Starting phenix.real_space_refine on Tue Apr 9 19:46:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwe_35055/04_2024/8hwe_35055_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwe_35055/04_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_35055/04_2024/8hwe_35055.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwe_35055/04_2024/8hwe_35055.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwe_35055/04_2024/8hwe_35055_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwe_35055/04_2024/8hwe_35055_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= 0.002 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 9.41, per 1000 atoms: 0.55 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: 6.34 Conformation dependent library (CDL) restraints added in 3.2 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... running ksdssp... Secondary structure from input PDB file: 100 helices and 31 sheets defined 36.6% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.44 Creating SS restraints... Processing helix chain 'D' and resid 325 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 374 removed outlier: 4.550A pdb=" N ILE D 371 " --> pdb=" O ILE D 368 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N HIS D 373 " --> pdb=" O SER D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 379 No H-bonds generated for 'chain 'D' and resid 377 through 379' Processing helix chain 'D' and resid 381 through 384 removed outlier: 3.727A pdb=" N LEU D 384 " --> pdb=" O SER D 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 381 through 384' Processing helix chain 'D' and resid 386 through 398 removed outlier: 3.600A pdb=" N ASP D 398 " --> pdb=" O ALA D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 434 No H-bonds generated for 'chain 'D' and resid 431 through 434' 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 456 through 468 Processing helix chain 'D' and resid 476 through 487 Processing helix chain 'D' and resid 509 through 520 Processing helix chain 'D' and resid 529 through 531 No H-bonds generated for 'chain 'D' and resid 529 through 531' Processing helix chain 'D' and resid 542 through 545 No H-bonds generated for 'chain 'D' and resid 542 through 545' Processing helix chain 'D' and resid 571 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 615 through 620 removed outlier: 3.831A pdb=" N ARG D 619 " --> pdb=" O ASN D 615 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ARG D 620 " --> pdb=" O ALA D 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 615 through 620' Processing helix chain 'D' and resid 633 through 635 No H-bonds generated for 'chain 'D' and resid 633 through 635' Processing helix chain 'D' and resid 637 through 640 No H-bonds generated for 'chain 'D' and resid 637 through 640' Processing helix chain 'D' and resid 657 through 660 No H-bonds generated for 'chain 'D' and resid 657 through 660' Processing helix chain 'D' and resid 665 through 679 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 690 through 692 No H-bonds generated for 'chain 'D' and resid 690 through 692' Processing helix chain 'D' and resid 694 through 699 Processing helix chain 'C' and resid 325 through 335 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 374 removed outlier: 3.740A pdb=" N ILE C 368 " --> pdb=" O THR C 365 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE C 371 " --> pdb=" O ILE C 368 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N HIS C 373 " --> pdb=" O SER C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 379 No H-bonds generated for 'chain 'C' and resid 377 through 379' 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 398 removed outlier: 4.128A pdb=" N THR C 391 " --> pdb=" O ARG C 387 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP C 398 " --> pdb=" O ALA C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 434 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 476 through 487 Processing helix chain 'C' and resid 509 through 520 Processing helix chain 'C' and resid 542 through 546 Processing helix chain 'C' and resid 571 through 577 removed outlier: 3.638A pdb=" N LYS C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 618 No H-bonds generated for 'chain 'C' and resid 615 through 618' Processing helix chain 'C' and resid 633 through 640 removed outlier: 5.051A pdb=" N GLU C 637 " --> pdb=" O SER C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 660 No H-bonds generated for 'chain 'C' and resid 657 through 660' Processing helix chain 'C' and resid 665 through 679 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 690 through 692 No H-bonds generated for 'chain 'C' and resid 690 through 692' Processing helix chain 'C' and resid 694 through 700 Processing helix chain 'F' and resid 325 through 335 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 374 removed outlier: 4.332A pdb=" N ILE F 371 " --> pdb=" O ILE F 368 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS F 373 " --> pdb=" O SER F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 380 No H-bonds generated for 'chain 'F' and resid 377 through 380' Processing helix chain 'F' and resid 386 through 388 No H-bonds generated for 'chain 'F' and resid 386 through 388' Processing helix chain 'F' and resid 390 through 397 Processing helix chain 'F' and resid 431 through 434 No H-bonds generated for 'chain 'F' and resid 431 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 456 through 468 Processing helix chain 'F' and resid 476 through 