid 199 through 588 or resid 599 through 764)) selection = (chain 'F' and (resid 199 through 588 or resid 599 through 764)) } 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.450 Check model and map are aligned: 0.410 Set scattering table: 0.250 Process input model: 63.790 Find NCS groups from input model: 2.580 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25771 Z= 0.299 Angle : 1.094 18.037 34753 Z= 0.611 Chirality : 0.063 0.553 3906 Planarity : 0.008 0.088 4595 Dihedral : 15.344 90.685 9957 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 0.04 % Allowed : 0.70 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.12), residues: 3194 helix: -2.32 (0.10), residues: 1594 sheet: -2.41 (0.28), residues: 276 loop : -2.49 (0.15), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP C 551 HIS 0.005 0.001 HIS A 340 PHE 0.023 0.002 PHE D 360 TYR 0.029 0.003 TYR D 244 ARG 0.010 0.001 ARG C 638 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 749 time to evaluate : 2.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 PHE cc_start: 0.6742 (t80) cc_final: 0.6475 (t80) REVERT: A 333 ASP cc_start: 0.8737 (p0) cc_final: 0.8516 (p0) REVERT: A 488 GLU cc_start: 0.7784 (pt0) cc_final: 0.7572 (pp20) REVERT: A 515 LEU cc_start: 0.9387 (tt) cc_final: 0.9167 (pp) REVERT: A 538 ASN cc_start: 0.8946 (m-40) cc_final: 0.8734 (m-40) REVERT: A 578 GLU cc_start: 0.7802 (tp30) cc_final: 0.6989 (tp30) REVERT: A 611 MET cc_start: 0.7379 (tpp) cc_final: 0.7156 (tpt) REVERT: A 639 LEU cc_start: 0.7706 (mt) cc_final: 0.7399 (mt) REVERT: B 219 MET cc_start: 0.8701 (mmt) cc_final: 0.8274 (mmt) REVERT: B 241 ILE cc_start: 0.8958 (mt) cc_final: 0.8512 (mm) REVERT: B 244 TYR cc_start: 0.6585 (p90) cc_final: 0.4738 (p90) REVERT: B 312 LYS cc_start: 0.8681 (mmmm) cc_final: 0.7041 (mtpp) REVERT: B 348 ASN cc_start: 0.8340 (t0) cc_final: 0.8009 (m110) REVERT: B 381 LEU cc_start: 0.8944 (tp) cc_final: 0.8667 (mt) REVERT: B 406 HIS cc_start: 0.8779 (m-70) cc_final: 0.8461 (m90) REVERT: B 417 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8534 (tm-30) REVERT: B 449 MET cc_start: 0.9108 (tmm) cc_final: 0.8363 (tpt) REVERT: B 492 LEU cc_start: 0.9062 (mt) cc_final: 0.8529 (pp) REVERT: B 538 ASN cc_start: 0.7876 (m-40) cc_final: 0.7531 (t0) REVERT: B 689 GLU cc_start: 0.8412 (tp30) cc_final: 0.8032 (tm-30) REVERT: B 690 ILE cc_start: 0.8719 (pt) cc_final: 0.8069 (pt) REVERT: C 286 LEU cc_start: 0.8508 (tp) cc_final: 0.8251 (tp) REVERT: C 303 ILE cc_start: 0.8155 (mt) cc_final: 0.7337 (mm) REVERT: C 328 LEU cc_start: 0.9098 (tt) cc_final: 0.8838 (tt) REVERT: C 379 GLU cc_start: 0.8776 (pt0) cc_final: 0.8129 (tm-30) REVERT: C 427 MET cc_start: 0.8574 (mpp) cc_final: 0.8321 (tmm) REVERT: C 492 LEU cc_start: 0.8900 (mp) cc_final: 0.8170 (tp) REVERT: C 541 SER cc_start: 0.8239 (p) cc_final: 0.8037 (t) REVERT: C 567 ARG cc_start: 0.8152 (tmt170) cc_final: 0.7937 (tmt170) REVERT: C 609 ASP cc_start: 0.9149 (m-30) cc_final: 0.8755 (m-30) REVERT: C 678 MET cc_start: 0.7508 (mtp) cc_final: 0.7199 (mtp) REVERT: D 329 LEU cc_start: 0.8625 (mt) cc_final: 0.8397 (mt) REVERT: D 332 MET cc_start: 0.8529 (mmm) cc_final: 0.8273 (mmm) REVERT: D 335 LEU cc_start: 0.8485 (pp) cc_final: 0.8158 (pp) REVERT: D 415 CYS cc_start: 0.8737 (m) cc_final: 0.8418 (p) REVERT: D 449 MET cc_start: 0.9299 (tmm) cc_final: 0.8923 (tmm) REVERT: D 487 ARG cc_start: 0.8509 (tpm170) cc_final: 0.7919 (tpt170) REVERT: D 489 LEU cc_start: 0.8999 (tp) cc_final: 0.8739 (tp) REVERT: D 548 LEU cc_start: 0.9021 (tp) cc_final: 0.8781 (tp) REVERT: D 552 PHE cc_start: 0.8305 (m-80) cc_final: 0.7393 (m-80) REVERT: D 606 THR cc_start: 0.8642 (p) cc_final: 0.8339 (p) REVERT: D 629 ILE cc_start: 0.7877 (tt) cc_final: 0.7631 (pt) REVERT: E 204 ASP cc_start: 0.8584 (t0) cc_final: 0.8322 (t70) REVERT: E 241 ILE cc_start: 0.9191 (mt) cc_final: 0.8496 (mp) REVERT: E 306 LEU cc_start: 0.8315 (tt) cc_final: 0.8049 (tt) REVERT: E 307 ASP cc_start: 0.6982 (t0) cc_final: 0.6611 (t70) REVERT: E 315 LYS cc_start: 0.9239 (mtpt) cc_final: 0.8479 (tptt) REVERT: E 420 LEU cc_start: 0.9394 (tp) cc_final: 0.9175 (tp) REVERT: E 514 VAL cc_start: 0.9012 (m) cc_final: 0.8767 (m) REVERT: E 542 ILE cc_start: 0.8837 (mm) cc_final: 0.8484 (mt) REVERT: E 548 LEU cc_start: 0.9302 (tp) cc_final: 0.9057 (tp) REVERT: E 550 MET cc_start: 0.8784 (mpp) cc_final: 0.8142 (mpp) REVERT: E 624 ASN cc_start: 0.7958 (m-40) cc_final: 0.7545 (m-40) REVERT: E 740 MET cc_start: 0.9130 (tpt) cc_final: 0.8860 (tpt) REVERT: F 301 ILE cc_start: 0.8498 (mt) cc_final: 0.8280 (mp) REVERT: F 319 GLU cc_start: 0.8017 (pm20) cc_final: 0.7479 (mp0) REVERT: F 332 MET cc_start: 0.8177 (tpt) cc_final: 0.7897 (tpt) REVERT: F 354 ASP cc_start: 0.8195 (t0) cc_final: 0.7863 (t0) REVERT: F 456 LEU cc_start: 0.9176 (mt) cc_final: 0.8836 (mt) REVERT: F 580 ASP cc_start: 0.7215 (p0) cc_final: 0.6354 (t0) REVERT: F 599 ARG cc_start: 0.7526 (ttm-80) cc_final: 0.6823 (ttm110) REVERT: F 618 PHE cc_start: 0.8196 (t80) cc_final: 0.7893 (t80) REVERT: F 625 ARG cc_start: 0.8874 (mtt-85) cc_final: 0.8043 (mmm160) outliers start: 1 outliers final: 0 residues processed: 750 average time/residue: 0.4270 time to fit residues: 472.4575 Evaluate side-chains 444 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 444 time to evaluate : 3.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 271 optimal weight: 9.9990 chunk 244 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 164 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 252 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 153 optimal weight: 0.9980 chunk 187 optimal weight: 10.0000 chunk 292 optimal weight: 7.