Starting phenix.real_space_refine on Fri Feb 16 10:17:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwd_35054/02_2024/8hwd_35054_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwd_35054/02_2024/8hwd_35054.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwd_35054/02_2024/8hwd_35054.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwd_35054/02_2024/8hwd_35054.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwd_35054/02_2024/8hwd_35054_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwd_35054/02_2024/8hwd_35054_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 79 5.16 5 C 9553 2.51 5 N 2554 2.21 5 O 2831 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 459": "OE1" <-> "OE2" Residue "F ASP 473": "OD1" <-> "OD2" Residue "F PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 343": "OE1" <-> "OE2" Residue "D GLU 405": "OE1" <-> "OE2" Residue "D ASP 411": "OD1" <-> "OD2" Residue "D ASP 431": "OD1" <-> "OD2" Residue "D GLU 504": "OE1" <-> "OE2" Residue "D ASP 603": "OD1" <-> "OD2" Residue "D GLU 637": "OE1" <-> "OE2" Residue "D ASP 656": "OD1" <-> "OD2" Residue "E PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 402": "OD1" <-> "OD2" Residue "E TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 405": "OE1" <-> "OE2" Residue "C PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 522": "OD1" <-> "OD2" Residue "C GLU 579": "OE1" <-> "OE2" Residue "C PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 637": "OE1" <-> "OE2" Residue "C ASP 646": "OD1" <-> "OD2" Residue "B GLU 360": "OE1" <-> "OE2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "B ASP 411": "OD1" <-> "OD2" Residue "B GLU 453": "OE1" <-> "OE2" Residue "B PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 522": "OD1" <-> "OD2" Residue "B ASP 537": "OD1" <-> "OD2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 695": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15029 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2505 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 11, 'TRANS': 296} Chain breaks: 5 Chain: "F" Number of atoms: 2092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2092 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 9, 'TRANS': 248} Chain breaks: 4 Chain: "D" Number of atoms: 2427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2427 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 11, 'TRANS': 287} Chain breaks: 4 Chain: "E" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2012 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 9, 'TRANS': 237} Chain breaks: 4 Chain: "C" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 3 Chain: "B" Number of atoms: 3045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3045 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 359} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.05, per 1000 atoms: 0.54 Number of scatterers: 15029 At special positions: 0 Unit cell: (107.2, 127.568, 128.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 79 16.00 P 12 15.00 O 2831 8.00 N 2554 7.00 C 9553 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: 5.60 Conformation dependent library (CDL) restraints added in 2.6 seconds 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3498 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 77 helices and 21 sheets defined 36.5% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.78 Creating SS restraints... Processing helix chain 'A' and resid 325 through 336 Processing helix chain 'A' and resid 364 through 374 removed outlier: 3.512A pdb=" N ARG A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N HIS A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLN A 374 " --> pdb=" O SER A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 383 removed outlier: 3.934A pdb=" N SER A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLU A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU A 383 " --> pdb=" O TYR A 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 377 through 383' Processing helix chain 'A' and resid 391 through 397 Processing helix chain 'A' and resid 430 through 433 Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 459 through 468 Processing helix chain 'A' and resid 476 through 487 Processing helix chain 'A' and resid 509 through 520 Processing helix chain 'A' and resid 571 through 576 Processing helix chain 'A' and resid 615 through 620 removed outlier: 3.631A pdb=" N ARG A 620 " --> pdb=" O ALA A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 660 No H-bonds generated for 'chain 'A' and resid 657 through 660' Processing helix chain 'A' and resid 665 through 679 Processing helix chain 'F' and resid 325 through 336 removed outlier: 3.772A pdb=" N ALA F 330 " --> pdb=" O LEU F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 374 removed outlier: 3.682A pdb=" N ARG F 372 " --> pdb=" O ILE F 368 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N HIS F 373 " --> pdb=" O LEU F 369 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLN F 374 " --> pdb=" O SER F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 399 removed outlier: 3.785A pdb=" N VAL F 392 " --> pdb=" O LYS F 388 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU F 393 " --> pdb=" O ARG F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 430 through 434 Processing helix chain 'F' and resid 448 through 450 No H-bonds generated for 'chain 'F' and resid 448 through 450' Processing helix chain 'F' and resid 458 through 468 Processing helix chain 'F' and resid 476 through 487 Processing helix chain 'F' and resid 509 through 519 Processing helix chain 'F' and resid 657 through 660 No H-bonds generated for 'chain 'F' and resid 657 through 660' Processing helix chain 'F' and resid 665 through 679 Processing helix chain 'D' and resid 325 through 335 removed outlier: 3.680A pdb=" N ALA D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 374 removed outlier: 3.683A pdb=" N ARG D 372 " --> pdb=" O ILE D 368 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N HIS D 373 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLN D 374 " --> pdb=" O SER D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 383 removed outlier: 3.556A pdb=" N SER D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU D 383 " --> pdb=" O TYR D 