Starting phenix.real_space_refine on Mon Jul 22 07:40:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwe_35055/07_2024/8hwe_35055_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwe_35055/07_2024/8hwe_35055.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/8hwe_35055/07_2024/8hwe_35055.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwe_35055/07_2024/8hwe_35055.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwe_35055/07_2024/8hwe_35055_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwe_35055/07_2024/8hwe_35055_neut.cif" } 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= 0.002 sd= 0.117 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: 6 Type Number sf(0) Gaussians P 17 5.49 5 Mg 5 5.21 5 S 91 5.16 5 C 10938 2.51 5 N 2930 2.21 5 O 3266 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 405": "OE1" <-> "OE2" Residue "D ASP 432": "OD1" <-> "OD2" Residue "D GLU 457": "OE1" <-> "OE2" Residue "D PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 557": "OE1" <-> "OE2" Residue "C ASP 603": "OD1" <-> "OD2" Residue "C PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 652": "OD1" <-> "OD2" Residue "C TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 346": "OD1" <-> "OD2" Residue "F ASP 411": "OD1" <-> "OD2" Residue "F ASP 432": "OD1" <-> "OD2" Residue "F ASP 522": "OD1" <-> "OD2" Residue "F PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 335": "OD1" <-> "OD2" Residue "A ASP 411": "OD1" <-> "OD2" Residue "A ASP 431": "OD1" <-> "OD2" Residue "A ASP 432": "OD1" <-> "OD2" Residue "A PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 346": "OD1" <-> "OD2" Residue "E GLU 360": "OE1" <-> "OE2" Residue "E GLU 483": "OE1" <-> "OE2" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 378": "OE1" <-> "OE2" Residue "B ASP 402": "OD1" <-> "OD2" Residue "B ASP 431": "OD1" <-> "OD2" Residue "B PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 643": "OD1" <-> "OD2" Residue "B TYR 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 691": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 17247 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3054 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 360} 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: "C" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3054 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 360} 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: "F" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2230 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 10, 'TRANS': 263} Chain breaks: 5 Chain: "A" Number of atoms: 2666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2666 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 14, 'TRANS': 314} Chain breaks: 4 Chain: "E" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 3002 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 17, 'TRANS': 354} Chain breaks: 1 Chain: "B" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3054 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 360} 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: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.07, per 1000 atoms: 0.53 Number of scatterers: 17247 At special positions: 0 Unit cell: (106.653, 127.121, 130.353, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 91 16.00 P 17 15.00 Mg 5 11.99 O 3266 8.00 N 2930 7.00 C 10938 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: 6.15 Conformation dependent library (CDL) restraints added in 2.9 seconds 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4028 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 27 sheets defined 43.9% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'D' and resid 324 through 336 removed outlier: 3.691A pdb=" N ALA D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR D 336 " --> pdb=" O ARG D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 371 removed outlier: 3.522A pdb=" N LEU D 367 " --> pdb=" O LEU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 375 removed outlier: 3.783A pdb=" N LEU D 375 " --> pdb=" O ARG D 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 372 through 375' Processing helix chain 'D' and resid 376 through 384 removed outlier: 4.861A pdb=" N SER D 381 " --> pdb=" O GLU D 378 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLU D 382 " --> pdb=" O TYR D 379 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU D 384 " --> pdb=" O SER D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 397 Processing helix chain 'D' and resid 430 through 435 removed outlier: 3.828A pdb=" N LYS D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 451 removed outlier: 3.501A pdb=" N PHE D 451 " --> pdb=" O ASP D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 469 Processing helix chain 'D' and resid 475 through 488 Processing helix chain 'D' and resid 508 through 521 removed outlier: 3.504A pdb=" N THR D 512 " --> pdb=" O GLY D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 528 through 532 removed outlier: 3.909A pdb=" N ILE D 531 " --> pdb=" O GLY D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 546 removed outlier: 3.715A pdb=" N ALA D 545 " --> pdb=" O ASN D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 578 removed outlier: 3.599A pdb=" N THR D 578 " --> pdb=" O ILE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 619 removed outlier: 3.831A pdb=" N ARG D 619 " --> pdb=" O ASN D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 635 Processing helix chain 'D' and resid 636 through 641 removed outlier: 3.601A pdb=" N GLU D 640 " --> pdb=" O ARG D 636 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASN D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 636 through 641' Processing helix chain 'D' and resid 656 through 661 removed outlier: 3.895A pdb=" N GLN D 660 " --> pdb=" O ASP D 656 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN D 661 " --> pdb=" O GLY D 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 656 through 661' Processing helix chain 'D' and resid 664 through 680 removed outlier: 3.650A pdb=" N LYS D 678 " --> pdb=" O LYS D 674 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR D 679 " --> pdb=" O TRP D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 692 removed outlier: 3.757A pdb=" N GLU D 692 " --> pdb=" O THR D 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 689 through 692' Processing helix chain 'D' and resid 693 through 700 Processing helix chain 'C' and resid 324 through 336 removed outlier: 3.722A pdb=" N ALA C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 371 Processing helix chain 'C' and resid 372 through 375 removed outlier: 4.029A pdb=" N LEU C 375 " --> pdb=" O ARG C 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 372 through 375' Processing helix chain 'C' and resid 376 through 384 removed outlier: 4.647A pdb=" N SER C 381 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU C 382 " --> pdb=" O TYR C 379 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU C 384 " --> pdb=" O SER C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 397 Processing helix chain 'C' and resid 430 through 435 removed outlier: 3.673A pdb=" N LYS C 435 " --> pdb=" O ASP C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 451 removed outlier: 3.773A pdb=" N LYS C 450 " --> pdb=" O ASP C 447 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE C 451 " --> pdb=" O ASP C 448 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 447 through 451' Processing helix chain 'C' and resid 455 through 469 Processing helix chain 'C' and resid 475 through 488 removed outlier: 3.512A pdb=" N ARG C 479 " --> pdb=" O ASN C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 541 through 547 removed outlier: 3.855A pdb=" N MET C 547 " --> pdb=" O PHE C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 578 removed outlier: 3.790A pdb=" N ILE C 574 " --> pdb=" O ARG C 570 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 619 removed outlier: 3.730A pdb=" N ARG C 619 " --> pdb=" O ASN C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 634 No H-bonds generated for 'chain 'C' and resid 632 through 634' Processing helix chain 'C' and resid 635 through 641 removed outlier: 3.909A pdb=" N ASN C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 661 removed outlier: 4.237A pdb=" N GLN C 660 " --> pdb=" O ASP C 656 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN C 661 " --> pdb=" O GLY C 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 656 through 661' Processing helix chain 'C' and resid 664 through 680 removed outlier: 3.809A pdb=" N LYS C 678 " --> pdb=" O LYS C 674 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR C 679 " --> pdb=" O TRP C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 692 removed outlier: 3.625A pdb=" N GLU C 692 " --> pdb=" O THR C 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 689 through 692' Processing helix chain 'C' and resid 693 through 701 removed outlier: 4.275A pdb=" N LYS C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 336 removed outlier: 3.891A pdb=" N ALA F 330 " --> pdb=" O LEU F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 371 removed outlier: 3.536A pdb=" N LEU F 367 " --> pdb=" O LEU F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 375 removed outlier: 3.792A pdb=" N LEU F 375 " --> pdb=" O ARG F 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 372 through 375' Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'F' and resid 385 through 388 Processing helix chain 'F' and resid 389 through 398 removed outlier: 3.505A pdb=" N GLU F 393 " --> pdb=" O ARG F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 430 through 435 Processing helix chain 'F' and resid 447 through 451 removed outlier: 3.502A pdb=" N LYS F 450 " --> pdb=" O ASP F 447 