Starting phenix.real_space_refine on Sat Mar 16 14:14:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb8_21586/03_2024/6wb8_21586.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb8_21586/03_2024/6wb8_21586.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb8_21586/03_2024/6wb8_21586.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb8_21586/03_2024/6wb8_21586.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb8_21586/03_2024/6wb8_21586.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb8_21586/03_2024/6wb8_21586.pdb" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 9864 2.51 5 N 2360 2.21 5 O 2596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 251": "NH1" <-> "NH2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "A PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 361": "NH1" <-> "NH2" Residue "A TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 397": "NH1" <-> "NH2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 504": "NH1" <-> "NH2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 654": "NH1" <-> "NH2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 361": "NH1" <-> "NH2" Residue "B TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 397": "NH1" <-> "NH2" Residue "B ARG 399": "NH1" <-> "NH2" Residue "B PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 504": "NH1" <-> "NH2" Residue "B ARG 528": "NH1" <-> "NH2" Residue "B PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 654": "NH1" <-> "NH2" Residue "C ARG 251": "NH1" <-> "NH2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 361": "NH1" <-> "NH2" Residue "C TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 397": "NH1" <-> "NH2" Residue "C ARG 399": "NH1" <-> "NH2" Residue "C PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 504": "NH1" <-> "NH2" Residue "C ARG 528": "NH1" <-> "NH2" Residue "C PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 654": "NH1" <-> "NH2" Residue "D ARG 251": "NH1" <-> "NH2" Residue "D ARG 327": "NH1" <-> "NH2" Residue "D PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 361": "NH1" <-> "NH2" Residue "D TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 397": "NH1" <-> "NH2" Residue "D ARG 399": "NH1" <-> "NH2" Residue "D PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 504": "NH1" <-> "NH2" Residue "D ARG 528": "NH1" <-> "NH2" Residue "D PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 654": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14888 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3680 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'CIS': 5, 'PTRANS': 10, 'TRANS': 447} Chain breaks: 2 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 95 Chain: "B" Number of atoms: 3680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3680 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'CIS': 5, 'PTRANS': 10, 'TRANS': 447} Chain breaks: 2 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 95 Chain: "C" Number of atoms: 3680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3680 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'CIS': 5, 'PTRANS': 10, 'TRANS': 447} Chain breaks: 2 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 95 Chain: "D" Number of atoms: 3680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3680 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'CIS': 5, 'PTRANS': 10, 'TRANS': 447} Chain breaks: 2 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 95 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.65, per 1000 atoms: 0.51 Number of scatterers: 14888 At special positions: 0 Unit cell: (112.35, 112.35, 101.