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 377 through 383' Processing helix chain 'D' and resid 386 through 399 removed outlier: 3.626A pdb=" N LYS D 390 " --> pdb=" O PRO D 386 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR D 391 " --> pdb=" O ARG D 387 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL D 392 " --> pdb=" O LYS D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 433 Processing helix chain 'D' and resid 448 through 450 No H-bonds generated for 'chain 'D' and resid 448 through 450' Processing helix chain 'D' and resid 458 through 468 Processing helix chain 'D' and resid 476 through 488 Processing helix chain 'D' and resid 509 through 519 Processing helix chain 'D' and resid 576 through 578 No H-bonds generated for 'chain 'D' and resid 576 through 578' Processing helix chain 'D' and resid 633 through 638 removed outlier: 4.267A pdb=" N GLU D 637 " --> pdb=" O PRO D 633 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA D 638 " --> pdb=" O SER D 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 633 through 638' Processing helix chain 'D' and resid 653 through 660 removed outlier: 4.030A pdb=" N GLY D 657 " --> pdb=" O GLU D 653 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN D 660 " --> pdb=" O ASP D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 679 removed outlier: 3.884A pdb=" N LYS D 678 " --> pdb=" O LYS D 674 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR D 679 " --> pdb=" O TRP D 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 336 removed outlier: 3.826A pdb=" N ALA E 330 " --> pdb=" O LEU E 326 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 374 removed outlier: 3.683A pdb=" N ARG E 372 " --> pdb=" O ILE E 368 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N HIS E 373 " --> pdb=" O LEU E 369 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N GLN E 374 " --> pdb=" O SER E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 380 No H-bonds generated for 'chain 'E' and resid 377 through 380' Processing helix chain 'E' and resid 389 through 399 removed outlier: 3.666A pdb=" N GLU E 393 " --> pdb=" O ARG E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 433 Processing helix chain 'E' and resid 448 through 450 No H-bonds generated for 'chain 'E' and resid 448 through 450' Processing helix chain 'E' and resid 456 through 468 removed outlier: 3.866A pdb=" N GLU E 460 " --> pdb=" O PRO E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 475 No H-bonds generated for 'chain 'E' and resid 473 through 475' Processing helix chain 'E' and resid 477 through 488 Processing helix chain 'E' and resid 509 through 520 Processing helix chain 'E' and resid 668 through 679 Processing helix chain 'C' and resid 325 through 336 Processing helix chain 'C' and resid 363 through 374 removed outlier: 3.942A pdb=" N ILE C 368 " --> pdb=" O THR C 365 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE C 371 " --> pdb=" O ILE C 368 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS C 373 " --> pdb=" O SER C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 383 No H-bonds generated for 'chain 'C' and resid 381 through 383' Processing helix chain 'C' and resid 386 through 397 removed outlier: 3.791A pdb=" N THR C 391 " --> pdb=" O ARG C 387 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 450 No H-bonds generated for 'chain 'C' and resid 448 through 450' Processing helix chain 'C' and resid 456 through 468 Processing helix chain 'C' and resid 473 through 475 No H-bonds generated for 'chain 'C' and resid 473 through 475' Processing helix chain 'C' and resid 477 through 488 Processing helix chain 'C' and resid 509 through 520 Processing helix chain 'C' and resid 571 through 577 removed outlier: 3.750A pdb=" N LYS C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 620 No H-bonds generated for 'chain 'C' and resid 618 through 620' Processing helix chain 'C' and resid 636 through 638 No H-bonds generated for 'chain 'C' and resid 636 through 638' Processing helix chain 'C' and resid 655 through 660 Processing helix chain 'C' and resid 665 through 679 removed outlier: 3.829A pdb=" N LYS C 678 " --> pdb=" O LYS C 674 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR C 679 " --> pdb=" O TRP C 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 335 Processing helix chain 'B' and resid 363 through 374 removed outlier: 3.692A pdb=" N ILE B 368 " --> pdb=" O THR B 365 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE B 371 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N HIS B 373 " --> pdb=" O SER B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 383 No H-bonds generated for 'chain 'B' and resid 381 through 383' Processing helix chain 'B' and resid 386 through 399 removed outlier: 3.740A pdb=" N THR B 391 " --> pdb=" O ARG B 387 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 434 Processing helix chain 'B' and resid 448 through 450 No H-bonds generated for 'chain 'B' and resid 448 through 450' Processing helix chain 'B' and resid 456 through 468 Processing helix chain 'B' and resid 476 through 488 Processing helix chain 'B' and resid 509 through 520 Processing helix chain 'B' and resid 529 through 531 No H-bonds generated for 'chain 'B' and resid 529 through 531' Processing helix chain 'B' and resid 542 through 545 No H-bonds generated for 'chain 'B' and resid 542 through 545' Processing helix chain 'B' and resid 571 through 577 Processing helix chain 'B' and resid 633 through 640 removed outlier: 4.353A pdb=" N GLU B 637 " --> pdb=" O PRO B 633 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ALA B 638 " --> pdb=" O SER B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 660 Processing helix chain 'B' and resid 665 through 679 Processing helix chain 'B' and resid 694 through 699 Processing sheet with id= A, first strand: chain 'A' and resid 339 through 341 Processing sheet with id= B, first strand: chain 'A' and resid 412 through 415 Processing sheet with id= C, first strand: chain 'A' and resid 498 through 500 Processing sheet with id= D, first strand: chain 'A' and resid 629 through 631 Processing sheet with id= E, first strand: chain 'F' and resid 339 through 342 Processing sheet with id= F, first strand: chain 'F' and resid 412 through 415 removed outlier: 3.772A pdb=" N MET F 426 " --> pdb=" O ASP F 421 