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN A 660 ASN B 398 GLN B 533 ASN ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN C 602 ASN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN ** D 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN E 660 ASN ** E 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 692 GLN F 763 GLN ** F 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25771 Z= 0.261 Angle : 0.706 10.921 34753 Z= 0.372 Chirality : 0.046 0.220 3906 Planarity : 0.006 0.073 4595 Dihedral : 6.156 32.665 3493 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.17 % Favored : 92.80 % Rotamer: Outliers : 0.22 % Allowed : 6.13 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: -2.51 (0.14), residues: 3194 helix: -0.96 (0.12), residues: 1610 sheet: -2.42 (0.27), residues: 272 loop : -2.30 (0.16), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 476 HIS 0.014 0.001 HIS B 384 PHE 0.027 0.002 PHE B 563 TYR 0.021 0.003 TYR B 244 ARG 0.009 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 530 time to evaluate : 3.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 PHE cc_start: 0.7273 (t80) cc_final: 0.6919 (t80) REVERT: A 427 MET cc_start: 0.8692 (pmm) cc_final: 0.8455 (pmm) REVERT: A 515 LEU cc_start: 0.9404 (tt) cc_final: 0.9160 (pp) REVERT: A 578 GLU cc_start: 0.8076 (tp30) cc_final: 0.7307 (tp30) REVERT: A 638 ARG cc_start: 0.7599 (mpp80) cc_final: 0.7316 (mpp80) REVERT: B 219 MET cc_start: 0.8706 (mmt) cc_final: 0.8336 (mmp) REVERT: B 319 GLU cc_start: 0.8303 (pm20) cc_final: 0.8089 (pm20) REVERT: B 329 LEU cc_start: 0.8852 (pp) cc_final: 0.8609 (pp) REVERT: B 348 ASN cc_start: 0.8784 (t0) cc_final: 0.8065 (m110) REVERT: B 395 ASP cc_start: 0.9092 (m-30) cc_final: 0.8691 (m-30) REVERT: B 406 HIS cc_start: 0.9032 (m-70) cc_final: 0.8297 (m90) REVERT: B 417 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8338 (tp30) REVERT: B 538 ASN cc_start: 0.7907 (m-40) cc_final: 0.7461 (t0) REVERT: B 689 GLU cc_start: 0.8520 (tp30) cc_final: 0.8200 (tm-30) REVERT: B 690 ILE cc_start: 0.8696 (pt) cc_final: 0.7814 (pt) REVERT: C 303 ILE cc_start: 0.8105 (mt) cc_final: 0.7846 (mt) REVERT: C 379 GLU cc_start: 0.8910 (pt0) cc_final: 0.8167 (tm-30) REVERT: C 492 LEU cc_start: 0.8546 (mp) cc_final: 0.8316 (tp) REVERT: C 586 ARG cc_start: 0.6545 (ppt170) cc_final: 0.5296 (ptt180) REVERT: D 251 LYS cc_start: 0.8429 (mtpt) cc_final: 0.8052 (mttt) REVERT: D 335 LEU cc_start: 0.8121 (pp) cc_final: 0.7697 (pp) REVERT: D 359 ARG cc_start: 0.8764 (tmt170) cc_final: 0.8313 (tmt170) REVERT: D 415 CYS cc_start: 0.8829 (m) cc_final: 0.8589 (p) REVERT: D 449 MET cc_start: 0.9215 (tmm) cc_final: 0.8868 (tmm) REVERT: D 487 ARG cc_start: 0.8496 (tpm170) cc_final: 0.7714 (tpm170) REVERT: D 552 PHE cc_start: 0.8200 (m-80) cc_final: 0.7194 (m-10) REVERT: D 561 GLU cc_start: 0.7169 (pp20) cc_final: 0.6864 (pm20) REVERT: E 204 ASP cc_start: 0.8548 (t0) cc_final: 0.8249 (t70) REVERT: E 315 LYS cc_start: 0.8969 (mtpt) cc_final: 0.8707 (tptt) REVERT: E 367 VAL cc_start: 0.8532 (m) cc_final: 0.8100 (p) REVERT: E 420 LEU cc_start: 0.9394 (tp) cc_final: 0.8988 (tp) REVERT: E 456 LEU cc_start: 0.9181 (tp) cc_final: 0.8883 (tp) REVERT: E 538 ASN cc_start: 0.8135 (m-40) cc_final: 0.7798 (m-40) REVERT: E 550 MET cc_start: 0.8522 (mpp) cc_final: 0.8198 (mpp) REVERT: E 624 ASN cc_start: 0.8097 (m-40) cc_final: 0.7761 (m-40) REVERT: E 740 MET cc_start: 0.9114 (tpt) cc_final: 0.8840 (tpt) REVERT: F 268 LEU cc_start: 0.8795 (tp) cc_final: 0.8571 (pp) REVERT: F 319 GLU cc_start: 0.8120 (pm20) cc_final: 0.7268 (mp0) REVERT: F 332 MET cc_start: 0.8321 (tpt) cc_final: 0.8011 (tpt) REVERT: F 580 ASP cc_start: 0.7155 (p0) cc_final: 0.6420 (t0) REVERT: F 618 PHE cc_start: 0.7868 (t80) cc_final: 0.7602 (t80) REVERT: F 625 ARG cc_start: 0.8953 (mtt-85) cc_final: 0.8084 (mmm160) REVERT: F 736 PHE cc_start: 0.8266 (m-10) cc_final: 0.7951 (m-10) REVERT: F 740 MET cc_start: 0.6235 (ptt) cc_final: 0.5716 (ptt) outliers start: 6 outliers final: 1 residues processed: 534 average time/residue: 0.3972 time to fit residues: 321.8720 Evaluate side-chains 399 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 398 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 162 optimal weight: 10.0000 chunk 90 optimal weight: 0.0770 chunk 243 optimal weight: 6.9990 chunk 199 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 292 optimal weight: 3.9990 chunk 316 optimal weight: 5.9990 chunk 260 optimal weight: 6.9990 chunk 290 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 235 optimal weight: 0.9980 overall best weight: 2.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 GLN B 384 HIS B 533 ASN B 602 ASN ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 GLN C 533 ASN C 602 ASN ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 GLN E 533 ASN E 603 GLN E 692 GLN ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 HIS ** F 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25771 Z= 0.222 Angle : 0.663 10.800 34753 Z= 0.345 Chirality : 0.045 0.223 3906 Planarity : 0.005 0.064 4595 Dihedral : 5.826 30.085 3493 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 0.04 % Allowed : 5.83 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.15), residues: 3194 helix: -0.33 (0.13), residues: 1634 sheet: -2.27 (0.28), residues: 268 loop : -2.19 (0.17), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 476 HIS 0.005 0.001 HIS F 406 PHE 0.024 0.002 PHE F 267 TYR 0.019 0.002 TYR A 244 ARG 0.009 0.001 ARG F 700 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 498 time to evaluate : 3.