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 2596 8.00 N 2360 7.00 C 9864 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 Links applied NAG-ASN " NAG A 801 " - " ASN A 328 " " NAG A 802 " - " ASN A 362 " " NAG A 803 " - " ASN A 375 " " NAG B 801 " - " ASN B 328 " " NAG B 802 " - " ASN B 362 " " NAG B 803 " - " ASN B 375 " " NAG C 801 " - " ASN C 328 " " NAG C 802 " - " ASN C 362 " " NAG C 803 " - " ASN C 375 " " NAG D 801 " - " ASN D 328 " " NAG D 802 " - " ASN D 362 " " NAG D 803 " - " ASN D 375 " Time building additional restraints: 6.69 Conformation dependent library (CDL) restraints added in 2.7 seconds 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3552 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 12 sheets defined 62.7% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 216 through 242 Processing helix chain 'A' and resid 245 through 258 removed outlier: 3.721A pdb=" N TYR A 249 " --> pdb=" O ASN A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 275 through 285 Processing helix chain 'A' and resid 285 through 292 removed outlier: 3.550A pdb=" N ASP A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 363 through 367 Processing helix chain 'A' and resid 398 through 412 Processing helix chain 'A' and resid 467 through 491 removed outlier: 3.584A pdb=" N PHE A 483 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 484 " --> pdb=" O PHE A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 528 removed outlier: 3.508A pdb=" N VAL A 513 " --> pdb=" O CYS A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 531 No H-bonds generated for 'chain 'A' and resid 529 through 531' Processing helix chain 'A' and resid 532 through 541 Processing helix chain 'A' and resid 548 through 573 removed outlier: 3.669A pdb=" N LEU A 573 " --> pdb=" O VAL A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 removed outlier: 4.661A pdb=" N ASN A 578 " --> pdb=" O LYS A 575 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE A 579 " --> pdb=" O PHE A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 619 removed outlier: 4.362A pdb=" N LYS A 595 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE A 607 " --> pdb=" O MET A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 627 Processing helix chain 'A' and resid 628 through 642 Processing helix chain 'A' and resid 645 through 653 removed outlier: 4.102A pdb=" N ILE A 649 " --> pdb=" O ASN A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 668 Processing helix chain 'A' and resid 670 through 693 removed outlier: 4.008A pdb=" N ASN A 674 " --> pdb=" O PHE A 670 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 242 Processing helix chain 'B' and resid 245 through 258 removed outlier: 3.722A pdb=" N TYR B 249 " --> pdb=" O ASN B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'B' and resid 275 through 285 Processing helix chain 'B' and resid 285 through 292 removed outlier: 3.549A pdb=" N ASP B 289 " --> pdb=" O GLY B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 363 through 367 Processing helix chain 'B' and resid 398 through 412 Processing helix chain 'B' and resid 467 through 491 removed outlier: 3.584A pdb=" N PHE B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 484 " --> pdb=" O PHE B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 528 removed outlier: 3.508A pdb=" N VAL B 513 " --> pdb=" O CYS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 531 No H-bonds generated for 'chain 'B' and resid 529 through 531' Processing helix chain 'B' and resid 532 through 541 Processing helix chain 'B' and resid 548 through 573 removed outlier: 3.669A pdb=" N LEU B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 579 removed outlier: 4.661A pdb=" N ASN B 578 " --> pdb=" O LYS B 575 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE B 579 " --> pdb=" O PHE B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 619 removed outlier: 4.362A pdb=" N LYS B 595 " --> pdb=" O SER B 591 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE B 607 " --> pdb=" O MET B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 627 Processing helix chain 'B' and resid 628 through 642 Processing helix chain 'B' and resid 645 through 653 removed outlier: 4.101A pdb=" N ILE B 649 " --> pdb=" O ASN B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 668 Processing helix chain 'B' and resid 670 through 693 removed outlier: 4.007A pdb=" N ASN B 674 " --> pdb=" O PHE B 670 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 676 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 242 Processing helix chain 'C' and resid 245 through 258 removed outlier: 3.722A pdb=" N TYR C 249 " --> pdb=" O ASN C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 275 through 285 Processing helix chain 'C' and resid 285 through 292 removed outlier: 3.550A pdb=" N ASP C 289 " --> pdb=" O GLY