Starting phenix.real_space_refine (version: dev) on Sat Feb 25 17:16:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbk_33104/02_2023/7xbk_33104_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbk_33104/02_2023/7xbk_33104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbk_33104/02_2023/7xbk_33104.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbk_33104/02_2023/7xbk_33104.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbk_33104/02_2023/7xbk_33104_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xbk_33104/02_2023/7xbk_33104_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.037 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 PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 545": "OE1" <-> "OE2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B GLU 443": "OE1" <-> "OE2" Residue "B PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 553": "OE1" <-> "OE2" Residue "C GLU 359": "OE1" <-> "OE2" Residue "C TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 443": "OE1" <-> "OE2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C TYR 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 310": "OE1" <-> "OE2" Residue "D GLU 321": "OE1" <-> "OE2" Residue "D PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 389": "OE1" <-> "OE2" Residue "D PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 471": "OE1" <-> "OE2" Residue "D GLU 534": "OE1" <-> "OE2" Residue "D TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 321": "OE1" <-> "OE2" Residue "E TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 527": "OE1" <-> "OE2" Residue "E GLU 545": "OE1" <-> "OE2" Residue "E TYR 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 597": "OE1" <-> "OE2" Residue "F GLU 303": "OE1" <-> "OE2" Residue "F GLU 359": "OE1" <-> "OE2" Residue "F ASP 371": "OD1" <-> "OD2" Residue "F GLU 534": "OE1" <-> "OE2" Residue "F GLU 553": "OE1" <-> "OE2" Residue "F TYR 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 342": "OE1" <-> "OE2" Residue "G GLU 359": "OE1" <-> "OE2" Residue "G GLU 386": "OE1" <-> "OE2" Residue "G TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 432": "OD1" <-> "OD2" Residue "G PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 526": "OD1" <-> "OD2" Residue "G GLU 527": "OE1" <-> "OE2" Residue "H GLU 386": "OE1" <-> "OE2" Residue "H PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 608": "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: 25745 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2968 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 13, 'TRANS': 353} Chain: "B" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2842 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 10, 'TRANS': 340} Chain breaks: 1 Chain: "C" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2822 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 10, 'TRANS': 338} Chain breaks: 3 Chain: "D" Number of atoms: 2857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2857 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 10, 'TRANS': 342} Chain breaks: 2 Chain: "E" Number of atoms: 2813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2813 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 10, 'TRANS': 337} Chain breaks: 2 Chain: "F" Number of atoms: 2766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2766 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 9, 'TRANS': 332} Chain breaks: 1 Chain: "G" Number of atoms: 2690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2690 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 9, 'TRANS': 322} Chain breaks: 2 Chain: "H" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2796 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 13, 'TRANS': 331} Chain breaks: 1 Chain: "I" Number of atoms: 2850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2850 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 10, 'TRANS': 341} Chain breaks: 1 Chain: "L" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.79, per 1000 atoms: 0.54 Number of scatterers: 25745 At special positions: 0 Unit cell: (166.32, 132.84, 153.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 80 16.00 P 24 15.00 Mg 8 11.99 O 4782 8.00 N 4674 7.00 C 16177 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.48 Conformation dependent library (CDL) restraints added in 3.9 seconds 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5938 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 142 helices and 25 sheets defined 47.0% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 300 through 306 Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 321 through 336 Processing helix chain 'A' and resid 357 through 368 Processing helix chain 'A' and resid 387 through 394 removed outlier: 3.648A pdb=" N ALA A 391 " --> pdb=" O ARG A 387 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS A 392 " --> pdb=" O HIS A 388 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE A 394 " --> pdb=" O VAL A 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 387 through 394' Processing helix chain 'A' and resid 408 through 415 Processing helix chain 'A' and resid 431 through 443 removed outlier: 4.485A pdb=" N ILE A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET A 437 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN A 439 " --> pdb=" O THR A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 492 Processing helix chain 'A' and resid 508 through 523 removed outlier: 5.123A pdb=" N ARG A 516 " --> pdb=" O GLU A 512 " (cutoff:3.500A) Proline residue: A 517 - end of helix Processing helix chain 'A' and resid 526 through 530 Processing helix chain 'A' and resid 543 through 565 removed outlier: 4.052A pdb=" N TRP A 557 " --> pdb=" O