488 Processing helix chain 'F' and resid 509 through 523 removed outlier: 7.430A pdb=" N ASP F 522 " --> pdb=" O SER F 518 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N LEU F 523 " --> pdb=" O ALA F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 576 No H-bonds generated for 'chain 'F' and resid 573 through 576' Processing helix chain 'F' and resid 615 through 620 removed outlier: 3.730A pdb=" N ARG F 619 " --> pdb=" O ASN F 615 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ARG F 620 " --> pdb=" O ALA F 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 615 through 620' Processing helix chain 'F' and resid 666 through 679 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 325 through 335 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 374 removed outlier: 3.935A pdb=" N ILE A 368 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE A 371 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS A 373 " --> pdb=" O SER A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 391 through 399 Processing helix chain 'A' and resid 430 through 434 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 456 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 544 through 546 No H-bonds generated for 'chain 'A' and resid 544 through 546' Processing helix chain 'A' and resid 571 through 577 removed outlier: 3.633A pdb=" N LYS A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 635 No H-bonds generated for 'chain 'A' and resid 633 through 635' Processing helix chain 'A' and resid 637 through 640 No H-bonds generated for 'chain 'A' and resid 637 through 640' 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 678 removed outlier: 3.889A pdb=" N LYS A 678 " --> pdb=" O LYS A 674 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 335 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 374 removed outlier: 4.028A pdb=" N ILE E 371 " --> pdb=" O ILE E 368 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS E 373 " --> pdb=" O SER E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 383 removed outlier: 4.575A pdb=" N GLU E 382 " --> pdb=" O GLU E 378 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU E 383 " --> pdb=" O TYR E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 399 removed outlier: 4.571A pdb=" N LYS E 390 " --> pdb=" O ARG E 387 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N THR E 391 " --> pdb=" O LYS E 388 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL E 392 " --> pdb=" O ARG E 389 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU E 393 " --> pdb=" O LYS E 390 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP E 398 " --> pdb=" O ASN E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 434 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 Processing helix chain 'E' and resid 477 through 488 Processing helix chain 'E' and resid 509 through 520 Processing helix chain 'E' and resid 542 through 546 Processing helix chain 'E' and resid 571 through 577 Processing helix chain 'E' and resid 615 through 618 No H-bonds generated for 'chain 'E' and resid 615 through 618' Processing helix chain 'E' and resid 633 through 635 No H-bonds generated for 'chain 'E' and resid 633 through 635' Processing helix chain 'E' and resid 657 through 660 No H-bonds generated for 'chain 'E' and resid 657 through 660' Processing helix chain 'E' and resid 665 through 679 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 690 through 692 No H-bonds generated for 'chain 'E' and resid 690 through 692' Processing helix chain 'E' and resid 694 through 699 Processing helix chain 'B' and resid 325 through 335 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 374 removed outlier: 3.809A pdb=" N ILE B 368 " --> pdb=" O THR B 365 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE B 371 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N HIS B 373 " --> pdb=" O SER B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 379 No H-bonds generated for 'chain 'B' and resid 377 through 379' Processing helix chain 'B' and resid 386 through 389 No H-bonds generated for 'chain 'B' and resid 386 through 389' Processing helix chain 'B' and resid 391 through 398 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 542 through 546 Processing helix chain 'B' and resid 571 through 578 removed outlier: 3.660A pdb=" N LYS B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 618 No H-bonds generated for 'chain 'B' and resid 615 through 618' Processing helix chain 'B' and resid 633 through 635 No H-bonds generated for 'chain 'B' and resid 633 through 635' Processing helix chain 'B' and resid 657 through 660 No H-bonds generated for 'chain 'B' and resid 657 through 660' Processing helix chain 'B' and resid 665 through 679 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 694 through 699 Processing sheet with id= A, first strand: chain 'D' and resid 339 through 341 Processing sheet with id= B, first strand: chain 'D' and resid 412 through 415 Processing sheet with id= C, first strand: chain 'D' and resid 621 through 626 removed outlier: 5.910A pdb=" N LEU D 498 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL D 624 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N PHE D 500 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N PHE D 626 " --> pdb=" O PHE D 500 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N PHE D 502 " --> pdb=" O PHE D 626 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE D 600 " --> pdb=" O THR D 499 