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE F 451 " --> pdb=" O ASP F 448 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 447 through 451' Processing helix chain 'F' and resid 455 through 469 Processing helix chain 'F' and resid 475 through 489 removed outlier: 3.841A pdb=" N CYS F 489 " --> pdb=" O THR F 485 " (cutoff:3.500A) Processing helix chain 'F' and resid 508 through 521 Processing helix chain 'F' and resid 522 through 524 No H-bonds generated for 'chain 'F' and resid 522 through 524' Processing helix chain 'F' and resid 573 through 577 Processing helix chain 'F' and resid 615 through 619 removed outlier: 3.730A pdb=" N ARG F 619 " --> pdb=" O ASN F 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 615 through 619' Processing helix chain 'F' and resid 665 through 680 removed outlier: 3.746A pdb=" N LYS F 678 " --> pdb=" O LYS F 674 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR F 679 " --> pdb=" O TRP F 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.809A pdb=" N ALA A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 371 removed outlier: 3.885A pdb=" N LEU A 369 " --> pdb=" O THR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 375 removed outlier: 3.869A pdb=" N LEU A 375 " --> pdb=" O ARG A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 372 through 375' Processing helix chain 'A' and resid 376 through 384 removed outlier: 4.524A pdb=" N SER A 381 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLU A 382 " --> pdb=" O TYR A 379 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU A 384 " --> pdb=" O SER A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 400 Processing helix chain 'A' and resid 430 through 435 removed outlier: 3.676A pdb=" N LYS A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 451 removed outlier: 3.690A pdb=" N LYS A 450 " --> pdb=" O ASP A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 475 through 488 Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 543 through 547 Processing helix chain 'A' and resid 571 through 578 removed outlier: 3.633A pdb=" N LYS A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 635 Processing helix chain 'A' and resid 636 through 641 removed outlier: 3.551A pdb=" N GLU A 640 " --> pdb=" O ARG A 636 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASN A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 636 through 641' Processing helix chain 'A' and resid 656 through 661 removed outlier: 4.039A pdb=" N GLN A 660 " --> pdb=" O ASP A 656 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN A 661 " --> pdb=" O GLY A 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 656 through 661' Processing helix chain 'A' and resid 664 through 677 Processing helix chain 'E' and resid 324 through 336 removed outlier: 3.700A pdb=" N ALA E 330 " --> pdb=" O LEU E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 371 Processing helix chain 'E' and resid 372 through 375 removed outlier: 3.709A pdb=" N LEU E 375 " --> pdb=" O ARG E 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 372 through 375' Processing helix chain 'E' and resid 376 through 381 Processing helix chain 'E' and resid 382 through 384 No H-bonds generated for 'chain 'E' and resid 382 through 384' Processing helix chain 'E' and resid 385 through 387 No H-bonds generated for 'chain 'E' and resid 385 through 387' Processing helix chain 'E' and resid 388 through 398 removed outlier: 3.882A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 435 removed outlier: 3.710A pdb=" N LYS E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 451 removed outlier: 3.852A pdb=" N LYS E 450 " --> pdb=" O ASP E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 469 Processing helix chain 'E' and resid 476 through 489 removed outlier: 3.775A pdb=" N CYS E 489 " --> pdb=" O THR E 485 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 521 Processing helix chain 'E' and resid 541 through 547 Processing helix chain 'E' and resid 570 through 578 Processing helix chain 'E' and resid 614 through 619 removed outlier: 3.712A pdb=" N ARG E 619 " --> pdb=" O ASN E 615 " (cutoff:3.500A) Processing helix chain 'E' and resid 632 through 636 Processing helix chain 'E' and resid 656 through 661 removed outlier: 3.969A pdb=" N GLN E 660 " --> pdb=" O ASP E 656 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN E 661 " --> pdb=" O GLY E 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 656 through 661' Processing helix chain 'E' and resid 664 through 680 removed outlier: 3.572A pdb=" N PHE E 668 " --> pdb=" O TYR E 664 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS E 678 " --> pdb=" O LYS E 674 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR E 679 " --> pdb=" O TRP E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 689 through 692 removed outlier: 3.798A pdb=" N GLU E 692 " --> pdb=" O THR E 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 