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 PHE cc_start: 0.7528 (t80) cc_final: 0.7077 (t80) REVERT: A 611 MET cc_start: 0.7175 (tpt) cc_final: 0.6712 (tpt) REVERT: B 219 MET cc_start: 0.8697 (mmt) cc_final: 0.8295 (mmt) REVERT: B 305 GLU cc_start: 0.7398 (mm-30) cc_final: 0.6991 (mm-30) REVERT: B 329 LEU cc_start: 0.8712 (pp) cc_final: 0.8462 (pp) REVERT: B 381 LEU cc_start: 0.8899 (tp) cc_final: 0.8655 (tt) REVERT: B 406 HIS cc_start: 0.9144 (m-70) cc_final: 0.8281 (m90) REVERT: B 550 MET cc_start: 0.8301 (mtm) cc_final: 0.8024 (mpp) REVERT: C 303 ILE cc_start: 0.8171 (mt) cc_final: 0.7962 (mt) REVERT: C 379 GLU cc_start: 0.8795 (pt0) cc_final: 0.8165 (tm-30) REVERT: C 586 ARG cc_start: 0.6528 (ppt170) cc_final: 0.5397 (ptt180) REVERT: C 678 MET cc_start: 0.8812 (ttt) cc_final: 0.8346 (ttt) REVERT: D 331 LEU cc_start: 0.9165 (mp) cc_final: 0.8936 (mp) REVERT: D 415 CYS cc_start: 0.9015 (m) cc_final: 0.8733 (p) REVERT: D 449 MET cc_start: 0.9294 (tmm) cc_final: 0.8965 (tmm) REVERT: D 487 ARG cc_start: 0.8331 (tpm170) cc_final: 0.6878 (tpm170) REVERT: D 526 LEU cc_start: 0.9558 (mt) cc_final: 0.9344 (mt) REVERT: D 552 PHE cc_start: 0.8156 (m-80) cc_final: 0.7417 (m-10) REVERT: D 561 GLU cc_start: 0.7167 (pp20) cc_final: 0.6865 (pm20) REVERT: D 577 ASP cc_start: 0.6906 (t0) cc_final: 0.6616 (t0) REVERT: D 578 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8029 (mm-30) REVERT: E 204 ASP cc_start: 0.8684 (t0) cc_final: 0.8368 (t70) REVERT: E 420 LEU cc_start: 0.9356 (tp) cc_final: 0.8998 (tp) REVERT: E 538 ASN cc_start: 0.8095 (m-40) cc_final: 0.7773 (m-40) REVERT: E 550 MET cc_start: 0.8578 (mpp) cc_final: 0.8271 (mpp) REVERT: E 624 ASN cc_start: 0.7821 (m-40) cc_final: 0.7497 (m-40) REVERT: E 740 MET cc_start: 0.9044 (tpt) cc_final: 0.8715 (tpt) REVERT: F 285 ASN cc_start: 0.7430 (m-40) cc_final: 0.7226 (m-40) REVERT: F 319 GLU cc_start: 0.8110 (pm20) cc_final: 0.7297 (mp0) REVERT: F 332 MET cc_start: 0.8270 (tpt) cc_final: 0.7999 (tpt) REVERT: F 388 MET cc_start: 0.8928 (ppp) cc_final: 0.7989 (ppp) REVERT: F 575 PHE cc_start: 0.8135 (t80) cc_final: 0.7917 (t80) REVERT: F 625 ARG cc_start: 0.8905 (mtt-85) cc_final: 0.8325 (mmm160) REVERT: F 736 PHE cc_start: 0.8515 (m-10) cc_final: 0.8084 (m-80) REVERT: F 740 MET cc_start: 0.6420 (ptt) cc_final: 0.6030 (ptt) outliers start: 1 outliers final: 0 residues processed: 499 average time/residue: 0.3920 time to fit residues: 300.3299 Evaluate side-chains 386 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 386 time to evaluate : 3.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 289 optimal weight: 0.9990 chunk 220 optimal weight: 7.9990 chunk 152 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 196 optimal weight: 0.8980 chunk 293 optimal weight: 0.0000 chunk 311 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 278 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 HIS B 387 ASN ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN C 602 ASN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 GLN D 317 HIS ** D 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 680 ASN E 317 HIS E 533 ASN ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS ** F 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25771 Z= 0.195 Angle : 0.656 11.152 34753 Z= 0.336 Chirality : 0.046 0.262 3906 Planarity : 0.005 0.063 4595 Dihedral : 5.696 31.781 3493 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.67 % Favored : 92.30 % Rotamer: Outliers : 0.04 % Allowed : 3.58 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: -1.70 (0.15), residues: 3194 helix: -0.12 (0.13), residues: 1620 sheet: -2.31 (0.27), residues: 276 loop : -2.12 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 454 HIS 0.004 0.001 HIS C 317 PHE 0.027 0.002 PHE F 618 TYR 0.023 0.002 TYR D 244 ARG 0.005 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 494 time to evaluate : 2.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 PHE cc_start: 0.7522 (t80) cc_final: 0.7157 (t80) REVERT: A 575 PHE cc_start: 0.7432 (t80) cc_final: 0.6680 (t80) REVERT: A 577 ASP cc_start: 0.7056 (t0) cc_final: 0.6571 (t0) REVERT: B 219 MET cc_start: 0.8594 (mmt) cc_final: 0.8298 (mmt) REVERT: B 305 GLU cc_start: 0.7332 (mm-30) cc_final: 0.6970 (mm-30) REVERT: B 312 LYS cc_start: 0.8754 (mmmm) cc_final: 0.7802 (mtpp) REVERT: B 315 LYS cc_start: 0.8799 (mtmt) cc_final: 0.8466 (pttt) REVERT: B 329 LEU cc_start: 0.8869 (pp) cc_final: 0.8641 (pp) REVERT: B 380 ILE cc_start: 0.9357 (pt) cc_final: 0.9095 (pt) REVERT: B 381 LEU cc_start: 0.8903 (tp) cc_final: 0.8658 (tt) REVERT: B 406 HIS cc_start: 0.9070 (m-70) cc_final: 0.8272 (m90) REVERT: B 414 LEU cc_start: 0.9361 (mt) cc_final: 0.9062 (tt) REVERT: B 527 LEU cc_start: 0.8624 (mt) cc_final: 0.8404 (mt) REVERT: C 353 ILE cc_start: 0.9085 (pt) cc_final: 0.8862 (pt) REVERT: C 359 ARG cc_start: 0.8434 (ttt180) cc_final: 0.8227 (ttt180) REVERT: C 379 GLU cc_start: 0.8758 (pt0) cc_final: 0.8170 (tm-30) REVERT: C 487 ARG cc_start: 0.8492 (tpm170) cc_final: 0.8275 (tpm170) REVERT: C 586 ARG cc_start: 0.6325 (ppt170) cc_final: 0.5276 (ptt180) REVERT: C 678 MET cc_start: 0.8824 (ttt) cc_final: 0.8347 (ttt) REVERT: D 331 LEU cc_start: 0.9174 (mp) cc_final: 0.8933 (mp) REVERT: D 359 ARG cc_start: 0.8598 (tmt170) cc_final: 0.7856 (tmt170) REVERT: D 415 CYS cc_start: 0.9052 (m) cc_final: 0.8697 (p) REVERT: D 424 ARG cc_start: 0.8291 (ttm110) cc_final: 0.7614 (ttp-110) REVERT: D 452 PHE cc_start: 0.7764 (m-10) cc_final: 0.7442 (m-80) REVERT: D 552 PHE cc_start: 0.8147 (m-80) cc_final: 0.7381 (m-10) REVERT: D 561 GLU cc_start: 0.6973 (pp20) cc_final: 0.6710 (pm20) REVERT: D 577 ASP cc_start: 0.6957 (t0) cc_final: 0.6640 (t0) REVERT: D 578 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7970 (mm-30) REVERT: D 606 THR cc_start: 0.8676 (p) cc_final: 0.8438 (p) REVERT: E 204 ASP cc_start: 0.8660 (t0) cc_final: 0.8348 (t70) REVERT: E 420 LEU cc_start: 0.9422 (tp) cc_final: 0.9115 (tp) REVERT: E 458 GLN cc_start: 0.7512 (mp10) cc_final: 0.7231 (mp10) REVERT: E 538 ASN cc_start: 0.8056 (m-40) cc_final: 0.7728 (m-40) REVERT: E 546 GLU cc_start: 0.8243 (tp30) cc_final: 0.7962 (tp30) REVERT: E 550 MET cc_start: 0.8476 (mpp) cc_final: 