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 339 through 341 removed outlier: 3.557A pdb=" N ILE D 351 " --> pdb=" O SER D 354 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 412 through 415 removed outlier: 3.668A pdb=" N GLY D 418 " --> pdb=" O PHE D 415 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 629 through 631 removed outlier: 3.834A pdb=" N LYS D 649 " --> pdb=" O HIS D 629 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 340 through 342 Processing sheet with id= K, first strand: chain 'E' and resid 412 through 415 Processing sheet with id= L, first strand: chain 'C' and resid 339 through 341 Processing sheet with id= M, first strand: chain 'C' and resid 412 through 415 Processing sheet with id= N, first strand: chain 'C' and resid 498 through 500 removed outlier: 6.326A pdb=" N ILE C 600 " --> pdb=" O THR C 499 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 581 through 583 Processing sheet with id= P, first strand: chain 'C' and resid 628 through 631 removed outlier: 6.014A pdb=" N LYS C 647 " --> pdb=" O HIS C 629 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N SER C 631 " --> pdb=" O LYS C 647 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LYS C 649 " --> pdb=" O SER C 631 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'B' and resid 412 through 414 Processing sheet with id= R, first strand: chain 'B' and resid 498 through 500 Processing sheet with id= S, first strand: chain 'B' and resid 552 through 555 removed outlier: 6.042A pdb=" N THR B 599 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N CYS B 555 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ILE B 601 " --> pdb=" O CYS B 555 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'B' and resid 581 through 583 Processing sheet with id= U, first strand: chain 'B' and resid 628 through 631 removed outlier: 6.500A pdb=" N LYS B 647 " --> pdb=" O HIS B 629 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N SER B 631 " --> pdb=" O LYS B 647 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LYS B 649 " --> pdb=" O SER B 631 " (cutoff:3.500A) No H-bonds generated for sheet with id= U 404 hydrogen bonds defined for protein. 1110 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.79 Time building geometry restraints manager: 6.03 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: 4318 1.33 - 1.46: 2555 1.46 - 1.58: 8313 1.58 - 1.70: 18 1.70 - 1.82: 118 Bond restraints: 15322 Sorted by residual: bond pdb=" N VAL D 673 " pdb=" CA VAL D 673 " ideal model delta sigma weight residual 1.461 1.493 -0.031 1.17e-02 7.31e+03 7.18e+00 bond pdb=" N HIS F 548 " pdb=" CA HIS F 548 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.22e-02 6.72e+03 6.31e+00 bond pdb=" N THR B 342 " pdb=" CA THR B 342 " ideal model delta sigma weight residual 1.454 1.483 -0.029 1.16e-02 7.43e+03 6.13e+00 bond pdb=" N ASP B 522 " pdb=" CA ASP B 522 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.51e+00 bond pdb=" N LYS D 674 " pdb=" CA LYS D 674 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.20e-02 6.94e+03 5.01e+00 ... (remaining 15317 not shown) Histogram of bond angle deviations from ideal: 99.23 - 106.61: 406 106.61 - 113.99: 8783 113.99 - 121.37: 7700 121.37 - 128.75: 3693 128.75 - 136.14: 92 Bond angle restraints: 20674 Sorted by residual: angle pdb=" N LYS D 450 " pdb=" CA LYS D 450 " pdb=" C LYS D 450 " ideal model delta sigma weight residual 114.56 107.59 6.97 1.27e+00 6.20e-01 3.01e+01 angle pdb=" CB GLU D 457 " pdb=" CG GLU D 457 " pdb=" CD GLU D 457 " ideal model delta sigma weight residual 112.60 104.04 8.56 1.70e+00 3.46e-01 2.53e+01 angle pdb=" N GLY D 521 " pdb=" CA GLY D 521 " pdb=" C GLY D 521 " ideal model delta sigma weight residual 111.67 116.07 -4.40 9.20e-01 1.18e+00 2.28e+01 angle pdb=" CB LYS C 647 " pdb=" CG LYS C 647 " pdb=" CD LYS C 647 " ideal model delta sigma weight residual 111.30 122.09 -10.79 2.30e+00 1.89e-01 2.20e+01 angle pdb=" C GLU D 457 " pdb=" CA GLU D 457 " pdb=" CB GLU D 457 " ideal model delta sigma weight residual 110.42 118.41 -7.99 1.99e+00 2.53e-01 1.61e+01 ... (remaining 20669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.77: 8803 31.77 - 63.54: 483 63.54 - 95.30: 24 95.30 - 127.07: 1 127.07 - 158.84: 2 Dihedral angle restraints: 9313 sinusoidal: 3942 harmonic: 5371 Sorted by residual: dihedral pdb=" C2' ADP B1001 " pdb=" C1' ADP B1001 " pdb=" N9 ADP B1001 " pdb=" C4 ADP B1001 " ideal model delta sinusoidal sigma weight residual 91.55 -67.29 158.84 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" C2' ADP E1001 " pdb=" C1' ADP E1001 " pdb=" N9 ADP E1001 " pdb=" C4 ADP E1001 " ideal model delta sinusoidal sigma weight residual 91.55 -129.70 -138.76 1 2.00e+01 2.50e-03 4.20e+01 dihedral pdb=" O2A ADP E1001 " pdb=" O3A ADP E1001 " pdb=" PA ADP E1001 " pdb=" PB ADP E1001 " ideal model delta sinusoidal sigma weight residual -60.00 66.45 -126.45 1 2.00e+01 2.50e-03 3.83e+01 ... (remaining 9310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1588 0.038 - 0.077: 559 0.077 - 0.115: 146 0.115 - 0.153: 25 0.153 - 0.191: 3 Chirality restraints: 2321 Sorted by residual: chirality pdb=" CA ASN D 641 " pdb=" N ASN D 641 " pdb=" C ASN D 641 " pdb=" CB ASN D 641 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.15e-01 chirality pdb=" CB ILE B 464 " pdb=" CA ILE B 464 " pdb=" CG1 ILE B 464 " pdb=" CG2 ILE B 464 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.55e-01 chirality pdb=" CB ILE B 681 " pdb=" CA ILE B 681 " pdb=" CG1 ILE B 681 " pdb=" CG2 ILE B 681 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.80e-01 ... (remaining 2318 not shown) Planarity restraints: 2583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 456 " -0.028 2.00e-02 2.50e+03 5.90e-02 3.48e+01 pdb=" C PRO D 456 " 0.102 2.00e-02 2.50e+03 pdb=" O PRO D 456 " -0.040 2.00e-02 2.50e+03 pdb=" N GLU D 457 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 628 " 0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C THR D 628 " -0.057 2.00e-02 2.50e+03 pdb=" O THR D 628 " 0.022 2.00e-02 2.50e+03 pdb=" N HIS D 629 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 448 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C ASP D 448 " -0.045 2.00e-02 2.50e+03 pdb=" O ASP D 448 " 0.017 2.00e-02 2.50e+03 pdb=" N THR D 449 " 0.015 2.00e-02 2.50e+03 ... (remaining 2580 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1311 2.74 - 3.28: 15370 3.28 - 3.82: 24987 3.82 - 4.36: 29784 4.36 - 4.90: 50256 Nonbonded interactions: 121708 Sorted by model distance: nonbonded pdb=" OG SER F 510 " pdb=" O2A ADP F1001 " model vdw 2.199 2.440 nonbonded pdb=" OG1 THR B 365 " pdb=" OE1 GLU B 393 " model vdw 2.204 2.440 nonbonded pdb=" OG SER A 455 " pdb=" OE1 GLU A 457 " model vdw 2.207 2.440 nonbonded pdb=" OD1 ASN D 395 " pdb=" NH2 ARG C 389 " model vdw 2.221 2.520 nonbonded pdb=" O LEU D 369 " pdb=" NH1 ARG D 372 " model vdw 2.237 2.520 ... (remaining 121703 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 323 through 526 or resid 544 through 554 or resid 575 thro \ ugh 581 or resid 595 through 614 or resid 623 through 688 or resid 1001)) selection = (chain 'C' and (resid 323 through 526 or resid 544 through 554 or resid 575 thro \ ugh 581 or resid 595 through 603 or resid 623 through 631 or resid 645 through 6 \ 88 or resid 1001)) selection = (chain 'D' and (resid 323 through 603 or resid 623 through 631 or resid 645 thro \ ugh 688 or resid 1001)) } ncs_group { reference = (chain 'E' and (resid 323 through 525 or resid 547 through 553 or resid 575 thro \ ugh 686 or resid 1001)) selection = (chain 'F' and (resid 323 through 525 or resid 547 through 580 or resid 595 thro \ ugh 600 or resid 664 through 686 or resid 1001)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.400 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 40.070 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 15322 Z= 0.234 Angle : 0.734 10.793 20674 Z= 0.382 Chirality : 0.042 0.191 2321 Planarity : 0.005 0.059 2583 Dihedral : 18.031 158.839 5815 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.64 % Favored : 91.30 % Rotamer: Outliers : 1.25 % Allowed : 32.48 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.20), residues: 1782 helix: 0.00 (0.20), residues: 689 sheet: -1.31 (0.35), residues: 232 loop : -2.03 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 355 HIS 0.005 0.001 HIS F 597 PHE 0.016 0.001 PHE E 666 TYR 0.018 0.001 TYR B 482 ARG 0.005 0.000 ARG B 625 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 265 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 LYS cc_start: 0.8336 (mmmt) cc_final: 0.7910 (mmmm) REVERT: A 618 MET cc_start: 0.8179 (tmm) cc_final: 0.7017 (tpp) REVERT: D 390 LYS cc_start: 0.6517 (mptt) cc_final: 0.6086 (mtmm) REVERT: D 500 PHE cc_start: 0.6804 (m-10) cc_final: 0.6602 (m-10) REVERT: D 650 LEU cc_start: 0.8161 (pp) cc_final: 0.7833 (pt) REVERT: D 651 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8472 (tt) REVERT: D 660 GLN cc_start: 0.7633 (mp10) cc_final: 0.7420 (mm-40) REVERT: C 436 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.8100 (m-80) REVERT: B 374 GLN cc_start: 0.7550 (mt0) cc_final: 0.7344 (mt0) outliers start: 21 outliers final: 7 residues processed: 277 average time/residue: 0.2801 time to fit residues: 112.1402 Evaluate side-chains 255 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 246 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain F residue 671 LEU Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 651 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 511 THR Chi-restraints excluded: chain B residue 351 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 151 optimal weight: 0.8980 chunk 135 optimal weight: 0.6980 chunk 75 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN E 331 GLN ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.0656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15322 Z= 0.194 Angle : 0.609 8.307 20674 Z= 0.287 Chirality : 0.040 0.147 2321 Planarity : 0.004 0.050 2583 Dihedral : 8.451 158.060 2051 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 4.23 % Allowed : 29.74 % Favored : 66.03 % 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: -1.53 (0.20), residues: 1782 helix: 0.14 (0.20), residues: 686 sheet: -1.34 (0.36), residues: 216 loop : -1.88 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 675 HIS 0.005 0.001 HIS D 629 PHE 0.017 0.001 PHE D 630 TYR 0.019 0.001 TYR F 482 ARG 0.010 0.000 ARG D 625 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 250 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 361 GLU cc_start: 0.5284 (OUTLIER) cc_final: 0.4928 (pp20) REVERT: D 372 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7956 (ttp-110) REVERT: D 481 LEU cc_start: 0.8385 (tp) cc_final: 0.8056 (tp) REVERT: D 502 PHE cc_start: 0.6669 (t80) cc_final: 0.6419 (t80) REVERT: D 660 GLN cc_start: 0.7881 (mp10) cc_final: 0.7619 (mm-40) REVERT: E 382 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7734 (tp30) REVERT: C 375 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7273 (mt) REVERT: C 484 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7636 (ttmm) REVERT: B 374 GLN cc_start: 0.7581 (mt0) cc_final: 0.7377 (mt0) REVERT: B 501 PHE cc_start: 0.7082 (OUTLIER) cc_final: 0.6712 (m-10) outliers start: 71 outliers final: 37 residues processed: 298 average time/residue: 0.2596 time to fit residues: 114.9119 Evaluate side-chains 282 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 239 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain F residue 361 GLU Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 387 ARG Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 489 CYS Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 579 GLU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 381 SER Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain E residue 411 ASP Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 664 TYR Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain B residue 544 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A 594 ASN ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 331 GLN ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 15322 Z= 0.320 Angle : 0.669 8.513 20674 Z= 0.318 Chirality : 0.043 0.203 2321 Planarity : 0.005 0.062 2583 Dihedral : 8.399 154.134 2042 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 6.62 % Allowed : 27.89 % Favored : 65.49 % 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: -1.86 (0.20), residues: 1782 helix: -0.23 (0.19), residues: 687 sheet: -1.34 (0.37), residues: 202 loop : -2.04 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 