689 through 692' Processing helix chain 'E' and resid 693 through 700 Processing helix chain 'B' and resid 324 through 336 removed outlier: 3.806A pdb=" N ALA B 330 " --> pdb=" O LEU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 371 removed outlier: 3.670A pdb=" N LEU B 369 " --> pdb=" O THR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 375 removed outlier: 3.691A pdb=" N LEU B 375 " --> pdb=" O ARG B 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 372 through 375' Processing helix chain 'B' and resid 376 through 380 Processing helix chain 'B' and resid 385 through 390 Processing helix chain 'B' and resid 390 through 398 Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.807A pdb=" N LYS B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 451 removed outlier: 3.521A pdb=" N PHE B 451 " --> pdb=" O ASP B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 469 Processing helix chain 'B' and resid 475 through 488 removed outlier: 3.522A pdb=" N ARG B 479 " --> pdb=" O ASN B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 541 through 547 Processing helix chain 'B' and resid 570 through 578 removed outlier: 3.804A pdb=" N ILE B 574 " --> pdb=" O ARG B 570 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 636 Processing helix chain 'B' and resid 656 through 661 removed outlier: 3.865A pdb=" N GLN B 660 " --> pdb=" O ASP B 656 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN B 661 " --> pdb=" O GLY B 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 656 through 661' Processing helix chain 'B' and resid 664 through 680 removed outlier: 3.667A pdb=" N LYS B 678 " --> pdb=" O LYS B 674 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR B 679 " --> pdb=" O TRP B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 700 Processing sheet with id=AA1, first strand: chain 'D' and resid 339 through 341 Processing sheet with id=AA2, first strand: chain 'D' and resid 412 through 415 Processing sheet with id=AA3, first strand: chain 'D' and resid 525 through 527 removed outlier: 6.613A pdb=" N VAL D 525 " --> pdb=" O PHE D 554 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LEU D 498 " --> pdb=" O ALA D 622 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 581 through 583 Processing sheet with id=AA5, first strand: chain 'D' and resid 629 through 631 removed outlier: 6.589A pdb=" N HIS D 629 " --> pdb=" O LYS D 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 339 through 341 Processing sheet with id=AA7, first strand: chain 'C' and resid 412 through 415 Processing sheet with id=AA8, first strand: chain 'C' and resid 525 through 527 removed outlier: 5.924A pdb=" N LEU C 498 " --> pdb=" O ALA C 622 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 581 through 582 Processing sheet with id=AB1, first strand: chain 'C' and resid 628 through 631 removed outlier: 6.167A pdb=" N HIS C 629 " --> pdb=" O LYS C 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'F' and resid 339 through 341 removed outlier: 3.582A pdb=" N ILE F 351 " --> pdb=" O SER F 354 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 412 through 415 Processing sheet with id=AB4, first strand: chain 'F' and resid 552 through 555 Processing sheet with id=AB5, first strand: chain 'A' and resid 339 through 341 Processing sheet with id=AB6, first strand: chain 'A' and resid 412 through 415 Processing sheet with id=AB7, first strand: chain 'A' and resid 525 through 526 removed outlier: 5.991A pdb=" N LEU A 498 " --> pdb=" O ALA A 622 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 629 through 631 removed outlier: 6.376A pdb=" N HIS A 629 " --> pdb=" O LYS A 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 339 through 341 Processing sheet with id=AC1, first strand: chain 'E' and resid 412 through 415 Processing sheet with id=AC2, first strand: chain 'E' and resid 525 through 526 removed outlier: 7.277A pdb=" N THR E 499 " --> pdb=" O ILE E 602 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU E 498 " --> pdb=" O ALA E 622 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 581 through 583 Processing sheet with id=AC4, first strand: chain 'E' and resid 628 through 631 Processing sheet with id=AC5, first strand: chain 'B' and resid 339 through 341 Processing sheet with id=AC6, first strand: chain 'B' and resid 412 through 415 removed outlier: 3.629A pdb=" N MET B 426 " --> pdb=" O ASP B 421 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 525 through 527 removed outlier: 6.430A pdb=" N VAL B 553 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR B 499 " --> pdb=" O ILE B 602 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 581 through 583 Processing sheet with id=AC9, first strand: chain 'B' and resid 629 through 631 removed outlier: 6.049A pdb=" N HIS B 629 " --> pdb=" O LYS B 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 553 hydrogen bonds defined for protein. 