GLU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 581 Processing helix chain 'A' and resid 588 through 609 removed outlier: 3.573A pdb=" N SER A 591 " --> pdb=" O GLY A 588 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A 598 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 600 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N VAL A 601 " --> pdb=" O ARG A 598 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ASN A 602 " --> pdb=" O ARG A 599 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A 609 " --> pdb=" O ALA A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 631 removed outlier: 4.107A pdb=" N GLN A 629 " --> pdb=" O ASP A 625 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 306 Processing helix chain 'B' and resid 309 through 316 Processing helix chain 'B' and resid 321 through 335 Processing helix chain 'B' and resid 357 through 368 Processing helix chain 'B' and resid 388 through 394 Processing helix chain 'B' and resid 408 through 415 Processing helix chain 'B' and resid 426 through 428 No H-bonds generated for 'chain 'B' and resid 426 through 428' Processing helix chain 'B' and resid 431 through 443 removed outlier: 3.967A pdb=" N ILE B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLN B 439 " --> pdb=" O THR B 435 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 440 " --> pdb=" O ILE B 436 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU B 443 " --> pdb=" O GLN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 492 Processing helix chain 'B' and resid 508 through 513 Processing helix chain 'B' and resid 515 through 523 Processing helix chain 'B' and resid 526 through 531 Processing helix chain 'B' and resid 543 through 564 Processing helix chain 'B' and resid 573 through 581 Processing helix chain 'B' and resid 589 through 599 removed outlier: 5.184A pdb=" N GLU B 597 " --> pdb=" O LYS B 593 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARG B 598 " --> pdb=" O HIS B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 606 Processing helix chain 'B' and resid 608 through 610 No H-bonds generated for 'chain 'B' and resid 608 through 610' Processing helix chain 'C' and resid 300 through 306 Processing helix chain 'C' and resid 309 through 314 Processing helix chain 'C' and resid 321 through 335 Processing helix chain 'C' and resid 357 through 369 Processing helix chain 'C' and resid 387 through 394 removed outlier: 3.604A pdb=" N VAL C 390 " --> pdb=" O ARG C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 415 Processing helix chain 'C' and resid 434 through 442 removed outlier: 4.002A pdb=" N GLN C 439 " --> pdb=" O ILE C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 493 removed outlier: 3.834A pdb=" N GLU C 493 " --> pdb=" O ASN C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 513 Processing helix chain 'C' and resid 515 through 523 Processing helix chain 'C' and resid 526 through 530 Processing helix chain 'C' and resid 543 through 560 removed outlier: 3.570A pdb=" N GLN C 548 " --> pdb=" O SER C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 580 Processing helix chain 'C' and resid 588 through 593 Processing helix chain 'C' and resid 596 through 599 No H-bonds generated for 'chain 'C' and resid 596 through 599' Processing helix chain 'C' and resid 601 through 610 Processing helix chain 'D' and resid 299 through 306 Processing helix chain 'D' and resid 309 through 316 Processing helix chain 'D' and resid 321 through 335 Processing helix chain 'D' and resid 357 through 368 Processing helix chain 'D' and resid 381 through 383 No H-bonds generated for 'chain 'D' and resid 381 through 383' Processing helix chain 'D' and resid 387 through 394 removed outlier: 4.210A pdb=" N ILE D 394 " --> pdb=" O ALA D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 415 removed outlier: 3.567A pdb=" N LYS D 412 " --> pdb=" O GLN D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 442 removed outlier: 4.408A pdb=" N ILE D 436 " --> pdb=" O ASP D 432 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N MET D 437 " --> pdb=" O VAL D 433 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU D 438 " --> pdb=" O LEU D 434 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLN D 439 " --> pdb=" O THR D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 492 Processing helix chain 'D' and resid 508 through 513 Processing helix chain 'D' and resid 515 through 523 Processing helix chain 'D' and resid 543 through 565 Processing helix chain 'D' and resid 573 through 578 Processing helix chain 'D' and resid 588 through 599 removed outlier: 3.534A pdb=" N ILE D 592 " --> pdb=" O GLY D 588 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG D 599 " --> pdb=" O GLU D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 609 Processing helix chain 'E' and resid 301 through 304 No H-bonds generated for 'chain 'E' and resid 301 through 304' Processing helix chain 'E' and resid 309 through 316 removed outlier: 3.696A pdb=" N GLU E 315 " --> pdb=" O GLN E 311 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N HIS E 316 " --> pdb=" O ARG E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 335 Processing helix chain 'E' and resid 357 through 368 Processing helix chain 'E' and resid 372 through 375 No H-bonds generated for 'chain 'E' and resid 372 through 375' Processing helix chain 'E' and resid 387 through 394 removed outlier: 3.816A pdb=" N ALA E 391 " --> pdb=" O HIS E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 415 Processing helix chain 'E' and resid 434 through 442 removed outlier: 4.151A pdb=" N GLN E 439 " --> pdb=" O ILE E 436 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP E 442 " --> pdb=" O GLN E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 