C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 341 Processing helix chain 'C' and resid 363 through 367 Processing helix chain 'C' and resid 398 through 412 Processing helix chain 'C' and resid 467 through 491 removed outlier: 3.584A pdb=" N PHE C 483 " --> pdb=" O ILE C 479 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE C 484 " --> pdb=" O PHE C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 528 removed outlier: 3.508A pdb=" N VAL C 513 " --> pdb=" O CYS C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 531 No H-bonds generated for 'chain 'C' and resid 529 through 531' Processing helix chain 'C' and resid 532 through 541 Processing helix chain 'C' and resid 548 through 573 removed outlier: 3.669A pdb=" N LEU C 573 " --> pdb=" O VAL C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 579 removed outlier: 4.661A pdb=" N ASN C 578 " --> pdb=" O LYS C 575 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE C 579 " --> pdb=" O PHE C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 619 removed outlier: 4.361A pdb=" N LYS C 595 " --> pdb=" O SER C 591 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASP C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE C 607 " --> pdb=" O MET C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 627 Processing helix chain 'C' and resid 628 through 642 Processing helix chain 'C' and resid 645 through 653 removed outlier: 4.101A pdb=" N ILE C 649 " --> pdb=" O ASN C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 668 Processing helix chain 'C' and resid 670 through 693 removed outlier: 4.008A pdb=" N ASN C 674 " --> pdb=" O PHE C 670 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE C 676 " --> pdb=" O LEU C 672 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 242 Processing helix chain 'D' and resid 245 through 258 removed outlier: 3.722A pdb=" N TYR D 249 " --> pdb=" O ASN D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'D' and resid 275 through 285 Processing helix chain 'D' and resid 285 through 292 removed outlier: 3.550A pdb=" N ASP D 289 " --> pdb=" O GLY D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 341 Processing helix chain 'D' and resid 363 through 367 Processing helix chain 'D' and resid 398 through 412 Processing helix chain 'D' and resid 467 through 491 removed outlier: 3.584A pdb=" N PHE D 483 " --> pdb=" O ILE D 479 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE D 484 " --> pdb=" O PHE D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 528 removed outlier: 3.508A pdb=" N VAL D 513 " --> pdb=" O CYS D 509 " (cutoff:3.500A) 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 532 through 541 Processing helix chain 'D' and resid 548 through 573 removed outlier: 3.669A pdb=" N LEU D 573 " --> pdb=" O VAL D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 579 removed outlier: 4.661A pdb=" N ASN D 578 " --> pdb=" O LYS D 575 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE D 579 " --> pdb=" O PHE D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 619 removed outlier: 4.360A pdb=" N LYS D 595 " --> pdb=" O SER D 591 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP D 596 " --> pdb=" O ARG D 592 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE D 607 " --> pdb=" O MET D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 627 Processing helix chain 'D' and resid 628 through 642 Processing helix chain 'D' and resid 645 through 653 removed outlier: 4.101A pdb=" N ILE D 649 " --> pdb=" O ASN D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 668 Processing helix chain 'D' and resid 670 through 693 removed outlier: 4.007A pdb=" N ASN D 674 " --> pdb=" O PHE D 670 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE D 676 " --> pdb=" O LEU D 672 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 308 through 309 Processing sheet with id=AA2, first strand: chain 'A' and resid 308 through 309 removed outlier: 6.355A pdb=" N LEU A 316 " --> pdb=" O TYR A 429 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR A 429 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL A 318 " --> pdb=" O SER A 427 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N SER A 427 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A 