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N PHE D 501 " --> pdb=" O ILE D 600 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ILE D 602 " --> pdb=" O PHE D 501 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N GLY D 503 " --> pdb=" O ILE D 602 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL D 525 " --> pdb=" O PHE D 554 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 581 through 583 Processing sheet with id= E, first strand: chain 'D' and resid 629 through 631 removed outlier: 3.772A pdb=" N SER D 631 " --> pdb=" O LYS D 649 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 339 through 341 Processing sheet with id= G, first strand: chain 'C' and resid 412 through 415 Processing sheet with id= H, first strand: chain 'C' and resid 498 through 500 Processing sheet with id= I, first strand: chain 'C' and resid 525 through 527 removed outlier: 5.983A pdb=" N THR C 599 " --> pdb=" O VAL C 553 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N CYS C 555 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ILE C 601 " --> pdb=" O CYS C 555 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 581 through 583 Processing sheet with id= K, first strand: chain 'C' and resid 628 through 631 removed outlier: 6.461A pdb=" N LYS C 647 " --> pdb=" O HIS C 629 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N SER C 631 " --> pdb=" O LYS C 647 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LYS C 649 " --> pdb=" O SER C 631 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, 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= M, first strand: chain 'F' and resid 412 through 415 Processing sheet with id= N, first strand: chain 'F' and resid 498 through 500 Processing sheet with id= O, first strand: chain 'F' and resid 552 through 555 removed outlier: 6.135A pdb=" N THR F 599 " --> pdb=" O VAL F 553 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N CYS F 555 " --> pdb=" O THR F 599 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ILE F 601 " --> pdb=" O CYS F 555 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'A' and resid 339 through 341 Processing sheet with id= Q, first strand: chain 'A' and resid 412 through 415 Processing sheet with id= R, first strand: chain 'A' and resid 498 through 500 Processing sheet with id= S, first strand: chain 'A' and resid 552 through 555 removed outlier: 5.758A pdb=" N THR A 599 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N CYS A 555 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE A 601 " --> pdb=" O CYS A 555 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'A' and resid 629 through 631 Processing sheet with id= U, first strand: chain 'E' and resid 339 through 341 Processing sheet with id= V, first strand: chain 'E' and resid 412 through 415 Processing sheet with id= W, first strand: chain 'E' and resid 498 through 500 Processing sheet with id= X, first strand: chain 'E' and resid 552 through 555 removed outlier: 5.894A pdb=" N THR E 599 " --> pdb=" O VAL E 553 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N CYS E 555 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE E 601 " --> pdb=" O CYS E 555 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'E' and resid 581 through 583 Processing sheet with id= Z, first strand: chain 'E' and resid 628 through 631 removed outlier: 6.377A pdb=" N LYS E 647 " --> pdb=" O HIS E 629 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N SER E 631 " --> pdb=" O LYS E 647 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LYS E 649 " --> pdb=" O SER E 631 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'B' and resid 339 through 341 Processing sheet with id= AB, 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= AC, first strand: chain 'B' and resid 621 through 623 removed outlier: 6.058A pdb=" N LEU B 498 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE B 600 " --> pdb=" O THR B 499 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL B 525 " --> pdb=" O PHE B 554 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'B' and resid 581 through 583 Processing sheet with id= AE, first strand: chain 'B' and resid 629 through 631 427 hydrogen bonds defined for protein. 1083 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: 5.10 Time building geometry restraints manager: 6.96 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: 153 2.54 - 3.13: 13020 3.13 - 3.72: 26536 3.72 - 4.31: 37071 4.31 - 4.90: 62508 Nonbonded interactions: 139288 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 139283 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 4.550 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 47.370 Find NCS groups from input model: 1.120 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: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.910 ------------------------------------------------------------------------------- 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= 0.199 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 : 2.074 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: 0.3166 time to fit residues: 119.4177 Evaluate side-chains 239 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 236 time to evaluate : 2.182 ------------------------------------------------------------------------------- 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: 0.5980 chunk 156 optimal weight: 10.0000 chunk 87 optimal weight: 0.0270 chunk 53 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 