492 Processing helix chain 'E' and resid 508 through 513 Processing helix chain 'E' and resid 515 through 523 Processing helix chain 'E' and resid 526 through 530 Processing helix chain 'E' and resid 543 through 565 Processing helix chain 'E' and resid 573 through 580 Processing helix chain 'E' and resid 588 through 599 removed outlier: 4.264A pdb=" N ARG E 599 " --> pdb=" O VAL E 596 " (cutoff:3.500A) Processing helix chain 'E' and resid 601 through 609 Processing helix chain 'E' and resid 628 through 630 No H-bonds generated for 'chain 'E' and resid 628 through 630' Processing helix chain 'F' and resid 309 through 316 Processing helix chain 'F' and resid 321 through 335 Processing helix chain 'F' and resid 357 through 368 Processing helix chain 'F' and resid 387 through 394 removed outlier: 3.711A pdb=" N VAL F 390 " --> pdb=" O ARG F 387 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA F 391 " --> pdb=" O HIS F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 415 Processing helix chain 'F' and resid 426 through 428 No H-bonds generated for 'chain 'F' and resid 426 through 428' Processing helix chain 'F' and resid 433 through 442 removed outlier: 3.576A pdb=" N PHE F 441 " --> pdb=" O LEU F 438 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP F 442 " --> pdb=" O GLN F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 469 through 493 Processing helix chain 'F' and resid 508 through 513 Processing helix chain 'F' and resid 515 through 523 Processing helix chain 'F' and resid 526 through 531 Processing helix chain 'F' and resid 543 through 564 Processing helix chain 'F' and resid 573 through 581 Processing helix chain 'F' and resid 588 through 599 removed outlier: 4.799A pdb=" N HIS F 594 " --> pdb=" O SER F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 601 through 609 Processing helix chain 'G' and resid 301 through 306 Processing helix chain 'G' and resid 309 through 316 Processing helix chain 'G' and resid 321 through 335 removed outlier: 3.518A pdb=" N ALA G 325 " --> pdb=" O GLU G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 357 through 368 Processing helix chain 'G' and resid 372 through 375 No H-bonds generated for 'chain 'G' and resid 372 through 375' Processing helix chain 'G' and resid 388 through 392 Processing helix chain 'G' and resid 408 through 415 Processing helix chain 'G' and resid 431 through 442 removed outlier: 3.552A pdb=" N THR G 435 " --> pdb=" O PRO G 431 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLN G 439 " --> pdb=" O THR G 435 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU G 440 " --> pdb=" O ILE G 436 " (cutoff:3.500A) Processing helix chain 'G' and resid 470 through 480 Processing helix chain 'G' and resid 510 through 513 No H-bonds generated for 'chain 'G' and resid 510 through 513' Processing helix chain 'G' and resid 515 through 522 Processing helix chain 'G' and resid 526 through 531 Processing helix chain 'G' and resid 543 through 564 Processing helix chain 'G' and resid 575 through 580 removed outlier: 3.786A pdb=" N LEU G 579 " --> pdb=" O VAL G 575 " (cutoff:3.500A) Processing helix chain 'G' and resid 589 through 599 Processing helix chain 'G' and resid 601 through 609 Processing helix chain 'H' and resid 299 through 306 Processing helix chain 'H' and resid 309 through 316 Processing helix chain 'H' and resid 321 through 335 Processing helix chain 'H' and resid 358 through 368 Processing helix chain 'H' and resid 372 through 375 No H-bonds generated for 'chain 'H' and resid 372 through 375' Processing helix chain 'H' and resid 388 through 394 removed outlier: 3.746A pdb=" N ILE H 394 " --> pdb=" O ALA H 391 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 415 Processing helix chain 'H' and resid 426 through 428 No H-bonds generated for 'chain 'H' and resid 426 through 428' Processing helix chain 'H' and resid 431 through 440 removed outlier: 3.982A pdb=" N THR H 435 " --> pdb=" O PRO H 431 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE H 436 " --> pdb=" O ASP H 432 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N GLN H 439 " --> pdb=" O THR H 435 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU H 440 " --> pdb=" O ILE H 436 " (cutoff:3.500A) Processing helix chain 'H' and resid 469 through 478 Processing helix chain 'H' and resid 508 through 513 Processing helix chain 'H' and resid 515 through 523 Processing helix chain 'H' and resid 526 through 531 Processing helix chain 'H' and resid 543 through 564 Processing helix chain 'H' and resid 573 through 581 Processing helix chain 'H' and resid 588 through 609 removed outlier: 3.748A pdb=" N ARG H 598 " --> pdb=" O GLU H 595 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG H 599 " --> pdb=" O VAL H 596 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL H 600 " --> pdb=" O GLU H 597 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL H 601 " --> pdb=" O ARG H 598 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASN H 602 " --> pdb=" O ARG H 599 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN H 603 " --> pdb=" O VAL H 600 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA H 607 " --> pdb=" O LEU H 604 " (cutoff:3.500A) Processing helix chain 'H' and resid 626 through 631 removed outlier: 4.072A pdb=" N LEU H 630 " --> pdb=" O SER H 626 " (cutoff:3.500A) Processing helix chain 'I' and resid 299 through 306 Processing helix chain 'I' and resid 309 through 316 Processing helix chain 'I' and resid 321 through 335 removed outlier: 3.891A pdb=" N LYS I 334 " --> pdb=" O ALA I 330 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU I 335 " --> pdb=" O ILE I 331 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 368 Processing helix chain 'I' and resid 387 through 