350 HIS 0.004 0.001 HIS C 629 PHE 0.020 0.002 PHE B 554 TYR 0.021 0.002 TYR B 482 ARG 0.006 0.000 ARG D 625 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 258 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.7033 (ptt90) REVERT: F 361 GLU cc_start: 0.5247 (OUTLIER) cc_final: 0.4835 (pp20) REVERT: D 481 LEU cc_start: 0.8460 (tp) cc_final: 0.8124 (tp) REVERT: D 502 PHE cc_start: 0.6829 (t80) cc_final: 0.6588 (t80) REVERT: D 645 TYR cc_start: 0.7373 (m-10) cc_final: 0.6704 (m-10) REVERT: E 382 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7886 (tp30) REVERT: E 384 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8284 (mt) REVERT: C 375 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7152 (mt) REVERT: C 436 TYR cc_start: 0.8490 (OUTLIER) cc_final: 0.8171 (m-80) REVERT: C 484 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7777 (ttmm) REVERT: B 374 GLN cc_start: 0.7344 (mt0) cc_final: 0.7089 (mt0) REVERT: B 501 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.6812 (m-10) outliers start: 111 outliers final: 67 residues processed: 334 average time/residue: 0.2533 time to fit residues: 127.1278 Evaluate side-chains 327 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 252 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 387 ARG Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 361 GLU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 485 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 387 ARG Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 489 CYS Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 579 GLU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 351 ILE Chi-restraints excluded: chain E residue 357 PHE Chi-restraints excluded: chain E residue 381 SER Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 576 LYS Chi-restraints excluded: chain E residue 664 TYR Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 556 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 160 optimal weight: 6.9990 chunk 122 optimal weight: 0.0970 chunk 84 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 173 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 154 optimal weight: 0.1980 chunk 46 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN A 594 ASN ** F 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 331 GLN ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 GLN C 573 ASN ** C 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15322 Z= 0.171 Angle : 0.608 12.375 20674 Z= 0.285 Chirality : 0.040 0.147 2321 Planarity : 0.004 0.052 2583 Dihedral : 7.945 158.181 2036 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 4.83 % Allowed : 29.02 % Favored : 66.15 % 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: -1.57 (0.20), residues: 1782 helix: 0.14 (0.20), residues: 687 sheet: -1.35 (0.38), residues: 191 loop : -1.95 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 350 HIS 0.007 0.001 HIS C 629 PHE 0.012 0.001 PHE B 501 TYR 0.018 0.001 TYR F 482 ARG 0.003 0.000 ARG D 625 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 261 time to evaluate : 1.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 439 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8253 (m) REVERT: F 361 GLU cc_start: 0.5214 (OUTLIER) cc_final: 0.4955 (pp20) REVERT: D 372 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7939 (ttp-110) REVERT: D 458 MET cc_start: 0.6240 (ppp) cc_final: 0.5885 (tmm) REVERT: D 481 LEU cc_start: 0.8449 (tp) cc_final: 0.8127 (tp) REVERT: D 502 PHE cc_start: 0.6860 (t80) cc_final: 0.6594 (t80) REVERT: E 382 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7684 (tp30) REVERT: E 384 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8294 (mt) REVERT: C 436 TYR cc_start: 0.8432 (OUTLIER) cc_final: 0.8183 (m-80) REVERT: C 484 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7649 (ttmm) REVERT: C 606 TYR cc_start: 0.6597 (OUTLIER) cc_final: 0.5689 (m-80) REVERT: B 501 PHE cc_start: 0.7016 (OUTLIER) cc_final: 0.6726 (m-10) outliers start: 81 outliers final: 49 residues processed: 315 average time/residue: 0.2967 time to fit residues: 140.2844 Evaluate side-chains 300 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 242 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 361 GLU Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 387 ARG Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 489 CYS Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 579 GLU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 357 PHE Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 576 LYS Chi-restraints excluded: chain E residue 664 TYR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 606 TYR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 656 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 144 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 147 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 155 optimal weight: 0.4980 chunk 43 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 331 GLN ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15322 Z= 0.171 Angle : 0.595 9.276 20674 Z= 0.279 Chirality : 0.040 0.147 2321 Planarity : 0.004 0.058 2583 Dihedral : 7.820 158.579 2036 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 5.42 % Allowed : 28.96 % Favored : 65.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.20), residues: 1782 helix: 0.29 (0.20), residues: 688 sheet: -1.34 (0.38), residues: 191 loop : -1.92 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 350 HIS 0.006 0.001 HIS C 629 PHE 0.024 0.001 PHE D 630 TYR 0.028 0.001 TYR D 645 ARG 0.002 0.000 ARG D 625 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 260 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8342 (mt) REVERT: A 343 GLU cc_start: 0.7011 (pm20) cc_final: 0.6091 (mp0) REVERT: A 387 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.6926 (ptt90) REVERT: A 439 THR cc_start: 0.8432 (OUTLIER) cc_final: 0.8210 (m) REVERT: F 361 GLU cc_start: 0.5168 (OUTLIER) cc_final: 0.4942 (pp20) REVERT: D 372 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7964 (ttp-110) REVERT: D 481 LEU cc_start: 0.8396 (tp) cc_final: 0.8083 (tp) REVERT: D 502 PHE cc_start: 0.6886 (t80) cc_final: 0.6616 (t80) REVERT: E 382 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7632 (tp30) REVERT: E 384 