83 optimal weight: 10.0000 chunk 162 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 187 optimal weight: 0.9980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 632 GLN ** 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: 0.7744 moved from start: 0.0499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 17594 Z= 0.148 Angle : 0.507 8.141 23782 Z= 0.253 Chirality : 0.041 0.235 2654 Planarity : 0.004 0.077 3003 Dihedral : 9.735 89.420 2469 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 2.29 % Allowed : 25.68 % Favored : 72.04 % 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 (0.19), residues: 2080 helix: 0.27 (0.20), residues: 743 sheet: -1.32 (0.29), residues: 352 loop : -1.66 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 675 HIS 0.009 0.001 HIS E 629 PHE 0.020 0.001 PHE A 524 TYR 0.014 0.001 TYR A 482 ARG 0.003 0.000 ARG A 332 *********************** 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 290 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 246 time to evaluate : 2.132 Fit side-chains revert: symmetry clash REVERT: D 649 LYS cc_start: 0.8138 (mmtt) cc_final: 0.7886 (mppt) REVERT: F 523 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7428 (pp) REVERT: F 554 PHE cc_start: 0.5737 (p90) cc_final: 0.5251 (p90) REVERT: A 474 GLU cc_start: 0.6447 (tp30) cc_final: 0.6139 (tp30) outliers start: 44 outliers final: 22 residues processed: 283 average time/residue: 0.2860 time to fit residues: 123.1376 Evaluate side-chains 257 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 234 time to evaluate : 2.172 ------------------------------------------------------------------------------- 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 683 ILE 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 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 523 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 361 GLU 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 465 ILE Chi-restraints excluded: chain B residue 544 ILE 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: 9.9990 chunk 128 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 203 optimal weight: 0.3980 chunk 167 optimal weight: 2.9990 chunk 186 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 593 ASN C 632 GLN A 352 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 B 546 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17594 Z= 0.307 Angle : 0.588 8.616 23782 Z= 0.292 Chirality : 0.044 0.237 2654 Planarity : 0.004 0.061 3003 Dihedral : 9.294 89.982 2465 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 4.47 % Allowed : 24.48 % Favored : 71.05 % 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: -1.56 (0.18), residues: 2080 helix: -0.02 (0.19), residues: 743 sheet: -1.37 (0.28), residues: 364 loop : -1.66 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 675 HIS 0.009 0.001 HIS E 629 PHE 0.015 0.002 PHE D 444 TYR 0.020 0.001 TYR D 482 ARG 0.005 0.000 ARG D 389 *********************** 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: 86 poor density : 233 time to evaluate : 2.159 Fit side-chains revert: symmetry clash REVERT: D 447 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.8011 (t70) REVERT: D 649 LYS cc_start: 0.8205 (mmtt) cc_final: 0.7988 (mptt) REVERT: F 523 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7265 (pp) REVERT: F 550 LYS cc_start: 0.6813 (mmtm) cc_final: 0.6594 (mmtm) REVERT: F 554 PHE cc_start: 0.5743 (p90) cc_final: 0.5098 (p90) REVERT: A 649 LYS cc_start: 0.8469 (tppt) cc_final: 0.8078 (tppp) REVERT: E 576 LYS cc_start: 0.8486 (mmtt) cc_final: 0.8057 (mttm) outliers start: 86 outliers final: 58 residues processed: 301 average time/residue: 0.2885 time to fit residues: 132.5901 Evaluate side-chains 282 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 222 time to evaluate : 2.092 ------------------------------------------------------------------------------- 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 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 571 SER Chi-restraints excluded: chain D residue 592 ILE 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 363 LEU 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 494 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 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 501 PHE 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 335 ASP Chi-restraints excluded: chain A residue 392 VAL 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 624 VAL Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 351 ILE 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 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 544 ILE Chi-restraints excluded: chain B residue 593 ASN Chi-restraints excluded: chain B residue 624 VAL 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: 0.9980 chunk 141 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 chunk 126 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 179 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 632 GLN ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN B 546 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1004 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= 0.212 Angle : 0.533 9.983 23782 Z= 0.265 Chirality : 0.042 0.188 2654 Planarity : 0.004 0.059 3003 Dihedral : 8.642 87.067 2465 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 4.16 % Allowed : 25.52 % 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: -1.39 (0.19), residues: 2080 helix: 