0.8176 (mpp) REVERT: E 624 ASN cc_start: 0.7869 (m-40) cc_final: 0.7484 (m-40) REVERT: E 740 MET cc_start: 0.9031 (tpt) cc_final: 0.8680 (tpt) REVERT: F 319 GLU cc_start: 0.8142 (pm20) cc_final: 0.7271 (mp0) REVERT: F 332 MET cc_start: 0.8295 (tpt) cc_final: 0.8051 (tpt) REVERT: F 333 ASP cc_start: 0.8739 (p0) cc_final: 0.8495 (p0) REVERT: F 388 MET cc_start: 0.9027 (ppp) cc_final: 0.8216 (ppp) REVERT: F 550 MET cc_start: 0.7857 (mmp) cc_final: 0.7488 (mmp) REVERT: F 625 ARG cc_start: 0.8882 (mtt-85) cc_final: 0.8402 (mmm160) REVERT: F 736 PHE cc_start: 0.8606 (m-10) cc_final: 0.8126 (m-10) REVERT: F 740 MET cc_start: 0.6408 (ptt) cc_final: 0.6026 (ptt) outliers start: 1 outliers final: 0 residues processed: 494 average time/residue: 0.3844 time to fit residues: 292.8579 Evaluate side-chains 388 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 388 time to evaluate : 2.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 259 optimal weight: 0.9990 chunk 176 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 231 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 265 optimal weight: 7.9990 chunk 215 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 158 optimal weight: 9.9990 chunk 279 optimal weight: 0.5980 chunk 78 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN C 602 ASN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 HIS ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS ** F 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN ** F 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25771 Z= 0.174 Angle : 0.645 11.248 34753 Z= 0.329 Chirality : 0.045 0.247 3906 Planarity : 0.005 0.056 4595 Dihedral : 5.508 31.596 3493 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.04 % Allowed : 3.51 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: -1.48 (0.15), residues: 3194 helix: 0.09 (0.13), residues: 1626 sheet: -2.41 (0.27), residues: 292 loop : -2.00 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 476 HIS 0.003 0.001 HIS F 406 PHE 0.029 0.001 PHE F 267 TYR 0.028 0.002 TYR F 495 ARG 0.007 0.000 ARG D 287 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 502 time to evaluate : 3.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 LYS cc_start: 0.9009 (tmtt) cc_final: 0.8727 (ttpt) REVERT: A 575 PHE cc_start: 0.7385 (t80) cc_final: 0.6559 (t80) REVERT: A 577 ASP cc_start: 0.6974 (t0) cc_final: 0.6630 (t0) REVERT: B 219 MET cc_start: 0.8600 (mmt) cc_final: 0.8339 (mmt) REVERT: B 305 GLU cc_start: 0.7441 (mm-30) cc_final: 0.7017 (mm-30) REVERT: B 312 LYS cc_start: 0.8748 (mmmm) cc_final: 0.7689 (mtpp) REVERT: B 315 LYS cc_start: 0.8952 (mtmt) cc_final: 0.8496 (pttt) REVERT: B 371 ILE cc_start: 0.8113 (mm) cc_final: 0.7846 (mm) REVERT: B 406 HIS cc_start: 0.9082 (m-70) cc_final: 0.8286 (m90) REVERT: B 522 CYS cc_start: 0.8286 (t) cc_final: 0.8037 (t) REVERT: C 379 GLU cc_start: 0.8758 (pt0) cc_final: 0.8161 (tm-30) REVERT: C 427 MET cc_start: 0.7763 (tmm) cc_final: 0.7548 (tmm) REVERT: C 487 ARG cc_start: 0.8478 (tpm170) cc_final: 0.8208 (tpm170) REVERT: C 586 ARG cc_start: 0.6327 (ppt170) cc_final: 0.5299 (ptt180) REVERT: C 678 MET cc_start: 0.8815 (ttt) cc_final: 0.8347 (ttt) REVERT: D 204 ASP cc_start: 0.8792 (t0) cc_final: 0.8514 (p0) REVERT: D 331 LEU cc_start: 0.9098 (mp) cc_final: 0.8874 (mp) REVERT: D 359 ARG cc_start: 0.8604 (tmt170) cc_final: 0.7856 (tmt170) REVERT: D 415 CYS cc_start: 0.9016 (m) cc_final: 0.8726 (p) REVERT: D 452 PHE cc_start: 0.7761 (m-10) cc_final: 0.7394 (m-80) REVERT: D 552 PHE cc_start: 0.8184 (m-80) cc_final: 0.7460 (m-10) REVERT: D 561 GLU cc_start: 0.6932 (pp20) cc_final: 0.6646 (pm20) REVERT: D 577 ASP cc_start: 0.6927 (t0) cc_final: 0.6590 (t0) REVERT: D 578 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7780 (mm-30) REVERT: D 606 THR cc_start: 0.8656 (p) cc_final: 0.8430 (p) REVERT: D 607 GLU cc_start: 0.8565 (mp0) cc_final: 0.8303 (mp0) REVERT: E 204 ASP cc_start: 0.8608 (t0) cc_final: 0.8312 (t70) REVERT: E 420 LEU cc_start: 0.9410 (tp) cc_final: 0.9107 (tp) REVERT: E 458 GLN cc_start: 0.7511 (mp10) cc_final: 0.7175 (mp10) REVERT: E 538 ASN cc_start: 0.8160 (m-40) cc_final: 0.7833 (m-40) REVERT: E 558 ASN cc_start: 0.8866 (m-40) cc_final: 0.8250 (t0) REVERT: E 624 ASN cc_start: 0.7692 (m-40) cc_final: 0.7245 (m-40) REVERT: E 740 MET cc_start: 0.9014 (tpt) cc_final: 0.8685 (tpt) REVERT: F 319 GLU cc_start: 0.8089 (pm20) cc_final: 0.7249 (mp0) REVERT: F 332 MET cc_start: 0.8254 (tpt) cc_final: 0.8006 (tpt) REVERT: F 333 ASP cc_start: 0.8822 (p0) cc_final: 0.8598 (p0) REVERT: F 493 VAL cc_start: 0.8834 (m) cc_final: 0.8577 (p) REVERT: F 625 ARG cc_start: 0.8855 (mtt-85) cc_final: 0.8405 (mmm160) REVERT: F 736 PHE cc_start: 0.8569 (m-10) cc_final: 0.8065 (m-10) REVERT: F 740 MET cc_start: 0.6389 (ptt) cc_final: 0.6011 (ptt) outliers start: 1 outliers final: 0 residues processed: 502 average time/residue: 0.3795 time to fit residues: 292.3425 Evaluate side-chains 390 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 390 time to evaluate : 2.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 104 optimal weight: 8.9990 chunk 280 optimal weight: 0.3980 chunk 61 optimal weight: 7.9990 chunk 182 optimal weight: 0.3980 chunk 76 optimal weight: 3.9990 chunk 311 optimal weight: 6.9990 chunk 258 optimal weight: 0.7980 chunk 144 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 163 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS B 384 HIS ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 GLN C 533 ASN C 602 ASN D 317 HIS ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS ** F 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25771 Z= 0.185 Angle : 0.660 11.136 34753 Z= 0.336 Chirality : 0.045 0.280 3906 Planarity : 0.005 0.056 4595 Dihedral : 5.421 30.783 3493 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.15), residues: 3194 helix: 0.20 (0.13), residues: 1634 sheet: -2.28 (0.28), residues: 292 loop : -1.97 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 454 HIS 0.008 0.001 HIS A 499 PHE 0.040 0.002 PHE F 265 TYR 0.042 0.002 TYR F 495 ARG 0.009 0.000 ARG D 256 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 494 time to evaluate : 2.