421 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 379 through 380 Processing sheet with id=AA4, first strand: chain 'B' and resid 308 through 309 Processing sheet with id=AA5, first strand: chain 'B' and resid 308 through 309 removed outlier: 6.356A pdb=" N LEU B 316 " --> pdb=" O TYR B 429 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR B 429 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL B 318 " --> pdb=" O SER B 427 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N SER B 427 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B 421 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 379 through 380 Processing sheet with id=AA7, first strand: chain 'C' and resid 308 through 309 Processing sheet with id=AA8, first strand: chain 'C' and resid 308 through 309 removed outlier: 6.356A pdb=" N LEU C 316 " --> pdb=" O TYR C 429 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR C 429 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL C 318 " --> pdb=" O SER C 427 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N SER C 427 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA C 421 " --> pdb=" O LEU C 324 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 379 through 380 Processing sheet with id=AB1, first strand: chain 'D' and resid 308 through 309 Processing sheet with id=AB2, first strand: chain 'D' and resid 308 through 309 removed outlier: 6.356A pdb=" N LEU D 316 " --> pdb=" O TYR D 429 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR D 429 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL D 318 " --> pdb=" O SER D 427 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N SER D 427 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA D 421 " --> pdb=" O LEU D 324 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 379 through 380 945 hydrogen bonds defined for protein. 2655 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: 4.82 Time building geometry restraints manager: 7.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.24: 2020 1.24 - 1.38: 4381 1.38 - 1.52: 7660 1.52 - 1.66: 1111 1.66 - 1.81: 104 Bond restraints: 15276 Sorted by residual: bond pdb=" C ALA D 356 " pdb=" N PRO D 357 " ideal model delta sigma weight residual 1.334 1.099 0.235 2.34e-02 1.83e+03 1.01e+02 bond pdb=" C ALA A 356 " pdb=" N PRO A 357 " ideal model delta sigma weight residual 1.334 1.099 0.235 2.34e-02 1.83e+03 1.01e+02 bond pdb=" C ALA C 356 " pdb=" N PRO C 357 " ideal model delta sigma weight residual 1.334 1.099 0.235 2.34e-02 1.83e+03 1.00e+02 bond pdb=" C ALA B 356 " pdb=" N PRO B 357 " ideal model delta sigma weight residual 1.334 1.099 0.235 2.34e-02 1.83e+03 1.00e+02 bond pdb=" CA ILE B 341 " pdb=" C ILE B 341 " ideal model delta sigma weight residual 1.523 1.558 -0.035 1.27e-02 6.20e+03 7.55e+00 ... (remaining 15271 not shown) Histogram of bond angle deviations from ideal: 99.40 - 106.32: 221 106.32 - 113.24: 8533 113.24 - 120.16: 5546 120.16 - 127.08: 6374 127.08 - 134.00: 126 Bond angle restraints: 20800 Sorted by residual: angle pdb=" N ALA B 303 " pdb=" CA ALA B 303 " pdb=" C ALA B 303 " ideal model delta sigma weight residual 111.36 118.20 -6.84 1.09e+00 8.42e-01 3.93e+01 angle pdb=" N ALA C 303 " pdb=" CA ALA C 303 " pdb=" C ALA C 303 " ideal model delta sigma weight residual 111.36 118.19 -6.83 1.09e+00 8.42e-01 3.93e+01 angle pdb=" N ALA A 303 " pdb=" CA ALA A 303 " pdb=" C ALA A 303 " ideal model delta sigma weight residual 111.36 118.19 -6.83 1.09e+00 8.42e-01 3.93e+01 angle pdb=" N ALA D 303 " pdb=" CA ALA D 303 " pdb=" C ALA D 303 " ideal model delta sigma weight residual 111.36 118.16 -6.80 1.09e+00 8.42e-01 3.89e+01 angle pdb=" CA ILE C 341 " pdb=" C ILE C 341 " pdb=" N LYS C 342 " ideal model delta sigma weight residual 116.60 124.56 -7.96 1.45e+00 4.76e-01 3.01e+01 ... (remaining 20795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.09: 8640 16.09 - 32.19: 184 32.19 - 48.28: 56 48.28 - 64.37: 0 64.37 - 80.47: 12 Dihedral angle restraints: 8892 sinusoidal: 3408 harmonic: 5484 Sorted by residual: dihedral pdb=" CA ASN A 432 " pdb=" C ASN A 432 " pdb=" N ILE A 433 " pdb=" CA ILE A 433 " ideal model delta harmonic sigma weight residual 180.00 150.00 30.00 