393 removed outlier: 3.645A pdb=" N VAL I 390 " --> pdb=" O ARG I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 408 through 415 Processing helix chain 'I' and resid 426 through 428 No H-bonds generated for 'chain 'I' and resid 426 through 428' Processing helix chain 'I' and resid 431 through 442 removed outlier: 3.760A pdb=" N LEU I 440 " --> pdb=" O ILE I 436 " (cutoff:3.500A) Processing helix chain 'I' and resid 469 through 492 removed outlier: 3.754A pdb=" N ASN I 489 " --> pdb=" O GLU I 485 " (cutoff:3.500A) Processing helix chain 'I' and resid 510 through 513 No H-bonds generated for 'chain 'I' and resid 510 through 513' Processing helix chain 'I' and resid 515 through 523 Processing helix chain 'I' and resid 526 through 530 Processing helix chain 'I' and resid 543 through 565 Processing helix chain 'I' and resid 573 through 581 Processing helix chain 'I' and resid 588 through 609 removed outlier: 3.700A pdb=" N HIS I 594 " --> pdb=" O SER I 591 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG I 599 " --> pdb=" O VAL I 596 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL I 600 " --> pdb=" O GLU I 597 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL I 601 " --> pdb=" O ARG I 598 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASN I 602 " --> pdb=" O ARG I 599 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU I 604 " --> pdb=" O VAL I 601 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU I 609 " --> pdb=" O ALA I 606 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 534 through 537 removed outlier: 6.163A pdb=" N VAL A 421 " --> pdb=" O ILE A 462 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N THR A 464 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE A 423 " --> pdb=" O THR A 464 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 445 through 447 Processing sheet with id= C, first strand: chain 'A' and resid 568 through 570 removed outlier: 4.037A pdb=" N THR A 618 " --> pdb=" O ILE A 653 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LEU A 650 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 662 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 534 through 538 removed outlier: 3.928A pdb=" N GLY B 351 " --> pdb=" O SER B 465 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 445 through 447 Processing sheet with id= F, first strand: chain 'B' and resid 568 through 571 removed outlier: 4.554A pdb=" N THR B 618 " --> pdb=" O ILE B 653 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 534 through 537 Processing sheet with id= H, first strand: chain 'C' and resid 445 through 447 removed outlier: 3.939A pdb=" N LEU C 446 " --> pdb=" O ILE C 454 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 568 through 571 removed outlier: 3.586A pdb=" N LEU C 619 " --> pdb=" O THR C 568 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 621 " --> pdb=" O LEU C 570 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR C 618 " --> pdb=" O ILE C 653 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS C 658 " --> pdb=" O ASP C 654 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 534 through 537 Processing sheet with id= K, first strand: chain 'D' and resid 445 through 447 Processing sheet with id= L, first strand: chain 'D' and resid 568 through 571 removed outlier: 4.204A pdb=" N THR D 618 " --> pdb=" O ILE D 653 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 534 through 537 Processing sheet with id= N, first strand: chain 'E' and resid 445 through 447 removed outlier: 3.744A pdb=" N LEU E 446 " --> pdb=" O ILE E 454 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 568 through 571 removed outlier: 4.314A pdb=" N THR E 618 " --> pdb=" O ILE E 653 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 534 through 537 Processing sheet with id= Q, first strand: chain 'F' and resid 568 through 570 removed outlier: 3.621A pdb=" N ILE F 621 " --> pdb=" O LEU F 570 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR F 618 " --> pdb=" O ILE F 653 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU F 650 " --> pdb=" O LEU F 662 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 534 through 537 removed outlier: 3.525A pdb=" N THR G 464 " --> pdb=" O PHE G 423 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 445 through 447 Processing sheet with id= T, first strand: chain 'G' and resid 568 through 571 removed outlier: 4.325A pdb=" N THR G 618 " --> pdb=" O ILE G 653 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'H' and resid 534 through 537 Processing sheet with id= V, first strand: chain 'H' and resid 568 through 571 removed outlier: 5.178A pdb=" N THR H 618 " --> pdb=" O ILE H 653 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 534 through 536 Processing sheet with id= X, first strand: chain 'I' and resid 445 through 447 Processing sheet with id= Y, first strand: chain 'I' and resid 568 through 570 removed outlier: 4.549A pdb=" N THR I 618 " --> pdb=" O ILE I 653 " (cutoff:3.500A) 1097 hydrogen bonds defined for protein. 2961 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: 8.45 Time building geometry restraints manager: 11.