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 219 MET cc_start: 0.8585 (mmt) cc_final: 0.8310 (mmt) REVERT: B 305 GLU cc_start: 0.7398 (mm-30) cc_final: 0.6997 (mm-30) REVERT: B 312 LYS cc_start: 0.8674 (mmmm) cc_final: 0.7595 (mtpp) REVERT: B 315 LYS cc_start: 0.8916 (mtmt) cc_final: 0.8635 (pttt) REVERT: B 371 ILE cc_start: 0.7998 (mm) cc_final: 0.7779 (mm) REVERT: B 388 MET cc_start: 0.8666 (mmp) cc_final: 0.6627 (ppp) REVERT: B 406 HIS cc_start: 0.9095 (m-70) cc_final: 0.8304 (m90) REVERT: B 522 CYS cc_start: 0.8275 (t) cc_final: 0.7122 (p) REVERT: B 567 ARG cc_start: 0.8268 (ttp80) cc_final: 0.8062 (ttm-80) REVERT: C 379 GLU cc_start: 0.8767 (pt0) cc_final: 0.8168 (tm-30) REVERT: C 609 ASP cc_start: 0.8898 (m-30) cc_final: 0.8542 (m-30) REVERT: C 678 MET cc_start: 0.8674 (ttt) cc_final: 0.8171 (ttt) REVERT: D 331 LEU cc_start: 0.9103 (mp) cc_final: 0.8897 (mp) REVERT: D 359 ARG cc_start: 0.8553 (tmt170) cc_final: 0.8009 (tmt170) REVERT: D 415 CYS cc_start: 0.9004 (m) cc_final: 0.8748 (p) REVERT: D 452 PHE cc_start: 0.7796 (m-10) cc_final: 0.7415 (m-80) REVERT: D 493 VAL cc_start: 0.9316 (t) cc_final: 0.8852 (p) REVERT: D 531 ILE cc_start: 0.9145 (tp) cc_final: 0.8897 (tp) REVERT: D 552 PHE cc_start: 0.8137 (m-80) cc_final: 0.7501 (m-10) REVERT: D 561 GLU cc_start: 0.6742 (pp20) cc_final: 0.6415 (pm20) REVERT: D 678 MET cc_start: 0.8637 (mtt) cc_final: 0.8399 (mmm) REVERT: E 204 ASP cc_start: 0.8610 (t0) cc_final: 0.8310 (t70) REVERT: E 420 LEU cc_start: 0.9357 (tp) cc_final: 0.9009 (tp) REVERT: E 538 ASN cc_start: 0.8166 (m-40) cc_final: 0.7845 (m-40) REVERT: E 558 ASN cc_start: 0.8894 (m-40) cc_final: 0.8413 (t0) REVERT: E 624 ASN cc_start: 0.7675 (m-40) cc_final: 0.7219 (m-40) REVERT: E 740 MET cc_start: 0.9015 (tpt) cc_final: 0.8684 (tpt) REVERT: F 319 GLU cc_start: 0.8084 (pm20) cc_final: 0.7250 (mp0) REVERT: F 332 MET cc_start: 0.8252 (tpt) cc_final: 0.7973 (tpt) REVERT: F 333 ASP cc_start: 0.8816 (p0) cc_final: 0.8566 (p0) REVERT: F 388 MET cc_start: 0.8941 (ppp) cc_final: 0.8251 (ppp) REVERT: F 493 VAL cc_start: 0.8584 (m) cc_final: 0.8343 (p) REVERT: F 736 PHE cc_start: 0.8599 (m-10) cc_final: 0.8083 (m-10) REVERT: F 740 MET cc_start: 0.6468 (ptt) cc_final: 0.6085 (ptt) outliers start: 0 outliers final: 0 residues processed: 494 average time/residue: 0.3955 time to fit residues: 302.3962 Evaluate side-chains 388 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 388 time to evaluate : 2.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 300 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 177 optimal weight: 7.9990 chunk 227 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 262 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 310 optimal weight: 0.0000 chunk 194 optimal weight: 0.0370 chunk 189 optimal weight: 0.1980 chunk 143 optimal weight: 0.8980 overall best weight: 0.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 ASN B 384 HIS ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 GLN C 533 ASN C 602 ASN ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 660 ASN D 735 HIS E 458 GLN E 533 ASN ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS ** F 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25771 Z= 0.170 Angle : 0.672 11.575 34753 Z= 0.337 Chirality : 0.046 0.273 3906 Planarity : 0.005 0.107 4595 Dihedral : 5.312 32.780 3493 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.04 % Allowed : 2.03 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.15), residues: 3194 helix: 0.26 (0.13), residues: 1642 sheet: -2.21 (0.28), residues: 292 loop : -1.92 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 454 HIS 0.004 0.001 HIS D 735 PHE 0.036 0.002 PHE F 267 TYR 0.016 0.002 TYR D 244 ARG 0.010 0.000 ARG D 322 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 498 time to evaluate : 3.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 PHE cc_start: 0.7304 (t80) cc_final: 0.6721 (t80) REVERT: A 577 ASP cc_start: 0.6981 (t0) cc_final: 0.6405 (t0) REVERT: B 312 LYS cc_start: 0.8740 (mmmm) cc_final: 0.7780 (mtpp) REVERT: B 388 MET cc_start: 0.8650 (mmp) cc_final: 0.6815 (ppp) REVERT: B 406 HIS cc_start: 0.9110 (m-70) cc_final: 0.8319 (m90) REVERT: B 522 CYS cc_start: 0.8263 (t) cc_final: 0.7115 (p) REVERT: C 379 GLU cc_start: 0.8763 (pt0) cc_final: 0.8157 (tm-30) REVERT: C 427 MET cc_start: 0.8060 (tmm) cc_final: 0.7777 (tmm) REVERT: C 442 MET cc_start: 0.8101 (mmt) cc_final: 0.7695 (mmm) REVERT: C 550 MET cc_start: 0.7354 (mmt) cc_final: 0.7001 (mmt) REVERT: C 586 ARG cc_start: 0.6744 (ppt170) cc_final: 0.5629 (ptt180) REVERT: C 609 ASP cc_start: 0.8918 (m-30) cc_final: 0.8685 (m-30) REVERT: C 678 MET cc_start: 0.8657 (ttt) cc_final: 0.8153 (ttt) REVERT: D 204 ASP cc_start: 0.8832 (t0) cc_final: 0.8509 (p0) REVERT: D 335 LEU cc_start: 0.8449 (pp) cc_final: 0.8061 (pp) REVERT: D 359 ARG cc_start: 0.8659 (tmt170) cc_final: 0.7964 (tmt170) REVERT: D 411 LEU cc_start: 0.9347 (mm) cc_final: 0.8721 (tt) REVERT: D 452 PHE cc_start: 0.7850 (m-10) cc_final: 0.7452 (m-80) REVERT: D 493 VAL cc_start: 0.9363 (t) cc_final: 0.9015 (p) REVERT: D 531 ILE cc_start: 0.9119 (tp) cc_final: 0.8832 (tp) REVERT: D 552 PHE cc_start: 0.8279 (m-80) cc_final: 0.7683 (m-10) REVERT: D 561 GLU cc_start: 0.6673 (pp20) cc_final: 0.6335 (pm20) REVERT: D 606 THR cc_start: 0.8755 (p) cc_final: 0.8416 (p) REVERT: D 678 MET cc_start: 0.8574 (mtt) cc_final: 0.8284 (mmm) REVERT: D 740 MET cc_start: 