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA ASN C 432 " pdb=" C ASN C 432 " pdb=" N ILE C 433 " pdb=" CA ILE C 433 " ideal model delta harmonic sigma weight residual 180.00 150.04 29.96 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA ASN B 432 " pdb=" C ASN B 432 " pdb=" N ILE B 433 " pdb=" CA ILE B 433 " ideal model delta harmonic sigma weight residual 180.00 150.04 29.96 0 5.00e+00 4.00e-02 3.59e+01 ... (remaining 8889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2345 0.102 - 0.204: 79 0.204 - 0.306: 0 0.306 - 0.409: 0 0.409 - 0.511: 4 Chirality restraints: 2428 Sorted by residual: chirality pdb=" C1 NAG A 801 " pdb=" ND2 ASN A 328 " pdb=" C2 NAG A 801 " pdb=" O5 NAG A 801 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.52e+00 chirality pdb=" C1 NAG C 801 " pdb=" ND2 ASN C 328 " pdb=" C2 NAG C 801 " pdb=" O5 NAG C 801 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.49e+00 chirality pdb=" C1 NAG D 801 " pdb=" ND2 ASN D 328 " pdb=" C2 NAG D 801 " pdb=" O5 NAG D 801 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.48e+00 ... (remaining 2425 not shown) Planarity restraints: 2568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 458 " -0.035 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO D 459 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 459 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 459 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 458 " -0.035 5.00e-02 4.00e+02 5.35e-02 4.59e+00 pdb=" N PRO B 459 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 459 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 459 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 458 " -0.035 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO C 459 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 459 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 459 " -0.029 5.00e-02 4.00e+02 ... (remaining 2565 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 413 2.68 - 3.23: 16979 3.23 - 3.79: 25543 3.79 - 4.34: 32429 4.34 - 4.90: 52321 Nonbonded interactions: 127685 Sorted by model distance: nonbonded pdb=" OH TYR B 227 " pdb=" O VAL B 569 " model vdw 2.124 2.440 nonbonded pdb=" OH TYR D 227 " pdb=" O VAL D 569 " model vdw 2.124 2.440 nonbonded pdb=" OH TYR C 227 " pdb=" O VAL C 569 " model vdw 2.125 2.440 nonbonded pdb=" OH TYR A 227 " pdb=" O VAL A 569 " model vdw 2.125 2.440 nonbonded pdb=" O PRO A 334 " pdb=" NH1 ARG A 338 " model vdw 2.203 2.520 ... (remaining 127680 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' selection = chain 'C' selection = chain 'D' } 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: 0.620 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: 2.930 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 41.980 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.100 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 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 : 0.011 0.235 15276 Z= 0.689 Angle : 0.905 12.660 20800 Z= 0.504 Chirality : 0.051 0.511 2428 Planarity : 0.005 0.054 2556 Dihedral : 8.890 80.467 5340 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.91 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.11 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.16), residues: 1828 helix: -3.19 (0.11), residues: 996 sheet: 0.97 (0.33), residues: 184 loop : -1.92 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP C 380 HIS 0.004 0.002 HIS D 550 PHE 0.018 0.002 PHE A 310 TYR 0.014 0.002 TYR C 386 ARG 0.009 0.001 ARG B 420 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 383 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 675 MET cc_start: 0.8569 (tpt) cc_final: 0.7933 (tpt) REVERT: D 675 MET cc_start: 0.8600 (tpt) cc_final: 0.7693 (tpt) outliers start: 0 outliers final: 0 residues processed: 383 average time/residue: 0.2654 time to fit residues: 147.3235 Evaluate side-chains 221 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 0.0870 chunk 107 optimal weight: 0.9990 chunk 167 optimal weight: 0.9980 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN A 379 HIS A 458 GLN A 543 ASN A 550 HIS A 580 ASN A 636 GLN ** A 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 GLN B 379 HIS B 458 GLN B 543 ASN B 550 HIS B 580 ASN B 636 GLN ** B 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 GLN C 458 GLN C 543 ASN C 550 HIS C 580 ASN C 636 GLN ** C 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 GLN D 379 HIS D 458 GLN D 543 ASN D 550 HIS D 580 ASN D 636 GLN ** D 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15276 Z= 0.207 Angle : 0.642 7.468 20800 Z= 0.355 Chirality : 0.046 0.447 2428 Planarity : 0.004 0.046 2556 Dihedral : 5.414 33.136 2268 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.67 % Favored : 96.12 % Rotamer: Outliers : 1.84 % Allowed : 8.29 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.11 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.18), residues: 1828 helix: 0.79 (0.15), residues: 1040 sheet: 1.16 (0.34), residues: 184 loop : -1.42 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 293 HIS 0.002 0.001 HIS B 379 PHE 0.018 0.002 PHE A 676 TYR 0.019 0.002 TYR A 527 ARG 0.004 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 282 time to evaluate : 1.639 Fit side-chains revert: symmetry clash REVERT: A 675 MET cc_start: 0.7916 (tpt) cc_final: 0.7538 (tpt) REVERT: B 675 MET cc_start: 0.7905 (tpt) cc_final: 0.7556 (tpt) REVERT: C 675 MET cc_start: 0.7832 (tpt) cc_final: 0.7524 (tpt) outliers start: 28 outliers final: 14 residues processed: 291 average time/residue: 0.2924 time to fit residues: 120.7717 Evaluate side-chains 234 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 220 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 677 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 20.0000 chunk 51 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 46 optimal weight: 20.0000 chunk 167 optimal weight: 0.9990 chunk 180 optimal weight: 0.3980 chunk 149 optimal weight: 0.0040 chunk 165 optimal weight: 0.4980 chunk 57 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN B 313 ASN C 313 ASN D 313 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15276 Z= 0.164 Angle : 0.557 7.240 20800 Z= 0.304 Chirality : 0.043 0.406 2428 Planarity : 0.004 0.043 2556 Dihedral : 4.421 26.827 2268 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.39 % Favored : 96.39 % Rotamer: Outliers : 1.12 % Allowed : 13.36 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.11 % 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: 1.26 (0.20), residues: 1828 helix: 2.04 (0.16), residues: 1016 sheet: 1.13 (0.34), residues: 184 loop : -1.34 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 293 HIS 0.002 0.001 HIS B 379 PHE 0.016 0.001 PHE B 676 TYR 0.016 0.001 TYR A 527 ARG 0.004 0.000 ARG B 581 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 266 time to evaluate : 1.747 Fit side-chains revert: symmetry clash REVERT: A 675 MET cc_start: 0.7921 (tpt) cc_final: 0.7607 (tpt) REVERT: B 675 MET cc_start: 0.7938 (tpt) cc_final: 0.7547 (tpt) outliers start: 17 outliers final: 7 residues processed: 275 average time/residue: 0.2725 time to fit residues: 109.9864 Evaluate side-chains 224 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 217 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 228 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 0.5980 chunk 125 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 112 optimal weight: 5.9990 chunk 167 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15276 Z= 0.174 Angle : 0.525 7.153 20800 Z= 0.289 Chirality : 0.042 0.378 2428 Planarity : 0.003 0.044 2556 Dihedral : 4.190 21.341 2268 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.16 % Favored : 95.62 % Rotamer: Outliers : 1.78 % Allowed : 14.41 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.11 % 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: 1.50 (0.20), residues: 1828 helix: 2.30 (0.16), residues: 1004 sheet: 1.04 (0.35), residues: 184 loop : -1.23 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 293 HIS 0.002 0.001 HIS A 379 PHE 0.018 0.001 PHE D 600 TYR 0.015 0.001 TYR A 527 ARG 0.002 0.000 ARG B 581 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 226 time to evaluate : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 675 MET cc_start: 0.8065 (tpt) cc_final: 0.7727 (tpt) REVERT: B 675 MET cc_start: 0.8039 (tpt) cc_final: 0.7721 (tpt) outliers start: 27 outliers final: 11 residues processed: 240 average