1548 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: 5.68 Time building geometry restraints manager: 6.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5469 1.34 - 1.46: 2861 1.46 - 1.58: 9104 1.58 - 1.70: 27 1.70 - 1.82: 133 Bond restraints: 17594 Sorted by residual: bond pdb=" N GLU A 361 " pdb=" CA GLU A 361 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.25e-02 6.40e+03 7.50e+00 bond pdb=" N GLU A 360 " pdb=" CA GLU A 360 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.10e-02 8.26e+03 7.39e+00 bond pdb=" N GLU B 691 " pdb=" CA GLU B 691 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.43e+00 bond pdb=" N THR B 689 " pdb=" CA THR B 689 " ideal model delta sigma weight residual 1.464 1.488 -0.025 9.80e-03 1.04e+04 6.27e+00 bond pdb=" N GLU C 360 " pdb=" CA GLU C 360 " ideal model delta sigma weight residual 1.455 1.487 -0.033 1.37e-02 5.33e+03 5.63e+00 ... (remaining 17589 not shown) Histogram of bond angle deviations from ideal: 98.71 - 106.95: 534 106.95 - 115.19: 10721 115.19 - 123.44: 12011 123.44 - 131.68: 480 131.68 - 139.92: 36 Bond angle restraints: 23782 Sorted by residual: angle pdb=" N ILE A 371 " pdb=" CA ILE A 371 " pdb=" C ILE A 371 " ideal model delta sigma weight residual 112.98 106.83 6.15 1.25e+00 6.40e-01 2.42e+01 angle pdb=" N ILE E 371 " pdb=" CA ILE E 371 " pdb=" C ILE E 371 " ideal model delta sigma weight residual 112.98 107.35 5.63 1.25e+00 6.40e-01 2.03e+01 angle pdb=" N ILE D 371 " pdb=" CA ILE D 371 " pdb=" C ILE D 371 " ideal model delta sigma weight residual 112.98 107.67 5.31 1.25e+00 6.40e-01 1.80e+01 angle pdb=" CA PRO E 540 " pdb=" N PRO E 540 " pdb=" CD PRO E 540 " ideal model delta sigma weight residual 112.00 106.16 5.84 1.40e+00 5.10e-01 1.74e+01 angle pdb=" N GLU A 360 " pdb=" CA GLU A 360 " pdb=" C GLU A 360 " ideal model delta sigma weight residual 114.16 108.17 5.99 1.48e+00 4.57e-01 1.64e+01 ... (remaining 23777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 9093 17.98 - 35.96: 1341 35.96 - 53.94: 308 53.94 - 71.91: 61 71.91 - 89.89: 25 Dihedral angle restraints: 10828 sinusoidal: 4630 harmonic: 6198 Sorted by residual: dihedral pdb=" CA SER B 359 " pdb=" C SER B 359 " pdb=" N GLU B 360 " pdb=" CA GLU B 360 " ideal model delta harmonic sigma weight residual 180.00 158.76 21.24 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA ALA E 598 " pdb=" C ALA E 598 " pdb=" N THR E 599 " pdb=" CA THR E 599 " ideal model delta harmonic sigma weight residual 180.00 160.22 19.78 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA ALA B 598 " pdb=" C ALA B 598 " pdb=" N THR B 599 " pdb=" CA THR B 599 " ideal model delta harmonic sigma weight residual 180.00 161.65 18.35 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 10825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1853 0.039 - 0.079: 596 0.079 - 0.118: 186 0.118 - 0.158: 17 0.158 - 0.197: 2 Chirality restraints: 2654 Sorted by residual: chirality pdb=" CB THR A 689 " pdb=" CA THR A 689 " pdb=" OG1 THR A 689 " pdb=" CG2 THR A 689 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CB THR C 533 " pdb=" CA THR C 533 " pdb=" OG1 THR C 533 " pdb=" CG2 THR C 533 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.46e-01 chirality pdb=" CA ILE A 602 " pdb=" N ILE A 602 " pdb=" C ILE A 602 " pdb=" CB ILE A 602 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 2651 not shown) Planarity restraints: 3003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 361 " -0.072 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO D 362 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO D 362 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO D 362 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 675 " 0.024 2.00e-02 2.50e+03 1.92e-02 9.17e+00 pdb=" CG TRP A 675 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A 675 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 675 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 675 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 675 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 675 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 675 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 675 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 675 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 524 " 0.001 2.00e-02 2.50e+03 1.88e-02 6.19e+00 pdb=" CG PHE A 524 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 524 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 PHE A 524 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 524 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 PHE A 524 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 524 " 0.001 2.00e-02 2.50e+03 ... (remaining 3000 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 152 2.54 - 3.13: 12957 3.13 - 3.72: 26444 3.72 - 4.31: 36806 4.31 - 4.90: 62425 Nonbonded interactions: 138784 Sorted by model distance: nonbonded pdb=" O2B ATP D1001 " pdb="MG MG D1002 " model vdw 1.956 2.170 nonbonded pdb=" O2B ATP A1001 " pdb="MG MG A1002 " model vdw 1.992 2.170 nonbonded pdb=" O2B ATP B1001 " pdb="MG MG B1002 " model vdw 2.029 2.170 nonbonded pdb=" OG SER C 510 " pdb="MG MG C1002 " model vdw 2.046 2.170 nonbonded pdb=" OG SER E 510 " pdb="MG MG E1002 " model vdw 2.064 2.170 ... (remaining 138779 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 323 through 532 or resid 543 through 559 or resid 570 thro \ ugh 582 or resid 594 through 608 or resid 617 through 690 or resid 1001 through \ 1002)) selection = (chain 'C' and (resid 323 through 532 or resid 543 through 559 or resid 570 thro \ ugh 582 or resid 594 through 608 or resid 617 through 690 or resid 1001 through \ 1002)) selection = (chain 'D' and (resid 323 through 532 or resid 543 through 559 or resid 570 thro \ ugh 582 or resid 594 through 608 or resid 617 through 690 or resid 1001 through \ 1002)) selection = (chain 'E' and (resid 323 through 532 or resid 543 through 559 or resid 570 thro \ ugh 582 or resid 594 through 608 or resid 617 through 690 or resid 1001 through \ 1002)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 44.860 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.090 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 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 : 0.003 0.104 17594 Z= 0.189 Angle : 0.610 11.182 23782 Z= 0.326 Chirality : 0.042 0.197 2654 Planarity : 0.004 0.110 3003 Dihedral : 17.841 89.894 6800 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 0.62 % Allowed : 27.39 % Favored : 71.99 % 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: -1.52 (0.19), residues: 2080 helix: 0.08 (0.20), residues: 738 sheet: -1.36 (0.28), residues: 356 loop : -1.70 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP A 675 HIS 0.011 0.001 HIS E 629 PHE 0.036 0.001 PHE A 524 TYR 0.027 0.001 TYR F 670 ARG 0.004 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 242 time to evaluate : 1.928 Fit side-chains revert: symmetry clash REVERT: F 554 PHE cc_start: 0.6005 (p90) cc_final: 0.5775 (p90) outliers start: 12 outliers final: 3 residues processed: 250 average time/residue: 0.2842 time to fit residues: 107.1647 Evaluate side-chains 239 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 236 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain B residue 346 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.9980 chunk 156 optimal weight: 9.9990 chunk 87 optimal weight: 20.0000 chunk 53 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 475 ASN F 328 ASN ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.0709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17594 Z= 0.182 Angle : 0.537 8.023 23782 Z= 0.272 Chirality : 0.042 0.229 2654 Planarity : 0.004 0.078 3003 Dihedral : 9.779 89.274 2469 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 3.07 % Allowed : 25.31 % Favored : 71.62 % 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: -1.52 (0.18), residues: 2080 helix: 0.13 (0.19), residues: 771 sheet: -1.34 (0.29), residues: 352 loop : -1.80 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 675 HIS 0.009 0.001 HIS E 629 PHE 0.022 0.001 PHE A 524 TYR 0.014 0.001 TYR D 482 ARG 0.003 0.000 ARG E 570 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 242 time to evaluate : 1.942 Fit side-chains revert: symmetry clash REVERT: D 447 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7856 (t70) REVERT: D 649 LYS cc_start: 0.8158 (mmtt) cc_final: 0.7894 (mppt) REVERT: F 523 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7396 (pp) REVERT: F 554 PHE cc_start: 0.5866 (p90) cc_final: 0.5491 (p90) REVERT: A 474 GLU cc_start: 0.6461 (tp30) cc_final: 0.6161 (tp30) REVERT: A 649 LYS cc_start: 0.8459 (tppt) cc_final: 0.7992 (tppp) REVERT: B 617 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7826 (mt) outliers start: 59 outliers final: 28 residues processed: 288 average time/residue: 0.2680 time to fit residues: 118.6054 Evaluate side-chains 261 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 230 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 385 CYS Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 618 MET Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 501 PHE Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 650 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 156 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 203 optimal weight: 0.0670 chunk 167 optimal weight: 2.9990 chunk 186 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 overall best weight: 1.