0.7647 (ppp) cc_final: 0.7309 (tmm) REVERT: E 204 ASP cc_start: 0.8580 (t0) cc_final: 0.8267 (t70) REVERT: E 315 LYS cc_start: 0.9273 (mtmt) cc_final: 0.8953 (tptt) REVERT: E 420 LEU cc_start: 0.9331 (tp) cc_final: 0.8974 (tp) REVERT: E 458 GLN cc_start: 0.7407 (mp-120) cc_final: 0.7123 (mp10) REVERT: E 538 ASN cc_start: 0.8122 (m-40) cc_final: 0.7766 (m-40) REVERT: E 550 MET cc_start: 0.7976 (mpp) cc_final: 0.7546 (mpp) REVERT: E 558 ASN cc_start: 0.8964 (m-40) cc_final: 0.8164 (t0) REVERT: E 624 ASN cc_start: 0.7616 (m-40) cc_final: 0.7116 (m-40) REVERT: E 740 MET cc_start: 0.9006 (tpt) cc_final: 0.8682 (tpt) REVERT: F 319 GLU cc_start: 0.8007 (pm20) cc_final: 0.7536 (mp0) REVERT: F 333 ASP cc_start: 0.8775 (p0) cc_final: 0.8387 (p0) REVERT: F 625 ARG cc_start: 0.8876 (mtt-85) cc_final: 0.8298 (mmm-85) REVERT: F 736 PHE cc_start: 0.8587 (m-10) cc_final: 0.8068 (m-10) REVERT: F 740 MET cc_start: 0.6581 (ptt) cc_final: 0.6247 (ptt) outliers start: 1 outliers final: 0 residues processed: 498 average time/residue: 0.3993 time to fit residues: 306.6893 Evaluate side-chains 391 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 3.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 192 optimal weight: 3.9990 chunk 123 optimal weight: 0.0270 chunk 185 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 197 optimal weight: 1.9990 chunk 211 optimal weight: 9.9990 chunk 153 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 243 optimal weight: 3.9990 chunk 282 optimal weight: 4.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN C 602 ASN ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 660 ASN E 458 GLN E 533 ASN ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS ** F 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25771 Z= 0.181 Angle : 0.673 11.056 34753 Z= 0.339 Chirality : 0.046 0.324 3906 Planarity : 0.005 0.114 4595 Dihedral : 5.244 32.235 3493 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: -1.18 (0.15), residues: 3194 helix: 0.32 (0.13), residues: 1646 sheet: -2.19 (0.28), residues: 292 loop : -1.88 (0.18), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 454 HIS 0.002 0.001 HIS B 384 PHE 0.035 0.002 PHE F 267 TYR 0.030 0.002 TYR D 203 ARG 0.015 0.000 ARG F 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 483 time to evaluate : 2.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ILE cc_start: 0.8553 (tp) cc_final: 0.8046 (mm) REVERT: A 291 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8311 (mm-30) REVERT: A 575 PHE cc_start: 0.7358 (t80) cc_final: 0.6737 (t80) REVERT: A 577 ASP cc_start: 0.7054 (t0) cc_final: 0.6621 (t0) REVERT: A 638 ARG cc_start: 0.7721 (mpp80) cc_final: 0.7449 (mpp80) REVERT: B 312 LYS cc_start: 0.8691 (mmmm) cc_final: 0.8223 (mtpp) REVERT: B 388 MET cc_start: 0.8624 (mmp) cc_final: 0.6810 (ppp) REVERT: B 406 HIS cc_start: 0.9098 (m-70) cc_final: 0.8349 (m90) REVERT: B 522 CYS cc_start: 0.8280 (t) cc_final: 0.7118 (p) REVERT: B 611 MET cc_start: 0.7259 (mmm) cc_final: 0.6880 (mmm) REVERT: C 204 ASP cc_start: 0.8132 (t0) cc_final: 0.7893 (t0) REVERT: C 379 GLU cc_start: 0.8747 (pt0) cc_final: 0.8150 (tm-30) REVERT: C 427 MET cc_start: 0.8060 (tmm) cc_final: 0.7755 (tmm) REVERT: C 442 MET cc_start: 0.8241 (mmt) cc_final: 0.7853 (mmm) REVERT: C 550 MET cc_start: 0.7354 (mmt) cc_final: 0.7109 (mmt) REVERT: C 567 ARG cc_start: 0.8367 (tmt170) cc_final: 0.8043 (tmt170) REVERT: C 586 ARG cc_start: 0.6994 (ppt170) cc_final: 0.5813 (ptt180) REVERT: C 600 VAL cc_start: 0.9065 (t) cc_final: 0.8859 (t) REVERT: C 609 ASP cc_start: 0.8946 (m-30) cc_final: 0.8701 (m-30) REVERT: C 678 MET cc_start: 0.8654 (ttt) cc_final: 0.8155 (ttt) REVERT: D 203 TYR cc_start: 0.6253 (t80) cc_final: 0.5980 (t80) REVERT: D 204 ASP cc_start: 0.8794 (t0) cc_final: 0.8368 (p0) REVERT: D 327 GLN cc_start: 0.8611 (tt0) cc_final: 0.8265 (mm-40) REVERT: D 332 MET cc_start: 0.8150 (tpt) cc_final: 0.7842 (tpp) REVERT: D 335 LEU cc_start: 0.8473 (pp) cc_final: 0.8073 (pp) REVERT: D 359 ARG cc_start: 0.8724 (tmt170) cc_final: 0.8008 (tmt170) REVERT: D 411 LEU cc_start: 0.9359 (mm) cc_final: 0.8664 (tt) REVERT: D 452 PHE cc_start: 0.7823 (m-10) cc_final: 0.7464 (m-80) REVERT: D 493 VAL cc_start: 0.9344 (t) cc_final: 0.8995 (p) REVERT: D 531 ILE cc_start: 0.9153 (tp) cc_final: 0.8909 (tp) REVERT: D 552 PHE cc_start: 0.8239 (m-80) cc_final: 0.7949 (m-10) REVERT: D 561 GLU cc_start: 0.6852 (pp20) cc_final: 0.6365 (pm20) REVERT: D 563 PHE cc_start: 0.8760 (m-80) cc_final: 0.8546 (m-80) REVERT: D 607 GLU cc_start: 0.8597 (mp0) cc_final: 0.8319 (mp0) REVERT: D 678 MET cc_start: 0.8591 (mtt) cc_final: 0.8335 (mmm) REVERT: D 740 MET cc_start: 0.7692 (ppp) cc_final: 0.7333 (tmm) REVERT: E 204 ASP cc_start: 0.8572 (t0) cc_final: 0.8252 (t70) REVERT: E 315 LYS cc_start: 0.9208 (mtmt) cc_final: 0.8943 (tptt) REVERT: E 335 LEU cc_start: 0.9204 (mt) cc_final: 0.8720 (pp) REVERT: E 388 MET cc_start: 0.8362 (ppp) cc_final: 0.8103 (ppp) REVERT: E 420 LEU cc_start: 0.9284 (tp) cc_final: 0.9023 (tp) REVERT: E 538 ASN cc_start: 0.8104 (m-40) cc_final: 0.7705 (m-40) REVERT: E 558 ASN cc_start: 0.8801 (m-40) cc_final: 0.8308 (t0) REVERT: E 624 ASN cc_start: 0.7726 (m-40) cc_final: 0.7353 (m-40) REVERT: E 740 MET cc_start: 0.9002 (tpt) cc_final: 0.8678 (tpt) REVERT: F 319 GLU cc_start: 0.8186 (pm20) cc_final: 0.7540 (mm-30) REVERT: F 333 ASP cc_start: 0.8735 (p0) cc_final: 0.8425 (p0) REVERT: F 625 ARG cc_start: 0.8827 (mtt-85) cc_final: 0.8285 (mmm-85) REVERT: F 736 PHE cc_start: 0.8608 (m-10) cc_final: 0.8094 (m-80) REVERT: F 740 MET cc_start: 0.6717 (ptt) cc_final: 0.6353 (ptt) outliers start: 0 outliers final: 0 residues processed: 483 average time/residue: 0.3863 time to fit residues: 286.4043 Evaluate side-chains 388 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 388 time to evaluate : 3.