Starting phenix.real_space_refine (version: dev) on Sat Feb 25 12:11:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7u_24305/02_2023/7r7u_24305.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7u_24305/02_2023/7r7u_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_24305/02_2023/7r7u_24305.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7u_24305/02_2023/7r7u_24305.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7u_24305/02_2023/7r7u_24305.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7u_24305/02_2023/7r7u_24305.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 14.46, per 1000 atoms: 0.57 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: 10.56 Conformation dependent library (CDL) restraints added in 4.1 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: 1.38 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: 8.60 Time building geometry restraints manager: 11.31 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 5.570 Check model and map are aligned: 0.440 Process input model: 68.080 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.210 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 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 % 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 *********************** 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 : 3.165 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 outliers start: 1 outliers final: 0 residues processed: 750 average time/residue: 0.4476 time to fit residues: 495.8240 Evaluate side-chains 426 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 426 time to evaluate : 3.357 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5250 ------------------------------------------------------------------------------- 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: 1.9990 chunk 135 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 252 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 153 optimal weight: 7.9990 chunk 187 optimal weight: 10.0000 chunk 292 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 GLN B 348 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 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 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 763 GLN ** 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: 0.7314 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 25771 Z= 0.268 Angle : 0.723 10.722 34753 Z= 0.383 Chirality : 0.046 0.210 3906 Planarity : 0.006 0.071 4595 Dihedral : 6.168 32.732 3493 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.26 % Favored : 92.71 % Rotamer Outliers : 0.22 % 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: -2.52 (0.14), residues: 3194 helix: -0.95 (0.12), residues: 1618 sheet: -2.44 (0.28), residues: 268 loop : -2.33 (0.16), residues: 1308 *********************** 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 521 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 515 time to evaluate : 3.323 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 outliers start: 6 outliers final: 1 residues processed: 519 average time/residue: 0.4138 time to fit residues: 327.6817 Evaluate side-chains 377 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 376 time to evaluate : 3.211 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2680 time to fit residues: 5.1901 ------------------------------------------------------------------------------- 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: 3.9990 chunk 90 optimal weight: 2.9990 chunk 243 optimal weight: 10.0000 chunk 199 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 292 optimal weight: 5.9990 chunk 316 optimal weight: 5.9990 chunk 260 optimal weight: 8.9990 chunk 290 optimal weight: 0.5980 chunk 99 optimal weight: 8.9990 chunk 235 optimal weight: 0.8980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 ASN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN B 602 ASN ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 GLN ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 692 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: 0.7319 moved from start: 0.3238 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= 0.224 Angle : 0.670 10.880 34753 Z= 0.348 Chirality : 0.046 0.225 3906 Planarity : 0.005 0.066 4595 Dihedral : 5.878 31.086 3493 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.03 % 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: -1.88 (0.15), residues: 3194 helix: -0.34 (0.13), residues: 1624 sheet: -2.33 (0.28), residues: 264 loop : -2.10 (0.17), residues: 1306 *********************** 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 503 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 500 time to evaluate : 3.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 502 average time/residue: 0.4089 time to fit residues: 312.8346 Evaluate side-chains 373 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 3.080 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9589 ------------------------------------------------------------------------------- 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: 4.9990 chunk 32 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 196 optimal weight: 1.9990 chunk 293 optimal weight: 0.9980 chunk 311 optimal weight: 10.0000 chunk 153 optimal weight: 3.9990 chunk 278 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 317 HIS B 384 HIS B 387 ASN 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 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 538 ASN F 603 GLN ** F 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 25771 Z= 0.209 Angle : 0.672 10.989 34753 Z= 0.347 Chirality : 0.046 0.233 3906 Planarity : 0.005 0.070 4595 Dihedral : 5.745 33.244 3493 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer Outliers : 0.07 % 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: -0.18 (0.13), residues: 1622 sheet: -2.29 (0.28), residues: 260 loop : -2.03 (0.17), residues: 1312 *********************** 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 