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 593 ASN A 352 ASN ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17594 Z= 0.297 Angle : 0.602 8.657 23782 Z= 0.300 Chirality : 0.044 0.259 2654 Planarity : 0.004 0.064 3003 Dihedral : 9.289 89.347 2465 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 4.52 % Allowed : 24.64 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.18), residues: 2080 helix: -0.09 (0.19), residues: 786 sheet: -1.49 (0.28), residues: 370 loop : -1.82 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 675 HIS 0.011 0.001 HIS B 629 PHE 0.014 0.001 PHE D 444 TYR 0.019 0.001 TYR D 482 ARG 0.004 0.000 ARG D 372 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 232 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 447 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.7939 (t70) REVERT: D 649 LYS cc_start: 0.8196 (mmtt) cc_final: 0.7994 (mppt) REVERT: C 501 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.8096 (m-10) REVERT: F 523 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7314 (pp) REVERT: F 554 PHE cc_start: 0.6040 (p90) cc_final: 0.5820 (p90) REVERT: A 526 GLU cc_start: 0.7677 (pm20) cc_final: 0.7433 (pm20) REVERT: E 363 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8798 (mp) REVERT: E 576 LYS cc_start: 0.8621 (mmtt) cc_final: 0.8085 (mttm) outliers start: 87 outliers final: 62 residues processed: 301 average time/residue: 0.2847 time to fit residues: 130.2863 Evaluate side-chains 288 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 222 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 385 CYS Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain D residue 618 MET Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 653 GLU Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 501 PHE Chi-restraints excluded: chain C residue 523 LEU Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 585 ARG Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 520 ILE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 553 VAL Chi-restraints excluded: chain F residue 573 ASN Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 351 ILE Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 501 PHE Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 614 ASP Chi-restraints excluded: chain E residue 615 ASN Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 593 ASN Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 681 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 188 optimal weight: 3.9990 chunk 200 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 179 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 324 ASN ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 ASN ** 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: 0.7780 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17594 Z= 0.171 Angle : 0.526 10.416 23782 Z= 0.263 Chirality : 0.042 0.183 2654 Planarity : 0.004 0.060 3003 Dihedral : 8.553 87.871 2465 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 3.64 % Allowed : 26.04 % Favored : 70.32 % 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: -1.40 (0.18), residues: 2080 helix: 0.21 (0.19), residues: 782 sheet: -1.38 (0.28), residues: 361 loop : -1.69 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 675 HIS 0.010 0.001 HIS E 629 PHE 0.021 0.001 PHE F 524 TYR 0.015 0.001 TYR A 482 ARG 0.003 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 232 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 447 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.7864 (t70) REVERT: D 533 THR cc_start: 0.8205 (OUTLIER) cc_final: 0.7961 (t) REVERT: D 649 LYS cc_start: 0.8185 (mmtt) cc_final: 0.7955 (mptt) REVERT: C 335 ASP cc_start: 0.7472 (t70) cc_final: 0.6924 (m-30) REVERT: F 523 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.7063 (pp) REVERT: A 524 PHE cc_start: 0.7602 (t80) cc_final: 0.7238 (t80) REVERT: E 558 LEU cc_start: 0.6616 (OUTLIER) cc_final: 0.6142 (mp) REVERT: E 576 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8294 (mtpp) outliers start: 70 outliers final: 42 residues processed: 288 average time/residue: 0.2736 time to fit residues: 120.8597 Evaluate side-chains 268 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 221 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 385 CYS Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 618 MET Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 653 GLU Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 502 PHE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain E residue 488 SER Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 501 PHE Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 576 LYS Chi-restraints excluded: chain E residue 615 ASN Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 593 ASN Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 650 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 179 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 358 ASN ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 ASN ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17594 Z= 0.199 Angle : 0.544 13.165 23782 Z= 0.270 Chirality : 0.042 0.157 2654 Planarity : 0.004 0.057 3003 Dihedral : 8.358 89.123 2465 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 4.31 % Allowed : 25.21 % Favored : 70.48 % 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: -1.32 (0.19), residues: 2080 helix: 0.29 (0.19), residues: 782 sheet: -1.34 (0.28), residues: 364 loop : -1.65 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 350 HIS 0.010 0.001 HIS E 629 PHE 0.013 0.001 PHE F 501 TYR 0.016 0.001 TYR D 482 ARG 0.004 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 229 time to evaluate : 2.