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6994 1.33 - 1.45: 4572 1.45 - 1.58: 14459 1.58 - 1.70: 35 1.70 - 1.82: 124 Bond restraints: 26184 Sorted by residual: bond pdb=" CB THR B 435 " pdb=" CG2 THR B 435 " ideal model delta sigma weight residual 1.521 1.447 0.074 3.30e-02 9.18e+02 5.05e+00 bond pdb=" CA ASN H 466 " pdb=" CB ASN H 466 " ideal model delta sigma weight residual 1.528 1.558 -0.031 1.49e-02 4.50e+03 4.29e+00 bond pdb=" CB THR C 435 " pdb=" CG2 THR C 435 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.21e+00 bond pdb=" CG LEU F 438 " pdb=" CD2 LEU F 438 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.74e+00 bond pdb=" CB MET C 368 " pdb=" CG MET C 368 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.72e+00 ... (remaining 26179 not shown) Histogram of bond angle deviations from ideal: 97.22 - 105.77: 435 105.77 - 114.31: 15429 114.31 - 122.86: 17123 122.86 - 131.40: 2195 131.40 - 139.95: 62 Bond angle restraints: 35244 Sorted by residual: angle pdb=" N ASP F 432 " pdb=" CA ASP F 432 " pdb=" C ASP F 432 " ideal model delta sigma weight residual 114.56 106.70 7.86 1.27e+00 6.20e-01 3.83e+01 angle pdb=" C HIS E 565 " pdb=" N ASN E 566 " pdb=" CA ASN E 566 " ideal model delta sigma weight residual 122.46 130.40 -7.94 1.41e+00 5.03e-01 3.17e+01 angle pdb=" N VAL D 596 " pdb=" CA VAL D 596 " pdb=" C VAL D 596 " ideal model delta sigma weight residual 112.50 105.85 6.65 1.39e+00 5.18e-01 2.29e+01 angle pdb=" N ILE C 355 " pdb=" CA ILE C 355 " pdb=" C ILE C 355 " ideal model delta sigma weight residual 113.43 108.41 5.02 1.09e+00 8.42e-01 2.12e+01 angle pdb=" CB MET B 381 " pdb=" CG MET B 381 " pdb=" SD MET B 381 " ideal model delta sigma weight residual 112.70 125.87 -13.17 3.00e+00 1.11e-01 1.93e+01 ... (remaining 35239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 14152 17.98 - 35.95: 1444 35.95 - 53.93: 279 53.93 - 71.91: 45 71.91 - 89.88: 25 Dihedral angle restraints: 15945 sinusoidal: 6811 harmonic: 9134 Sorted by residual: dihedral pdb=" CA PRO H 540 " pdb=" C PRO H 540 " pdb=" N PHE H 541 " pdb=" CA PHE H 541 " ideal model delta harmonic sigma weight residual -180.00 -154.81 -25.19 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA TYR D 400 " pdb=" C TYR D 400 " pdb=" N VAL D 401 " pdb=" CA VAL D 401 " ideal model delta harmonic sigma weight residual -180.00 -158.20 -21.80 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA PHE F 393 " pdb=" C PHE F 393 " pdb=" N ILE F 394 " pdb=" CA ILE F 394 " ideal model delta harmonic sigma weight residual -180.00 -158.40 -21.60 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 15942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3212 0.066 - 0.131: 549 0.131 - 0.197: 80 0.197 - 0.262: 13 0.262 - 0.328: 6 Chirality restraints: 3860 Sorted by residual: chirality pdb=" CB VAL E 580 " pdb=" CA VAL E 580 " pdb=" CG1 VAL E 580 " pdb=" CG2 VAL E 580 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CB VAL A 580 " pdb=" CA VAL A 580 " pdb=" CG1 VAL A 580 " pdb=" CG2 VAL A 580 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CB ILE B 535 " pdb=" CA ILE B 535 " pdb=" CG1 ILE B 535 " pdb=" CG2 ILE B 535 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 3857 not shown) Planarity restraints: 4540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG G 516 " 0.054 5.00e-02 4.00e+02 8.08e-02 1.04e+01 pdb=" N PRO G 517 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO G 517 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO G 517 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 430 " -0.053 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO A 431 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 431 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 431 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN H 466 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.87e+00 pdb=" C ASN H 466 " -0.045 2.00e-02 2.50e+03 pdb=" O ASN H 466 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL H 467 " 0.015 2.00e-02 2.50e+03 ... (remaining 4537 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 314 2.66 - 3.22: 22232 3.22 - 3.78: 40496 3.78 - 4.34: 54778 4.34 - 4.90: 88626 Nonbonded interactions: 206446 Sorted by model distance: nonbonded pdb="MG MG C 701 " pdb=" O3G ATP C 702 " model vdw 2.095 2.170 nonbonded pdb="MG MG F 701 " pdb=" O3G ATP F 702 " model vdw 2.109 2.170 nonbonded pdb=" O2B ATP H 703 " pdb="MG MG I 701 " model vdw 2.111 2.170 nonbonded pdb="MG MG D 701 " pdb=" O3G ATP D 702 " model vdw 2.112 2.170 nonbonded pdb="MG MG E 701 " pdb=" O3G ATP E 702 " model vdw 2.114 2.170 ... (remaining 206441 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' and (resid 304 through 480 or resid 503 through 625 or resid 648 thro \ ugh 662)) selection = (chain 'B' and (resid 304 through 480 or resid 503 through 625 or resid 648 thro \ ugh 662)) selection = (chain 'C' and (resid 304 through 480 or resid 503 through 625 or resid 648 thro \ ugh 662)) selection = (chain 'D' and (resid 304 through 480 or resid 503 through 625 or resid 648 thro \ ugh 662)) selection = (chain 'E' and (resid 304 through 480 or resid 503 through 625 or resid 648 thro \ ugh 662)) selection = (chain 'F' and (resid 304 through 480 or resid 503 through 625 or resid 648 thro \ ugh 662)) selection = (chain 'G' and (resid 304 through 480 or resid 503 through 625 or resid 648 thro \ ugh 662)) selection = (chain 'H' and (resid 304 through 625 or resid 648 through 662)) selection = (chain 'I' and (resid 304 through 480 or resid 503 through 625 or resid 648 thro \ ugh 662)) } 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: 6 Type Number sf(0) Gaussians P 24 5.49 5 Mg 8 5.21 5 S 80 5.16 5 C 16177 2.51 5 N 4674 2.21 5 O 4782 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: 0.890 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: 6.060 Check model and map are aligned: 0.390 Process input model: 63.070 Find NCS groups from input model: 2.490 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.250 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6274 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 0.074 26184 Z= 0.323 Angle : 0.863 13.166 35244 Z= 0.476 Chirality : 0.053 0.328 3860 Planarity : 0.007 0.081 4540 Dihedral : 15.007 89.885 10007 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.94 % Favored : 97.03 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.14), residues: 3096 helix: -1.64 (0.11), residues: 1497 sheet: -0.13 (0.23), residues: 509 loop : -0.52 (0.18), residues: 1090 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1078 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1078 time to evaluate : 3.148 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: 1078 average time/residue: 0.4766 time to fit residues: 743.4225 Evaluate side-chains 954 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 954 time to evaluate : 2.860 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 0.5980 chunk 235 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 159 optimal weight: 0.0670 chunk 125 optimal weight: 0.0370 chunk 243 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 282 optimal weight: 1.