0.16 (0.20), residues: 727 sheet: -1.37 (0.29), residues: 349 loop : -1.54 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 350 HIS 0.009 0.001 HIS E 629 PHE 0.019 0.001 PHE F 524 TYR 0.017 0.001 TYR D 482 ARG 0.004 0.000 ARG A 332 *********************** 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 308 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 228 time to evaluate : 2.169 Fit side-chains revert: symmetry clash REVERT: D 447 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.7931 (t70) REVERT: D 649 LYS cc_start: 0.8202 (mmtt) cc_final: 0.7919 (mppt) REVERT: F 523 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.7109 (pp) REVERT: F 550 LYS cc_start: 0.6792 (mmtm) cc_final: 0.6543 (mmtm) REVERT: A 371 ILE cc_start: 0.9077 (tt) cc_final: 0.8875 (tt) REVERT: A 602 ILE cc_start: 0.7459 (mm) cc_final: 0.7064 (mt) REVERT: E 558 LEU cc_start: 0.6612 (OUTLIER) cc_final: 0.6138 (mp) REVERT: E 576 LYS cc_start: 0.8489 (mmtt) cc_final: 0.8193 (mtpp) outliers start: 80 outliers final: 50 residues processed: 290 average time/residue: 0.2833 time to fit residues: 127.3669 Evaluate side-chains 279 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 226 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 558 LEU Chi-restraints excluded: chain D residue 571 SER Chi-restraints excluded: chain D residue 592 ILE 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 371 ILE 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 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 501 PHE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 553 VAL Chi-restraints excluded: chain F residue 664 TYR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 471 LEU 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 346 ASP 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 558 LEU 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 544 ILE 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 681 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 148 optimal weight: 8.9990 chunk 82 optimal weight: 0.8980 chunk 170 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 179 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 358 ASN A 374 GLN ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN B 546 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17594 Z= 0.171 Angle : 0.515 10.519 23782 Z= 0.256 Chirality : 0.041 0.160 2654 Planarity : 0.003 0.052 3003 Dihedral : 8.271 87.087 2463 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 4.21 % Allowed : 24.90 % Favored : 70.89 % 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: -1.22 (0.19), residues: 2080 helix: 0.36 (0.20), residues: 723 sheet: -1.30 (0.29), residues: 352 loop : -1.46 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 350 HIS 0.010 0.001 HIS E 629 PHE 0.015 0.001 PHE F 524 TYR 0.015 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 319 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 238 time to evaluate : 2.105 Fit side-chains revert: symmetry clash REVERT: D 447 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7967 (t70) REVERT: D 649 LYS cc_start: 0.8189 (mmtt) cc_final: 0.7962 (mptt) REVERT: F 523 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.7064 (pp) REVERT: A 602 ILE cc_start: 0.7552 (mm) cc_final: 0.7173 (mt) REVERT: A 649 LYS cc_start: 0.8472 (tppt) cc_final: 0.8097 (tppp) REVERT: E 558 LEU cc_start: 0.6596 (OUTLIER) cc_final: 0.6121 (mp) REVERT: E 576 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8098 (mttt) REVERT: B 334 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8533 (mm) outliers start: 81 outliers final: 59 residues processed: 303 average time/residue: 0.2884 time to fit residues: 133.8859 Evaluate side-chains 294 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 230 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 370 SER 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 471 LEU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 571 SER Chi-restraints excluded: chain D residue 592 ILE 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 363 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 371 ILE 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 523 LEU Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 558 LEU 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 479 ARG Chi-restraints excluded: chain F residue 501 PHE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain F residue 573 ASN Chi-restraints excluded: chain F residue 664 TYR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 502 PHE 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 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 558 LEU Chi-restraints excluded: chain E residue 576 LYS Chi-restraints excluded: chain B residue 334 LEU 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 558 LEU Chi-restraints excluded: chain B residue 593 ASN Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 681 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 1.9990 chunk 180 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 166 optimal weight: 0.6980 chunk 92 optimal weight: 6.9990 chunk 16 optimal weight: 0.0970 chunk 66 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 358 ASN F 328 ASN ** A 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN B 546 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17594 Z= 0.171 Angle : 0.525 10.525 23782 Z= 0.259 Chirality : 0.041 0.204 2654 Planarity : 0.004 0.053 3003 Dihedral : 8.110 87.146 