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8351 (mt) REVERT: E 684 MET cc_start: 0.7239 (mpp) cc_final: 0.6986 (mpp) REVERT: C 375 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7239 (mt) REVERT: C 436 TYR cc_start: 0.8400 (OUTLIER) cc_final: 0.8124 (m-80) REVERT: C 484 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7736 (ttmm) REVERT: C 606 TYR cc_start: 0.6620 (OUTLIER) cc_final: 0.5628 (m-80) REVERT: B 501 PHE cc_start: 0.7028 (OUTLIER) cc_final: 0.6725 (m-10) outliers start: 91 outliers final: 60 residues processed: 322 average time/residue: 0.2508 time to fit residues: 120.0174 Evaluate side-chains 319 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 247 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 387 ARG Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 361 GLU Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 520 ILE Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 387 ARG Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 489 CYS Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 579 GLU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 357 PHE Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 576 LYS Chi-restraints excluded: chain E residue 664 TYR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 606 TYR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 656 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 58 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 101 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 173 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 90 optimal weight: 0.3980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 331 GLN ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 GLN ** C 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15322 Z= 0.180 Angle : 0.609 15.027 20674 Z= 0.282 Chirality : 0.040 0.150 2321 Planarity : 0.004 0.049 2583 Dihedral : 7.761 158.818 2036 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 6.02 % Allowed : 28.61 % Favored : 65.38 % 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: -1.41 (0.20), residues: 1782 helix: 0.30 (0.20), residues: 690 sheet: -1.30 (0.38), residues: 191 loop : -1.88 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 350 HIS 0.007 0.001 HIS C 629 PHE 0.013 0.001 PHE D 415 TYR 0.021 0.001 TYR D 645 ARG 0.002 0.000 ARG D 625 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 253 time to evaluate : 1.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8353 (mt) REVERT: A 343 GLU cc_start: 0.6997 (pm20) cc_final: 0.6065 (mp0) REVERT: A 387 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.6937 (ptt90) REVERT: A 439 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.8188 (m) REVERT: D 372 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7968 (ttp-110) REVERT: D 481 LEU cc_start: 0.8401 (tp) cc_final: 0.8096 (tp) REVERT: D 502 PHE cc_start: 0.6898 (t80) cc_final: 0.6628 (t80) REVERT: E 382 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7624 (tp30) REVERT: E 384 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8394 (mt) REVERT: E 684 MET cc_start: 0.7302 (mpp) cc_final: 0.7054 (mpp) REVERT: C 375 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7265 (mt) REVERT: C 436 TYR cc_start: 0.8394 (OUTLIER) cc_final: 0.8124 (m-80) REVERT: C 484 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7741 (ttmm) REVERT: C 606 TYR cc_start: 0.6609 (OUTLIER) cc_final: 0.5619 (m-80) REVERT: B 501 PHE cc_start: 0.7042 (OUTLIER) cc_final: 0.6725 (m-10) outliers start: 101 outliers final: 70 residues processed: 320 average time/residue: 0.2562 time to fit residues: 123.1342 Evaluate side-chains 327 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 246 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 387 ARG Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 520 ILE Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 387 ARG Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 489 CYS Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 579 GLU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 357 PHE Chi-restraints excluded: chain E residue 381 SER Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 421 ASP Chi-restraints excluded: chain E residue 481 LEU Chi-restraints excluded: chain E residue 576 LYS Chi-restraints excluded: chain E residue 664 TYR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 606 TYR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 659 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 166 optimal weight: 20.0000 chunk 19 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 chunk 96 optimal weight: 0.4980 chunk 172 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 331 GLN ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 15322 Z= 0.386 Angle : 0.722 14.410 20674 Z= 0.343 Chirality : 0.045 0.228 2321 Planarity : 0.005 0.056 2583 Dihedral : 8.108 151.262 2036 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 6.50 % Allowed : 28.43 % Favored : 65.08 % 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: -1.91 (0.20), residues: 1782 helix: -0.35 (0.19), residues: 697 sheet: -1.29 (0.36), residues: 212 loop : -2.04 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 350 HIS 0.006 0.001 HIS C 629 PHE 0.016 0.002 PHE B 501 TYR 0.029 0.002 TYR F 482 ARG 0.004 0.000 ARG E 397 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 255 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 GLU cc_start: 0.7057 (pm20) cc_final: 0.6112 (mp0) REVERT: A 387 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7090 (ptt90) REVERT: A 618 MET cc_start: 0.8309 (tmm) cc_final: 0.7145 (tpp) REVERT: F 343 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7602 (mp0) REVERT: D 458 MET cc_start: 0.6526 (ppp) cc_final: 0.6224 (tmm) REVERT: D 481 LEU cc_start: 0.8518 (tp) cc_final: 0.8223 (tp) REVERT: D 502 PHE cc_start: 0.6989 (t80) cc_final: 0.6759 (t80) REVERT: E 382 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7854 (tp30) REVERT: E 384 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8409 (mt) REVERT: E 684 MET cc_start: 0.7322 (mpp) cc_final: 0.7096 (mpp) REVERT: C 375 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7217 (mt) REVERT: C 436 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.8176 (m-80) REVERT: C 484 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7770 (ttmm) REVERT: C 509 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7085 (mttp) REVERT: C 606 TYR cc_start: 0.6630 (OUTLIER) cc_final: 0.5575 (m-80) REVERT: B 363 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7673 (tt) REVERT: B 501 PHE cc_start: 0.7189 (OUTLIER) cc_final: 0.6796 (m-10) REVERT: B 653 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6602 (mm-30) outliers start: 109 outliers final: 76 residues processed: 332 average time/residue: 0.2573 time to fit residues: 126.5388 Evaluate side-chains 333 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 246 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 387 ARG Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 387 ARG Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 489 CYS Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 579 GLU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 357 PHE Chi-restraints excluded: chain E residue 381 SER Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 421 ASP Chi-restraints excluded: chain E residue 513 LYS Chi-restraints excluded: chain E residue 576 LYS Chi-restraints excluded: chain E residue 664 TYR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 606 TYR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 653 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 106 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 135 optimal weight: 0.8980 chunk 156 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 331 GLN ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 15322 Z= 0.221 Angle : 0.650 13.718 20674 Z= 0.306 Chirality : 0.041 0.159 2321 Planarity : 0.004 0.053 2583 Dihedral : 7.895 155.182 2036 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 5.90 % Allowed : 29.56 % Favored : 64.54 % 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: -1.68 (0.20), residues: 1782 helix: -0.03 (0.20), residues: 692 sheet: -1.22 (0.37), residues: 201 loop : -2.00 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 350 HIS 0.007 0.001 HIS C 629 PHE 0.014 0.001 PHE A 630 TYR 0.026 0.001 TYR F 482 ARG 0.002 0.000 ARG D 387 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 247 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8354 (mt) REVERT: A 343 GLU cc_start: 0.6919 (pm20) cc_final: 0.6022 (mp0) REVERT: A 387 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.6948 (ptt90) REVERT: A 618 MET cc_start: 0.8270 (tmm) cc_final: 0.7207 (tpp) REVERT: D 372 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7906 (ttp-110) REVERT: D 390 LYS cc_start: 0.6585 (mptt) cc_final: 0.6259 (mtmm) REVERT: D 481 LEU cc_start: 0.8475 (tp) cc_final: 0.8173 (tp) REVERT: D 502 PHE cc_start: 0.6945 (t80) cc_final: 0.6736 (t80) REVERT: E 382 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7650 (tp30) REVERT: E 384 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8391 (mt) REVERT: E 684 MET cc_start: 0.7311 (mpp) cc_final: 0.7101 (mpp) REVERT: C 343 GLU cc_start: 0.7053 (mp0) cc_final: 0.6808 (mp0) REVERT: C 436 TYR cc_start: 0.8458 (OUTLIER) cc_final: 0.8191 (m-80) REVERT: C 484 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7719 (ttmm) REVERT: C 509 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7075 (mttp) REVERT: C 606 TYR cc_start: 0.6610 (OUTLIER) cc_final: 0.5566 (m-80) REVERT: B 363 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7609 (tt) REVERT: B 501 PHE cc_start: 0.7097 (OUTLIER) cc_final: 0.6767 (m-10) outliers start: 99 outliers final: 78 residues processed: 313 average time/residue: 0.2548 time to fit residues: 119.4535 Evaluate side-chains 327 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 238 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 387 ARG Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 387 ARG Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 489 CYS Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 579 GLU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 357 PHE Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 513 LYS Chi-restraints excluded: chain E residue 576 LYS Chi-restraints excluded: chain E residue 664 TYR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 606 TYR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 609 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 165 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 160 optimal weight: 8.9990 chunk 96 optimal weight: 0.0670 chunk 70 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 49 optimal weight: 0.0980 chunk 145 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 chunk 105 optimal weight: 8.9990 chunk 170 optimal weight: 1.9990 overall best weight: 0.5922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 GLN ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 331 GLN ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 GLN C 629 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 15322 Z= 0.181 Angle : 0.636 12.927 20674 Z= 0.296 Chirality : 0.040 0.154 2321 Planarity : 0.004 0.050 2583 Dihedral : 7.708 157.817 2036 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 5.30 % Allowed : 30.10 % Favored : 64.60 % 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: -1.43 (0.20), residues: 1782 helix: 0.24 (0.20), residues: 690 sheet: -1.16 (0.37), residues: 212 loop : -1.90 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 355 HIS 0.005 0.001 HIS C 629 PHE 0.014 0.001 PHE E 666 TYR 0.025 0.001 TYR F 482 ARG 0.008 0.000 ARG B 625 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 247 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8321 (mt) REVERT: A 343 GLU cc_start: 0.6985 (pm20) cc_final: 0.6043 (mp0) REVERT: A 387 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.6959 (ptt90) REVERT: A 618 MET cc_start: 0.8218 (tmm) cc_final: 0.7449 (tpp) REVERT: D 372 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7933 (ttp-110) REVERT: D 481 LEU cc_start: 0.8425 (tp) cc_final: 0.8159 (tp) REVERT: E 382 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7630 (tp30) REVERT: E 384 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8397 (mt) REVERT: E 684 MET cc_start: 0.7319 (mpp) cc_final: 0.7110 (mpp) REVERT: C 343 GLU cc_start: 0.6983 (mp0) cc_final: 0.6723 (mp0) REVERT: C 436 TYR cc_start: 0.8390 (OUTLIER) cc_final: 0.8112 (m-80) REVERT: C 484 