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 297 optimal weight: 0.7980 chunk 271 optimal weight: 0.0770 chunk 289 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 227 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 273 optimal weight: 1.9990 chunk 288 optimal weight: 0.6980 chunk 189 optimal weight: 0.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 494 GLN ** D 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 460 ASN E 533 ASN ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS F 404 HIS ** F 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25771 Z= 0.182 Angle : 0.676 10.789 34753 Z= 0.340 Chirality : 0.046 0.262 3906 Planarity : 0.005 0.100 4595 Dihedral : 5.236 31.800 3493 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.86 % Favored : 92.11 % Rotamer: Outliers : 0.04 % Allowed : 0.85 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: -1.17 (0.15), residues: 3194 helix: 0.32 (0.13), residues: 1648 sheet: -2.16 (0.28), residues: 292 loop : -1.88 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 551 HIS 0.002 0.001 HIS D 384 PHE 0.034 0.002 PHE F 267 TYR 0.025 0.002 TYR E 244 ARG 0.009 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 476 time to evaluate : 3.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ILE cc_start: 0.8579 (tp) cc_final: 0.8059 (mm) REVERT: A 291 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8297 (mm-30) REVERT: A 575 PHE cc_start: 0.7382 (t80) cc_final: 0.6859 (t80) REVERT: A 577 ASP cc_start: 0.7074 (t0) cc_final: 0.6632 (t0) REVERT: B 312 LYS cc_start: 0.8672 (mmmm) cc_final: 0.8236 (mtpp) REVERT: B 315 LYS cc_start: 0.9097 (pttt) cc_final: 0.8868 (pttm) REVERT: B 348 ASN cc_start: 0.8799 (t0) cc_final: 0.8577 (t0) REVERT: B 371 ILE cc_start: 0.7606 (mm) cc_final: 0.7375 (mm) REVERT: B 388 MET cc_start: 0.8608 (mmp) cc_final: 0.6806 (ppp) REVERT: B 406 HIS cc_start: 0.9145 (m-70) cc_final: 0.8295 (m90) REVERT: B 522 CYS cc_start: 0.8238 (t) cc_final: 0.7059 (p) REVERT: B 611 MET cc_start: 0.7246 (mmm) cc_final: 0.6886 (mmm) REVERT: C 332 MET cc_start: 0.7074 (ttm) cc_final: 0.6853 (ttt) REVERT: C 379 GLU cc_start: 0.8745 (pt0) cc_final: 0.8126 (tm-30) REVERT: C 442 MET cc_start: 0.8229 (mmt) cc_final: 0.7856 (mmm) REVERT: C 550 MET cc_start: 0.7396 (mmt) cc_final: 0.6876 (mmt) REVERT: C 567 ARG cc_start: 0.8055 (tmt170) cc_final: 0.7801 (tmt170) REVERT: C 586 ARG cc_start: 0.6985 (ppt170) cc_final: 0.5830 (ptt180) REVERT: C 609 ASP cc_start: 0.9017 (m-30) cc_final: 0.8751 (m-30) REVERT: C 678 MET cc_start: 0.8650 (ttt) cc_final: 0.8169 (ttt) REVERT: D 203 TYR cc_start: 0.6419 (t80) cc_final: 0.6009 (t80) REVERT: D 204 ASP cc_start: 0.8662 (t0) cc_final: 0.8285 (p0) REVERT: D 327 GLN cc_start: 0.8482 (tt0) cc_final: 0.7933 (mm-40) REVERT: D 332 MET cc_start: 0.8122 (tpt) cc_final: 0.7828 (tpp) REVERT: D 335 LEU cc_start: 0.8448 (pp) cc_final: 0.8042 (pp) REVERT: D 359 ARG cc_start: 0.8734 (tmt170) cc_final: 0.8005 (tmt170) REVERT: D 411 LEU cc_start: 0.9351 (mm) cc_final: 0.8690 (tt) REVERT: D 452 PHE cc_start: 0.7588 (m-10) cc_final: 0.7192 (m-80) REVERT: D 493 VAL cc_start: 0.9344 (t) cc_final: 0.8982 (p) REVERT: D 531 ILE cc_start: 0.9055 (tp) cc_final: 0.8802 (tp) REVERT: D 552 PHE cc_start: 0.8247 (m-80) cc_final: 0.7951 (m-10) REVERT: D 561 GLU cc_start: 0.6827 (pp20) cc_final: 0.6379 (pm20) REVERT: D 563 PHE cc_start: 0.8753 (m-80) cc_final: 0.8537 (m-80) REVERT: D 606 THR cc_start: 0.8742 (p) cc_final: 0.8517 (p) REVERT: D 607 GLU cc_start: 0.8652 (mp0) cc_final: 0.8387 (mp0) REVERT: D 678 MET cc_start: 0.8601 (mtt) cc_final: 0.8366 (mmm) REVERT: D 740 MET cc_start: 0.7691 (ppp) cc_final: 0.7360 (tmm) REVERT: E 204 ASP cc_start: 0.8555 (t0) cc_final: 0.8247 (t70) REVERT: E 315 LYS cc_start: 0.9288 (mtmt) cc_final: 0.8713 (tptt) REVERT: E 335 LEU cc_start: 0.9181 (mt) cc_final: 0.8688 (pp) REVERT: E 420 LEU cc_start: 0.9348 (tp) cc_final: 0.9106 (tp) REVERT: E 538 ASN cc_start: 0.8038 (m-40) cc_final: 0.7661 (m-40) REVERT: E 558 ASN cc_start: 0.8925 (m-40) cc_final: 0.8465 (t0) REVERT: E 624 ASN cc_start: 0.7772 (m-40) cc_final: 0.7372 (m-40) REVERT: E 740 MET cc_start: 0.9002 (tpt) cc_final: 0.8671 (tpt) REVERT: F 319 GLU cc_start: 0.7813 (pm20) cc_final: 0.7432 (mm-30) REVERT: F 328 LEU cc_start: 0.8723 (tp) cc_final: 0.8469 (pp) REVERT: F 333 ASP cc_start: 0.8776 (p0) cc_final: 0.8429 (p0) REVERT: F 625 ARG cc_start: 0.8832 (mtt-85) cc_final: 0.8279 (mmm-85) REVERT: F 736 PHE cc_start: 0.8620 (m-10) cc_final: 0.8079 (m-80) REVERT: F 740 MET cc_start: 0.6718 (ptt) cc_final: 0.6393 (ptt) outliers start: 1 outliers final: 0 residues processed: 476 average time/residue: 0.3702 time to fit residues: 273.1963 Evaluate side-chains 384 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 3.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 305 optimal weight: 0.9980 chunk 186 optimal weight: 0.2980 chunk 145 optimal weight: 5.9990 chunk 212 optimal weight: 5.9990 chunk 320 optimal weight: 9.9990 chunk 295 optimal weight: 5.9990 chunk 255 optimal weight: 0.0370 chunk 26 optimal weight: 0.5980 chunk 197 optimal weight: 0.9990 chunk 156 optimal weight: 6.9990 chunk 202 optimal weight: 7.9990 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 660 ASN E 458 GLN E 460 ASN E 533 ASN ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS ** F 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 25771 Z= 0.179 Angle : 0.685 12.292 34753 Z= 0.343 Chirality : 0.047 0.265 3906 Planarity : 0.005 0.104 4595 Dihedral : 5.202 31.451 3493 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.04 % Allowed : 0.48 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.15), residues: 3194 helix: 0.35 (0.13), residues: 1648 sheet: -2.33 (0.27), residues: 312 loop : -1.82 (0.18), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 476 HIS 0.016 0.001 HIS B 384 PHE 0.036 0.002 PHE F 267 TYR 0.025 0.002 TYR E 244 ARG 0.009 0.000 ARG A 313 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6388 Ramachandran restraints generated. 