490 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 488 time to evaluate : 3.189 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 outliers start: 2 outliers final: 0 residues processed: 489 average time/residue: 0.4065 time to fit residues: 306.9409 Evaluate side-chains 383 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 383 time to evaluate : 3.161 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3284 ------------------------------------------------------------------------------- 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: 0.0980 chunk 176 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 231 optimal weight: 0.6980 chunk 128 optimal weight: 5.9990 chunk 265 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 chunk 279 optimal weight: 0.0970 chunk 78 optimal weight: 10.0000 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 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** D 348 ASN ** 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 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 25771 Z= 0.166 Angle : 0.649 11.452 34753 Z= 0.328 Chirality : 0.045 0.247 3906 Planarity : 0.005 0.068 4595 Dihedral : 5.522 32.868 3493 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer Outliers : 0.04 % 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: -1.47 (0.15), residues: 3194 helix: 0.00 (0.13), residues: 1628 sheet: -2.28 (0.30), residues: 240 loop : -1.92 (0.17), residues: 1326 *********************** 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 498 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 497 time to evaluate : 3.117 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 outliers start: 1 outliers final: 0 residues processed: 497 average time/residue: 0.4054 time to fit residues: 309.6404 Evaluate side-chains 378 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 378 time to evaluate : 3.643 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7815 ------------------------------------------------------------------------------- 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: 10.0000 chunk 280 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 182 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 311 optimal weight: 1.9990 chunk 258 optimal weight: 0.9990 chunk 144 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 163 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 533 ASN ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN C 602 ASN D 348 ASN D 536 GLN ** D 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 GLN 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 404 HIS ** 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: 0.7324 moved from start: 0.4063 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= 0.212 Angle : 0.674 10.933 34753 Z= 0.346 Chirality : 0.046 0.243 3906 Planarity : 0.005 0.083 4595 Dihedral : 5.494 31.970 3493 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.05 % Favored : 91.92 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.03 % 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: -1.40 (0.15), residues: 3194 helix: 0.08 (0.13), residues: 1642 sheet: -2.21 (0.29), residues: 276 loop : -1.92 (0.18), residues: 1276 *********************** 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 465 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 465 time to evaluate : 3.331 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 outliers start: 0 outliers final: 0 residues processed: 465 average time/residue: 0.4031 time to fit residues: 288.7903 Evaluate side-chains 370 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 370 time to evaluate : 2.909 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2303 ------------------------------------------------------------------------------- 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: 4.9990 chunk 35 optimal weight: 0.6980 chunk 177 optimal weight: 2.9990 chunk 227 optimal weight: 7.9990 chunk 176 optimal weight: 10.0000 chunk 262 optimal weight: 0.6980 chunk 173 optimal weight: 4.9990 chunk 310 optimal weight: 9.9990 chunk 194 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 533 ASN ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 GLN ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN ** D 494 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 25771 Z= 0.201 Angle : 0.669 11.186 34753 Z= 0.342 Chirality : 0.046 0.245 3906 Planarity : 0.005 0.058 4595 Dihedral : 5.433 30.610 3493 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.03 % 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: -1.34 (0.15), residues: 3194 helix: 0.12 (0.13), residues: 1640 sheet: -2.15 (0.29), residues: 276 loop : -1.87 (0.18), residues: 1278 *********************** 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 467 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 466 time to evaluate : 3.563 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 outliers start: 1 outliers final: 0 residues processed: 466 average time/residue: 0.4068 time to fit residues: 294.6755 Evaluate side-chains 367 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 3.432 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8542 ------------------------------------------------------------------------------- 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: 1.9990 chunk 123 optimal weight: 0.1980 chunk 185 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 197 optimal weight: 0.9980 chunk 211 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 243 optimal weight: 0.6980 chunk 282 optimal weight: 8.