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7741 (ttmm) REVERT: C 509 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7110 (mttp) REVERT: C 606 TYR cc_start: 0.6583 (OUTLIER) cc_final: 0.5545 (m-80) REVERT: B 363 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7603 (tt) REVERT: B 501 PHE cc_start: 0.7009 (OUTLIER) cc_final: 0.6664 (m-10) outliers start: 89 outliers final: 73 residues processed: 306 average time/residue: 0.2446 time to fit residues: 111.9878 Evaluate side-chains 320 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 236 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 387 ARG Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 387 ARG Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 489 CYS Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 579 GLU Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 357 PHE Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 513 LYS Chi-restraints excluded: chain E residue 576 LYS Chi-restraints excluded: chain E residue 664 TYR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 606 TYR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 629 HIS Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 609 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 103 optimal weight: 9.9990 chunk 80 optimal weight: 20.0000 chunk 118 optimal weight: 0.6980 chunk 178 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 142 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 112 optimal weight: 0.3980 chunk 151 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 660 GLN ** D 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 331 GLN ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 15322 Z= 0.191 Angle : 0.646 12.492 20674 Z= 0.301 Chirality : 0.041 0.175 2321 Planarity : 0.004 0.047 2583 Dihedral : 7.669 157.787 2036 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 5.24 % Allowed : 30.27 % Favored : 64.48 % 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: -1.41 (0.20), residues: 1782 helix: 0.27 (0.20), residues: 696 sheet: -1.13 (0.37), residues: 212 loop : -1.92 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 350 HIS 0.010 0.001 HIS C 629 PHE 0.014 0.001 PHE E 666 TYR 0.024 0.001 TYR F 482 ARG 0.003 0.000 ARG B 625 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3564 Ramachandran restraints generated. 1782 Oldfield, 0 Emsley, 1782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 244 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8326 (mt) REVERT: A 343 GLU cc_start: 0.6983 (pm20) cc_final: 0.6049 (mp0) REVERT: A 387 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.6970 (ptt90) REVERT: A 618 MET cc_start: 0.8244 (tmm) cc_final: 0.7468 (tpp) REVERT: F 348 ILE cc_start: 0.8613 (pt) cc_final: 0.8126 (pt) REVERT: D 372 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7927 (ttp-110) REVERT: D 481 LEU cc_start: 0.8427 (tp) cc_final: 0.8156 (tp) REVERT: D 502 PHE cc_start: 0.6868 (t80) cc_final: 0.6360 (t80) REVERT: E 382 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7624 (tp30) REVERT: E 384 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8379 (mt) REVERT: E 684 MET cc_start: 0.7336 (mpp) cc_final: 0.7114 (mpp) REVERT: C 343 GLU cc_start: 0.7031 (mp0) cc_final: 0.6777 (mp0) REVERT: C 436 TYR cc_start: 0.8390 (OUTLIER) cc_final: 0.8112 (m-80) REVERT: C 484 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7726 (ttmm) REVERT: C 509 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7105 (mttp) REVERT: C 606 TYR cc_start: 0.6583 (OUTLIER) cc_final: 0.5531 (m-80) REVERT: B 363 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7579 (tt) REVERT: B 501 PHE cc_start: 0.6991 (OUTLIER) cc_final: 0.6600 (m-10) outliers start: 88 outliers final: 73 residues processed: 306 average time/residue: 0.2523 time to fit residues: 116.3619 Evaluate side-chains 324 residues out of total 1679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 240 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 387 ARG Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 407 ASP Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 387 ARG Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 436 TYR Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 489 CYS Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 579 GLU Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 357 PHE Chi-restraints excluded: chain E residue 381 SER Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 513 LYS Chi-restraints excluded: chain E residue 576 LYS Chi-restraints excluded: chain E residue 664 TYR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 368 ILE Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 509 LYS Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 606 TYR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 629 HIS Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 501 PHE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 555 CYS Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 609 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 43 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 20 optimal weight: 0.0970 chunk 39 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 18 optimal weight: 0.0670 chunk 26 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 overall best weight: 0.6316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 331 GLN ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.216773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.178454 restraints weight = 18406.814| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 4.01 r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 15322 Z= 0.183 Angle : 0.638 12.493 20674 Z= 0.297 Chirality : 0.040 0.165 2321 Planarity : 0.004 0.045 2583 Dihedral : 7.612 158.421 2036 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 5.30 % Allowed : 30.39 % Favored : 64.30 % 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: -1.37 (0.20), residues: 1782 helix: 0.32 (0.20), residues: 697 sheet: -1.07 (0.37), residues: 212 loop : -1.92 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 350 HIS 0.015 0.001 HIS C 629 PHE 0.013 0.001 PHE E 666 TYR 0.024 0.001 TYR F 482 ARG 0.008 0.000 ARG D 625 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3246.03 seconds wall clock time: 60 minutes 16.06 seconds (3616.06 seconds total)