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 360 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6987 (pt0) REVERT: D 447 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.7905 (t70) REVERT: D 533 THR cc_start: 0.8195 (OUTLIER) cc_final: 0.7900 (t) REVERT: D 649 LYS cc_start: 0.8193 (mmtt) cc_final: 0.7964 (mptt) REVERT: C 335 ASP cc_start: 0.7494 (t70) cc_final: 0.6910 (m-30) REVERT: F 523 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.7114 (pp) REVERT: F 618 MET cc_start: 0.6563 (mtt) cc_final: 0.5996 (mmp) REVERT: E 554 PHE cc_start: 0.7620 (OUTLIER) cc_final: 0.6895 (m-80) REVERT: E 558 LEU cc_start: 0.6622 (OUTLIER) cc_final: 0.6144 (mp) REVERT: E 576 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8309 (mtpp) outliers start: 83 outliers final: 58 residues processed: 296 average time/residue: 0.2663 time to fit residues: 121.7935 Evaluate side-chains 289 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 224 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 385 CYS Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain D residue 618 MET Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 653 GLU Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 520 ILE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 573 ASN Chi-restraints excluded: chain F residue 664 TYR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 502 PHE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain E residue 351 ILE Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain E residue 488 SER Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 554 PHE Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 576 LYS Chi-restraints excluded: chain E residue 615 ASN Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 534 ASP Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 593 ASN Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 650 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.965 > 50: distance: 101 - 106: 5.552 distance: 106 - 107: 12.438 distance: 107 - 108: 8.885 distance: 107 - 110: 12.602 distance: 108 - 109: 24.172 distance: 108 - 111: 8.655 distance: 111 - 112: 21.184 distance: 112 - 113: 18.078 distance: 112 - 115: 18.971 distance: 113 - 114: 35.953 distance: 113 - 118: 15.638 distance: 115 - 116: 38.185 distance: 115 - 117: 25.683 distance: 118 - 119: 7.827 distance: 119 - 120: 18.955 distance: 119 - 122: 10.292 distance: 120 - 121: 16.734 distance: 120 - 125: 16.027 distance: 122 - 123: 32.397 distance: 122 - 124: 15.119 distance: 125 - 126: 19.969 distance: 126 - 127: 13.405 distance: 126 - 129: 11.128 distance: 127 - 128: 7.649 distance: 127 - 136: 12.099 distance: 129 - 130: 21.465 distance: 130 - 131: 12.679 distance: 131 - 132: 12.799 distance: 132 - 133: 4.804 distance: 133 - 134: 7.632 distance: 136 - 137: 19.018 distance: 137 - 138: 21.816 distance: 137 - 140: 23.122 distance: 138 - 139: 21.106 distance: 138 - 147: 27.786 distance: 140 - 141: 8.924 distance: 141 - 142: 9.167 distance: 141 - 143: 14.604 distance: 142 - 144: 16.349 distance: 143 - 145: 23.577 distance: 144 - 146: 8.791 distance: 145 - 146: 19.433 distance: 147 - 148: 9.913 distance: 148 - 149: 36.813 distance: 148 - 151: 15.300 distance: 149 - 150: 13.921 distance: 149 - 158: 24.616 distance: 151 - 152: 28.178 distance: 152 - 153: 36.828 distance: 153 - 154: 29.811 distance: 154 - 155: 10.572 distance: 155 - 156: 13.660 distance: 155 - 157: 13.478 distance: 158 - 159: 9.481 distance: 159 - 160: 27.213 distance: 159 - 162: 9.407 distance: 160 - 161: 18.676 distance: 160 - 165: 30.828 distance: 162 - 163: 14.320 distance: 162 - 164: 21.465 distance: 165 - 166: 11.189 distance: 166 - 167: 15.532 distance: 166 - 169: 10.773 distance: 167 - 168: 9.560 distance: 167 - 175: 14.631 distance: 169 - 170: 15.449 distance: 170 - 171: 15.704 distance: 170 - 172: 8.213 distance: 171 - 173: 18.653 distance: 172 - 174: 22.252 distance: 173 - 174: 12.986 distance: 175 - 176: 6.812 distance: 176 - 177: 8.631 distance: 176 - 179: 4.733 distance: 177 - 178: 8.564 distance: 177 - 186: 11.887 distance: 179 - 180: 10.170 distance: 180 - 181: 5.206 distance: 180 - 182: 10.731 distance: 181 - 183: 10.629 distance: 182 - 184: 17.443 distance: 183 - 185: 12.377 distance: 184 - 185: 11.500 distance: 186 - 187: 4.049 distance: 187 - 188: 32.141 distance: 187 - 190: 20.978 distance: 188 - 189: 59.965 distance: 188 - 192: 29.938 distance: 190 - 191: 28.003