2463 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 4.52 % Allowed : 25.10 % Favored : 70.37 % 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: -1.13 (0.19), residues: 2080 helix: 0.45 (0.20), residues: 717 sheet: -1.28 (0.29), residues: 352 loop : -1.40 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 350 HIS 0.009 0.001 HIS E 629 PHE 0.016 0.001 PHE F 554 TYR 0.015 0.001 TYR D 482 ARG 0.006 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 6 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 324 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 237 time to evaluate : 2.025 Fit side-chains revert: symmetry clash REVERT: D 360 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7152 (pt0) REVERT: D 447 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7957 (t70) REVERT: F 523 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7192 (pp) REVERT: F 618 MET cc_start: 0.6931 (mmp) cc_final: 0.6340 (mtm) REVERT: A 602 ILE cc_start: 0.7531 (mm) cc_final: 0.7131 (mt) REVERT: A 649 LYS cc_start: 0.8459 (tppt) cc_final: 0.8101 (tppp) REVERT: E 558 LEU cc_start: 0.6580 (OUTLIER) cc_final: 0.6101 (mp) REVERT: E 576 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8123 (mttt) REVERT: B 334 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8554 (mm) REVERT: B 617 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7727 (mt) outliers start: 87 outliers final: 61 residues processed: 309 average time/residue: 0.2744 time to fit residues: 131.3946 Evaluate side-chains 299 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 231 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 370 SER 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 471 LEU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 571 SER Chi-restraints excluded: chain D residue 592 ILE 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 363 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 401 VAL 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 523 LEU 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 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 471 LEU Chi-restraints excluded: chain F residue 501 PHE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain F residue 573 ASN Chi-restraints excluded: chain F residue 664 TYR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 471 LEU 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 346 ASP 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 558 LEU Chi-restraints excluded: chain E residue 576 LYS Chi-restraints excluded: chain E residue 615 ASN Chi-restraints excluded: chain B residue 334 LEU 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 534 ASP Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 593 ASN Chi-restraints excluded: chain B residue 617 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/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-5288/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-5288/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-5288/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-5288/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-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/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-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.8665 > 50: distance: 39 - 43: 12.113 distance: 43 - 44: 16.249 distance: 44 - 45: 9.295 distance: 44 - 47: 9.347 distance: 45 - 46: 15.468 distance: 45 - 51: 18.906 distance: 46 - 76: 41.332 distance: 47 - 48: 5.232 distance: 48 - 49: 13.000 distance: 48 - 50: 17.984 distance: 51 - 52: 26.481 distance: 52 - 53: 30.489 distance: 52 - 55: 19.451 distance: 53 - 54: 37.329 distance: 53 - 59: 17.347 distance: 54 - 85: 35.298 distance: 55 - 56: 16.779 distance: 56 - 57: 9.819 distance: 56 - 58: 19.496 distance: 59 - 60: 26.466 distance: 60 - 61: 14.868 distance: 60 - 63: 39.603 distance: 61 - 62: 27.612 distance: 61 - 67: 37.143 distance: 63 - 64: 16.232 distance: 63 - 65: 10.168 distance: 64 - 66: 20.810 distance: 67 - 68: 24.762 distance: 68 - 69: 22.863 distance: 68 - 71: 39.270 distance: 69 - 70: 23.757 distance: 69 - 76: 11.719 distance: 71 - 72: 14.099 distance: 72 - 73: 12.924 distance: 73 - 74: 19.228 distance: 74 - 75: 31.330 distance: 76 - 77: 27.581 distance: 77 - 78: 10.809 distance: 77 - 80: 13.876 distance: 78 - 79: 22.104 distance: 78 - 85: 16.007 distance: 80 - 81: 17.555 distance: 81 - 82: 37.488 distance: 82 - 83: 22.023 distance: 83 - 84: 27.541 distance: 85 - 86: 4.724 distance: 86 - 87: 23.761 distance: 86 - 89: 14.741 distance: 87 - 88: 27.838 distance: 87 - 93: 15.782 distance: 89 - 90: 13.012 distance: 90 - 91: 20.374 distance: 90 - 92: 25.856 distance: 93 - 94: 6.116 distance: 94 - 95: 9.480 distance: 94 - 97: 18.015 distance: 95 - 96: 26.297 distance: 95 - 100: 16.121 distance: 97 - 98: 33.131 distance: 97 - 99: 16.030 distance: 100 - 101: 18.765 distance: 101 - 102: 15.723 distance: 101 - 104: 28.278 distance: 102 - 103: 16.978 distance: 102 - 109: 14.335 distance: 104 - 105: 28.350 distance: 105 - 106: 30.280 distance: 106 - 107: 13.513 distance: 106 - 108: 20.833 distance: 109 - 110: 15.196 distance: 109 - 115: 36.073 distance: 110 - 111: 35.592 distance: 110 - 113: 22.580 distance: 111 - 112: 30.657 distance: 111 - 116: 13.522 distance: 113 - 114: 9.949 distance: 114 - 115: 22.669 distance: 116 - 117: 12.193 distance: 117 - 118: 10.262 distance: 117 - 120: 37.280 distance: 118 - 119: 8.802 distance: 118 - 122: 26.273 distance: 120 - 121: 13.509