time/residue: 0.2645 time to fit residues: 93.7677 Evaluate side-chains 230 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 219 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 677 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 132 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 90 optimal weight: 0.8980 chunk 159 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15276 Z= 0.192 Angle : 0.522 7.189 20800 Z= 0.286 Chirality : 0.042 0.362 2428 Planarity : 0.003 0.044 2556 Dihedral : 4.099 18.726 2268 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.56 % Favored : 96.23 % Rotamer: Outliers : 1.78 % Allowed : 14.61 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.11 % 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: 1.38 (0.20), residues: 1828 helix: 2.09 (0.16), residues: 1028 sheet: 0.88 (0.34), residues: 184 loop : -1.15 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 293 HIS 0.002 0.001 HIS D 379 PHE 0.022 0.001 PHE A 469 TYR 0.015 0.001 TYR B 486 ARG 0.002 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 225 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 675 MET cc_start: 0.8042 (tpt) cc_final: 0.7688 (tpt) REVERT: B 675 MET cc_start: 0.8027 (tpt) cc_final: 0.7706 (tpt) outliers start: 27 outliers final: 14 residues processed: 243 average time/residue: 0.2494 time to fit residues: 90.9251 Evaluate side-chains 228 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 214 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 484 ILE Chi-restraints excluded: chain D residue 677 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 178 optimal weight: 0.9980 chunk 147 optimal weight: 0.2980 chunk 82 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 15276 Z= 0.163 Angle : 0.502 7.213 20800 Z= 0.278 Chirality : 0.041 0.352 2428 Planarity : 0.003 0.042 2556 Dihedral : 3.969 18.837 2268 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.83 % Favored : 95.95 % Rotamer: Outliers : 1.38 % Allowed : 15.07 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.11 % 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: 1.42 (0.20), residues: 1828 helix: 2.09 (0.16), residues: 1036 sheet: 0.84 (0.34), residues: 184 loop : -1.09 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 293 HIS 0.002 0.001 HIS D 379 PHE 0.041 0.001 PHE C 469 TYR 0.015 0.001 TYR A 486 ARG 0.002 0.000 ARG B 581 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 232 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 LEU cc_start: 0.7774 (mt) cc_final: 0.7303 (mt) REVERT: A 675 MET cc_start: 0.8037 (tpt) cc_final: 0.7753 (tpt) REVERT: B 597 LEU cc_start: 0.7766 (mt) cc_final: 0.7320 (mt) REVERT: B 675 MET cc_start: 0.8055 (tpt) cc_final: 0.7765 (tpt) REVERT: C 583 MET cc_start: 0.7420 (mmm) cc_final: 0.7027 (mmm) REVERT: C 597 LEU cc_start: 0.7766 (mt) cc_final: 0.7302 (mt) REVERT: D 583 MET cc_start: 0.7428 (mmm) cc_final: 0.7028 (mmm) REVERT: D 597 LEU cc_start: 0.7770 (mt) cc_final: 0.7308 (mt) outliers start: 21 outliers final: 12 residues processed: 238 average time/residue: 0.2716 time to fit residues: 94.8943 Evaluate side-chains 231 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 219 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 484 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 101 optimal weight: 0.0270 chunk 130 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 177 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 15276 Z= 0.150 Angle : 0.490 7.212 20800 Z= 0.271 Chirality : 0.041 0.345 2428 Planarity : 0.003 0.040 2556 Dihedral : 3.867 18.806 2268 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.61 % Favored : 96.17 % Rotamer: Outliers : 1.64 % Allowed : 15.59 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.11 % 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: 1.51 (0.20), residues: 1828 helix: 2.16 (0.16), residues: 1036 sheet: 0.91 (0.34), residues: 184 loop : -1.06 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 293 HIS 0.002 0.000 HIS D 379 PHE 0.023 0.001 PHE A 469 TYR 0.025 0.001 TYR C 239 ARG 0.002 0.000 ARG A 581 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 236 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 LEU cc_start: 0.7699 (mt) cc_final: 