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 HIS B 316 HIS B 320 GLN B 551 ASN C 439 GLN C 475 HIS C 533 ASN ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 ASN D 369 HIS D 408 GLN ** D 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 594 HIS D 603 GLN E 316 HIS E 320 GLN ** E 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 ASN ** E 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 594 HIS F 543 HIS F 584 ASN ** F 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 320 GLN G 474 GLN ** G 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 466 ASN I 475 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6341 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 26184 Z= 0.182 Angle : 0.565 11.123 35244 Z= 0.295 Chirality : 0.041 0.194 3860 Planarity : 0.005 0.063 4540 Dihedral : 5.729 76.706 3458 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.00 % Favored : 97.97 % Rotamer Outliers : 2.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.14), residues: 3096 helix: -0.37 (0.13), residues: 1511 sheet: -0.03 (0.23), residues: 492 loop : -0.20 (0.18), residues: 1093 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1031 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 971 time to evaluate : 3.259 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 outliers start: 60 outliers final: 30 residues processed: 981 average time/residue: 0.4850 time to fit residues: 690.4163 Evaluate side-chains 949 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 919 time to evaluate : 3.025 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2402 time to fit residues: 18.1468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 156 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 192 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 chunk 282 optimal weight: 0.0370 chunk 305 optimal weight: 10.0000 chunk 251 optimal weight: 1.9990 chunk 280 optimal weight: 30.0000 chunk 96 optimal weight: 0.9990 chunk 226 optimal weight: 10.0000 overall best weight: 1.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 ASN A 548 GLN B 320 GLN B 385 GLN ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 HIS D 603 GLN E 316 HIS E 439 GLN ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 555 ASN ** E 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 415 GLN ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 GLN F 584 ASN G 320 GLN ** G 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 594 HIS ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 26184 Z= 0.293 Angle : 0.595 12.900 35244 Z= 0.315 Chirality : 0.044 0.366 3860 Planarity : 0.005 0.057 4540 Dihedral : 5.557 67.706 3458 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.45 % Favored : 97.51 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 3096 helix: -0.09 (0.13), residues: 1511 sheet: -0.19 (0.22), residues: 509 loop : -0.11 (0.19), residues: 1076 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1071 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 1007 time to evaluate : 3.197 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 outliers start: 64 outliers final: 35 residues processed: 1024 average time/residue: 0.4950 time to fit residues: 730.4806 Evaluate side-chains 990 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 955 time to evaluate : 2.840 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 35 outliers final: 1 residues processed: 35 average time/residue: 0.2482 time to fit residues: 20.0796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 279 optimal weight: 20.0000 chunk 212 optimal weight: 0.0170 chunk 146 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 135 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 283 optimal weight: 10.0000 chunk 300 optimal weight: 0.5980 chunk 148 optimal weight: 0.8980 chunk 269 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 HIS ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 603 GLN ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 HIS F 548 GLN ** G 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 26184 Z= 0.208 Angle : 0.566 10.394 35244 Z= 0.295 Chirality : 0.042 0.333 3860 Planarity : 0.004 0.049 4540 Dihedral : 5.422 66.510 3458 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.13 % Favored : 97.84 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.15), residues: 3096 helix: 0.13 (0.13), residues: 1508 sheet: -0.19 (0.22), residues: 517 loop : 0.03 (0.19), residues: 1071 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1016 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 968 time to evaluate : 3.076 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: 48 outliers final: 25 residues processed: 977 average time/residue: 0.4796 time to fit residues: 679.3711 Evaluate side-chains 963 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 938 time to evaluate : 2.766 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2298 time to fit