3194 Oldfield, 0 Emsley, 3194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 473 time to evaluate : 2.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ILE cc_start: 0.8591 (tp) cc_final: 0.8091 (mm) REVERT: A 291 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8303 (mm-30) REVERT: A 575 PHE cc_start: 0.7382 (t80) cc_final: 0.6829 (t80) REVERT: A 577 ASP cc_start: 0.7019 (t0) cc_final: 0.6684 (t0) REVERT: A 578 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6444 (tp30) REVERT: B 312 LYS cc_start: 0.8591 (mmmm) cc_final: 0.8050 (mtpp) REVERT: B 313 ARG cc_start: 0.7414 (tpt90) cc_final: 0.7022 (tpt90) REVERT: B 315 LYS cc_start: 0.9037 (pttt) cc_final: 0.8758 (pttm) REVERT: B 348 ASN cc_start: 0.8825 (t0) cc_final: 0.8530 (t0) REVERT: B 388 MET cc_start: 0.8575 (mmp) cc_final: 0.6817 (ppp) REVERT: B 406 HIS cc_start: 0.9093 (m-70) cc_final: 0.8344 (m90) REVERT: B 449 MET cc_start: 0.8697 (tpt) cc_final: 0.8451 (tpt) REVERT: B 522 CYS cc_start: 0.8220 (t) cc_final: 0.7058 (p) REVERT: B 611 MET cc_start: 0.7359 (mmm) cc_final: 0.7008 (mmm) REVERT: C 379 GLU cc_start: 0.8711 (pt0) cc_final: 0.8133 (tm-30) REVERT: C 388 MET cc_start: 0.8460 (mmm) cc_final: 0.7811 (ppp) REVERT: C 442 MET cc_start: 0.8262 (mmt) cc_final: 0.7936 (mmm) REVERT: C 550 MET cc_start: 0.7387 (mmt) cc_final: 0.7126 (mmt) REVERT: C 567 ARG cc_start: 0.8302 (tmt170) cc_final: 0.7991 (tmt170) REVERT: C 586 ARG cc_start: 0.6845 (ppt170) cc_final: 0.5692 (ptt180) REVERT: C 609 ASP cc_start: 0.9014 (m-30) cc_final: 0.8778 (m-30) REVERT: C 678 MET cc_start: 0.8610 (ttt) cc_final: 0.8127 (ttt) REVERT: D 203 TYR cc_start: 0.6660 (t80) cc_final: 0.6077 (t80) REVERT: D 204 ASP cc_start: 0.8591 (t0) cc_final: 0.8335 (p0) REVERT: D 305 GLU cc_start: 0.7448 (mp0) cc_final: 0.7227 (mp0) REVERT: D 327 GLN cc_start: 0.8450 (tt0) cc_final: 0.7955 (mm-40) REVERT: D 332 MET cc_start: 0.8089 (tpt) cc_final: 0.7845 (tpp) REVERT: D 335 LEU cc_start: 0.8592 (pp) cc_final: 0.8089 (pp) REVERT: D 359 ARG cc_start: 0.8683 (tmt170) cc_final: 0.7878 (tmt170) REVERT: D 452 PHE cc_start: 0.7572 (m-10) cc_final: 0.7210 (m-80) REVERT: D 493 VAL cc_start: 0.9372 (t) cc_final: 0.9110 (t) REVERT: D 552 PHE cc_start: 0.8243 (m-80) cc_final: 0.7979 (m-10) REVERT: D 606 THR cc_start: 0.8753 (p) cc_final: 0.8512 (p) REVERT: D 607 GLU cc_start: 0.8667 (mp0) cc_final: 0.8375 (mp0) REVERT: D 678 MET cc_start: 0.8718 (mtt) cc_final: 0.8438 (mmm) REVERT: D 740 MET cc_start: 0.7668 (ppp) cc_final: 0.7339 (tmm) REVERT: D 753 ARG cc_start: 0.8481 (mmt-90) cc_final: 0.8035 (mmp80) REVERT: E 204 ASP cc_start: 0.8544 (t0) cc_final: 0.8222 (t70) REVERT: E 315 LYS cc_start: 0.9312 (mtmt) cc_final: 0.8819 (tptt) REVERT: E 335 LEU cc_start: 0.9144 (mt) cc_final: 0.8644 (pp) REVERT: E 388 MET cc_start: 0.8293 (ppp) cc_final: 0.8033 (ppp) REVERT: E 420 LEU cc_start: 0.9280 (tp) cc_final: 0.9040 (tp) REVERT: E 538 ASN cc_start: 0.8006 (m-40) cc_final: 0.7641 (m-40) REVERT: E 550 MET cc_start: 0.7956 (mpp) cc_final: 0.7483 (mpp) REVERT: E 558 ASN cc_start: 0.9158 (m-40) cc_final: 0.8353 (t0) REVERT: E 624 ASN cc_start: 0.7528 (m-40) cc_final: 0.7067 (m-40) REVERT: E 740 MET cc_start: 0.8999 (tpt) cc_final: 0.8681 (tpt) REVERT: F 319 GLU cc_start: 0.8136 (pm20) cc_final: 0.7660 (mm-30) REVERT: F 328 LEU cc_start: 0.8935 (tp) cc_final: 0.8510 (pp) REVERT: F 333 ASP cc_start: 0.8774 (p0) cc_final: 0.8456 (p0) REVERT: F 550 MET cc_start: 0.7891 (mmp) cc_final: 0.7657 (mmp) REVERT: F 625 ARG cc_start: 0.8824 (mtt-85) cc_final: 0.8270 (mmm-85) REVERT: F 736 PHE cc_start: 0.8605 (m-10) cc_final: 0.8105 (m-80) REVERT: F 740 MET cc_start: 0.6731 (ptt) cc_final: 0.6421 (ptt) outliers start: 1 outliers final: 0 residues processed: 473 average time/residue: 0.3733 time to fit residues: 274.8140 Evaluate side-chains 383 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 383 time to evaluate : 2.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 272 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 235 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 70 optimal weight: 8.9990 chunk 255 optimal weight: 0.0070 chunk 107 optimal weight: 10.0000 chunk 262 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 224 optimal weight: 3.9990 overall best weight: 1.7204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN C 603 GLN ** D 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 460 ASN E 533 ASN ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 HIS ** F 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.091619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.082594 restraints weight = 118439.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.084186 restraints weight = 85115.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.085403 restraints weight = 64820.553| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25771 Z= 0.204 Angle : 0.679 10.179 34753 Z= 0.346 Chirality : 0.047 0.264 3906 Planarity : 0.005 0.098 4595 Dihedral : 5.210 31.469 3493 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.83 % Favored : 92.14 % Rotamer: Outliers : 0.07 % Allowed : 0.52 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: -1.19 (0.15), residues: 3194 helix: 0.34 (0.13), residues: 1640 sheet: -2.31 (0.27), residues: 312 loop : -1.86 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 551 HIS 0.014 0.001 HIS B 384 PHE 0.034 0.002 PHE F 267 TYR 0.025 0.002 TYR E 244 ARG 0.014 0.000 ARG D 239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5747.83 seconds wall clock time: 104 minutes 14.90 seconds (6254.90 seconds total)