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 533 ASN B 536 GLN ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN ** D 490 GLN ** 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 458 GLN 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 25771 Z= 0.179 Angle : 0.688 11.278 34753 Z= 0.347 Chirality : 0.046 0.246 3906 Planarity : 0.005 0.057 4595 Dihedral : 5.389 30.110 3493 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.86 % Favored : 92.11 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.32 (0.15), residues: 3194 helix: 0.15 (0.13), residues: 1644 sheet: -2.36 (0.28), residues: 296 loop : -1.82 (0.18), residues: 1254 *********************** 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 462 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 462 time to evaluate : 4.105 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 outliers start: 0 outliers final: 0 residues processed: 462 average time/residue: 0.3972 time to fit residues: 285.0046 Evaluate side-chains 363 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 3.375 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4776 ------------------------------------------------------------------------------- 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: 4.9990 chunk 271 optimal weight: 6.9990 chunk 289 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 227 optimal weight: 5.9990 chunk 88 optimal weight: 0.3980 chunk 261 optimal weight: 6.9990 chunk 273 optimal weight: 4.9990 chunk 288 optimal weight: 5.9990 chunk 189 optimal weight: 0.9980 overall best weight: 2.4584 ------------------------------------------------------------------------------- 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 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN ** D 490 GLN ** 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 460 ASN E 533 ASN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 25771 Z= 0.248 Angle : 0.709 10.091 34753 Z= 0.364 Chirality : 0.047 0.280 3906 Planarity : 0.005 0.108 4595 Dihedral : 5.468 29.954 3493 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 22.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.55 % Favored : 91.42 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.15), residues: 3194 helix: 0.16 (0.13), residues: 1634 sheet: -2.07 (0.29), residues: 276 loop : -1.87 (0.17), residues: 1284 *********************** 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 458 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 456 time to evaluate : 3.315 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 outliers start: 2 outliers final: 0 residues processed: 456 average time/residue: 0.4116 time to fit residues: 294.8086 Evaluate side-chains 353 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 3.472 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7386 ------------------------------------------------------------------------------- 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: 0.9990 chunk 186 optimal weight: 0.5980 chunk 145 optimal weight: 0.9990 chunk 212 optimal weight: 9.9990 chunk 320 optimal weight: 4.9990 chunk 295 optimal weight: 8.9990 chunk 255 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 197 optimal weight: 0.9980 chunk 156 optimal weight: 5.9990 chunk 202 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN ** A 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 ** D 490 GLN ** 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 458 GLN E 460 ASN 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: 0.7287 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 25771 Z= 0.189 Angle : 0.704 10.599 34753 Z= 0.355 Chirality : 0.047 0.260 3906 Planarity : 0.005 0.055 4595 Dihedral : 5.428 30.005 3493 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 20.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.05 % Favored : 91.92 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.24 (0.15), residues: 3194 helix: 0.22 (0.13), residues: 1636 sheet: -2.31 (0.28), residues: 296 loop : -1.78 (0.18), residues: 1262 ********************** 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 460 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 459 time to evaluate : 3.332 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 outliers start: 1 outliers final: 0 residues processed: 459 average time/residue: 0.3821 time to fit residues: 274.9345 Evaluate side-chains 369 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 369 time to evaluate : 3.131 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2221 ------------------------------------------------------------------------------- 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: 3.9990 chunk 78 optimal weight: 5.9990 chunk 235 optimal weight: 9.9990 chunk 37 optimal weight: 0.0060 chunk 70 optimal weight: 6.9990 chunk 255 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 chunk 262 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 224 optimal weight: 0.7980 overall best weight: 1.0798 ------------------------------------------------------------------------------- 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 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN ** B 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 490 GLN ** 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 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 460 ASN E 533 ASN ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 ASN ** 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 = 0.3778 r_free = 0.3778 target = 0.091139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.082656 restraints weight = 114982.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.084250 restraints weight = 81044.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.085004 restraints weight = 60720.594| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 25771 Z= 0.190 Angle : 0.694 10.305 34753 Z= 0.350 Chirality : 0.047 0.266 3906 Planarity : 0.005 0.060 4595 Dihedral : 5.373 29.824 3493 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.23 % Favored : 91.73 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.15), residues: 3194 helix: 0.21 (0.13), residues: 1640 sheet: -2.28 (0.28), residues: 296 loop : -1.76 (0.18), residues: 1258 =============================================================================== Job complete usr+sys time: 5556.61 seconds wall clock time: 102 minutes 29.74 seconds (6149.74 seconds total)