residues: 15.0423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 250 optimal weight: 2.9990 chunk 170 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 256 optimal weight: 8.9990 chunk 207 optimal weight: 2.9990 chunk 0 optimal weight: 70.0000 chunk 153 optimal weight: 2.9990 chunk 269 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 584 ASN ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 603 GLN E 555 ASN F 543 HIS F 548 GLN G 320 GLN G 385 GLN ** G 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 316 HIS ** H 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 603 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 26184 Z= 0.258 Angle : 0.592 10.278 35244 Z= 0.310 Chirality : 0.044 0.339 3860 Planarity : 0.004 0.062 4540 Dihedral : 5.389 67.047 3458 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.58 % Favored : 97.38 % Rotamer Outliers : 2.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.15), residues: 3096 helix: 0.17 (0.13), residues: 1503 sheet: -0.24 (0.23), residues: 512 loop : -0.03 (0.19), residues: 1081 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1066 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 996 time to evaluate : 2.987 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: 70 outliers final: 41 residues processed: 1012 average time/residue: 0.4816 time to fit residues: 704.3036 Evaluate side-chains 995 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 954 time to evaluate : 3.680 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.2449 time to fit residues: 22.8382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 101 optimal weight: 0.8980 chunk 270 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 176 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 300 optimal weight: 1.9990 chunk 249 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 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 403 HIS C 320 GLN ** C 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 GLN D 385 GLN D 418 ASN ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 HIS D 551 ASN D 603 GLN F 513 ASN F 543 HIS ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 474 GLN ** H 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 603 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6436 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 26184 Z= 0.206 Angle : 0.593 11.053 35244 Z= 0.305 Chirality : 0.043 0.338 3860 Planarity : 0.004 0.047 4540 Dihedral : 5.333 65.951 3458 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.36 % Favored : 97.61 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.15), residues: 3096 helix: 0.34 (0.13), residues: 1505 sheet: -0.28 (0.22), residues: 520 loop : 0.08 (0.20), residues: 1071 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1021 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 976 time to evaluate : 3.090 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 outliers start: 45 outliers final: 25 residues processed: 989 average time/residue: 0.4768 time to fit residues: 686.2565 Evaluate side-chains 988 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 963 time to evaluate : 2.929 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 25 outliers final: 1 residues processed: 25 average time/residue: 0.2521 time to fit residues: 15.8007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 290 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 171 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 chunk 170 optimal weight: 0.6980 chunk 253 optimal weight: 0.9990 chunk 168 optimal weight: 0.6980 chunk 299 optimal weight: 10.0000 chunk 187 optimal weight: 0.7980 chunk 182 optimal weight: 0.1980 chunk 138 optimal weight: 10.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 GLN C 475 HIS D 385 GLN D 408 GLN D 418 ASN ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 603 GLN E 466 ASN ** E 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 513 ASN ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 GLN G 408 GLN ** G 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 586 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6417 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 26184 Z= 0.184 Angle : 0.597 12.099 35244 Z= 0.308 Chirality : 0.043 0.343 3860 Planarity : 0.004 0.052 4540 Dihedral : 5.246 63.831 3458 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.10 % Favored : 97.87 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.15), residues: 3096 helix: 0.42 (0.13), residues: 1507 sheet: -0.23 (0.23), residues: 518 loop : 0.15 (0.20), residues: 1071 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1012 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 974 time to evaluate : 3.385 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 outliers start: 38 outliers final: 23 residues processed: 979 average time/residue: 0.4927 time to fit residues: 702.4623 Evaluate side-chains 978 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 955 time to evaluate : 2.916 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2784 time to fit residues: 15.4660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 185 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 58 optimal weight: 0.4980 chunk 190 optimal weight: 0.8980 chunk 204 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 235 optimal weight: 0.8980 chunk 272 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 369 HIS C 425 GLN C 475 HIS D 385 GLN ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 ASN D 586 HIS D 594 HIS D 603 GLN ** F 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 GLN ** G 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 26184 Z= 0.207 Angle : 0.620 10.700 35244 Z= 0.319 Chirality : 0.043 0.348 3860 Planarity : 0.004 0.051 4540 Dihedral : 5.190 61.934 3458 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.26 % Favored : 97.71 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 3096 helix: 0.47 (0.13), residues: 1487 sheet: -0.18 (0.22), residues: 524 loop : 0.13 (0.20), residues: 1085 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1011 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 978 time to evaluate : 3.192 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: 33 outliers final: 17 residues processed: 984 average time/residue: 0.4947 time to fit residues: 706.5834 Evaluate side-chains 979 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 962 time to evaluate : 3.024 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 17 outliers final: 1 residues processed: 17 average time/residue: 0.2657 time to fit residues: 12.5333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 287 optimal weight: 6.9990 chunk 262 optimal weight: 0.7980 chunk 279 optimal weight: 0.5980 chunk 168 optimal weight: 0.5980 chunk 121 optimal weight: 2.9990 chunk 219 optimal weight: 0.0060 chunk 85 optimal weight: 0.0770 chunk 252 optimal weight: 1.9990 chunk 264 optimal weight: 0.8980 chunk 278 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 overall best weight: 0.4154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 HIS D 385 GLN D 408 GLN ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 ASN D 586 HIS D 594 HIS D 603 GLN ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 GLN ** G 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 551 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6401 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 26184 Z= 0.185 Angle : 0.639 11.457 35244 Z= 0.326 Chirality : 0.043 0.346 3860 Planarity : 0.004 0.056 4540 Dihedral : 5.127 60.304 3458 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.16 % Favored : 97.80 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.15), residues: 3096 helix: 0.51 (0.13), residues: 1487 sheet: -0.16 (0.22), residues: 520 loop : 0.11 (0.20), residues: 1089 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 981 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 960 time to evaluate : 2.975 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 outliers start: 21 outliers final: 14 residues processed: 965 average time/residue: 0.4896 time to fit residues: 688.1810 Evaluate side-chains 960 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 946 time to evaluate : 2.855 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2450 time to fit residues: 10.5540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 295 optimal weight: 10.0000 chunk 180 optimal weight: 2.9990 chunk 140 optimal weight: 0.0050 chunk 205 optimal weight: 6.9990 chunk 309 optimal weight: 0.0270 chunk 285 optimal weight: 0.0170 chunk 246 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 195 optimal weight: 0.9990 overall best weight: 0.3490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 GLN C 439 GLN C 475 HIS D 385 GLN D 418 ASN D 439 GLN ** D 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 HIS D 594 HIS D 603 GLN ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 336 ASN ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6386 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 26184 Z= 0.197 Angle : 0.672 10.962 35244 Z= 0.342 Chirality : 0.044 0.630 3860 Planarity : 0.004 0.055 4540 Dihedral : 5.095 58.083 3458 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.10 % Favored : 97.87 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 3096 helix: 0.52 (0.14), residues: 1483 sheet: -0.05 (0.23), residues: 509 loop : 0.05 (0.19), residues: 1104 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 977 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 962 time to evaluate : 3.099 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: 15 outliers final: 11 residues processed: 964 average time/residue: 0.4994 time to fit residues: 700.2303 Evaluate side-chains 954 residues out of total 2729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 943 time to evaluate : 2.843 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2437 time to fit residues: 9.1989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 0.1980 chunk 75 optimal weight: 2.9990 chunk 227 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 chunk 247 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 253 optimal weight: 0.6980 chunk 31 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 216 optimal weight: 0.0270 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 HIS C 475 HIS ** C 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 385 GLN ** D 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 HIS D 478 GLN D 603 GLN ** E 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.164779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.133560 restraints weight = 46623.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.137756 restraints weight = 21912.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.140435 restraints weight = 12979.486| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 26184 Z= 0.231 Angle : 0.696 12.197 35244 Z= 0.355 Chirality : 0.045 0.404 3860 Planarity : 0.004 0.052 4540 Dihedral : 5.252 77.065 3458 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.36 % Favored : 97.61 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 3096 helix: 0.47 (0.13), residues: 1478 sheet: -0.12 (0.22), residues: 516 loop : -0.04 (0.19), residues: 1102 =============================================================================== Job complete usr+sys time: 9555.43 seconds wall clock time: 171 minutes 38.76 seconds (10298.76 seconds total)