0.7272 (mt) REVERT: A 675 MET cc_start: 0.8051 (tpt) cc_final: 0.7720 (tpt) REVERT: B 597 LEU cc_start: 0.7697 (mt) cc_final: 0.7260 (mt) REVERT: B 675 MET cc_start: 0.8062 (tpt) cc_final: 0.7714 (tpt) REVERT: C 597 LEU cc_start: 0.7651 (mt) cc_final: 0.7214 (mt) REVERT: C 668 MET cc_start: 0.8449 (tpp) cc_final: 0.8186 (mmp) REVERT: D 597 LEU cc_start: 0.7660 (mt) cc_final: 0.7211 (mt) REVERT: D 668 MET cc_start: 0.8464 (tpp) cc_final: 0.8218 (mmp) outliers start: 25 outliers final: 16 residues processed: 247 average time/residue: 0.2859 time to fit residues: 101.9544 Evaluate side-chains 236 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 220 time to evaluate : 2.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 411 LYS Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 411 LYS Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 411 LYS Chi-restraints excluded: chain D residue 484 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 120 optimal weight: 0.0570 chunk 87 optimal weight: 0.0070 chunk 16 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 161 optimal weight: 0.9990 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 580 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15276 Z= 0.179 Angle : 0.500 7.223 20800 Z= 0.277 Chirality : 0.041 0.341 2428 Planarity : 0.003 0.040 2556 Dihedral : 4.000 22.158 2268 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.61 % Favored : 96.17 % Rotamer: Outliers : 1.51 % Allowed : 16.12 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.11 % 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: 1.46 (0.20), residues: 1828 helix: 2.12 (0.16), residues: 1036 sheet: 0.86 (0.34), residues: 184 loop : -1.06 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 293 HIS 0.001 0.000 HIS B 379 PHE 0.033 0.001 PHE B 469 TYR 0.016 0.001 TYR C 527 ARG 0.002 0.000 ARG B 397 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 226 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 LEU cc_start: 0.7769 (mt) cc_final: 0.7315 (mt) REVERT: A 675 MET cc_start: 0.7927 (tpt) cc_final: 0.7661 (tpt) REVERT: B 675 MET cc_start: 0.7935 (tpt) cc_final: 0.7661 (tpt) REVERT: C 597 LEU cc_start: 0.7757 (mt) cc_final: 0.7292 (mt) REVERT: D 597 LEU cc_start: 0.7746 (mt) cc_final: 0.7290 (mt) outliers start: 23 outliers final: 18 residues processed: 232 average time/residue: 0.2596 time to fit residues: 89.2808 Evaluate side-chains 240 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 222 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 411 LYS Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 411 LYS Chi-restraints excluded: chain C residue 483 PHE Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 411 LYS Chi-restraints excluded: chain D residue 484 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 0.4980 chunk 155 optimal weight: 8.9990 chunk 165 optimal weight: 0.4980 chunk 99 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 chunk 164 optimal weight: 0.0020 chunk 108 optimal weight: 8.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 ASN A 630 GLN B 580 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15276 Z= 0.148 Angle : 0.493 7.221 20800 Z= 0.273 Chirality : 0.041 0.338 2428 Planarity : 0.003 0.039 2556 Dihedral : 3.924 22.641 2268 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.50 % Favored : 96.28 % Rotamer: Outliers : 2.11 % Allowed : 15.92 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.20), residues: 1828 helix: 2.13 (0.16), residues: 1036 sheet: 0.94 (0.35), residues: 184 loop : -0.98 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 293 HIS 0.001 0.000 HIS B 379 PHE 0.032 0.001 PHE B 469 TYR 0.016 0.001 TYR C 527 ARG 0.002 0.000 ARG D 397 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 236 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 675 MET cc_start: 0.7864 (tpt) cc_final: 0.7651 (tpt) REVERT: B 597 LEU cc_start: 0.7696 (mt) cc_final: 0.7282 (mt) REVERT: B 675 MET cc_start: 0.7883 (tpt) cc_final: 0.7671 (tpt) REVERT: C 597 LEU cc_start: 0.7667 (mt) cc_final: 0.7246 (mt) REVERT: C 668 MET cc_start: 0.8515 (tpp) cc_final: 0.8237 (mmp) REVERT: D 597 LEU cc_start: 0.7657 (mt) cc_final: 0.7221 (mt) REVERT: D 668 MET cc_start: 0.8517 (tpp) cc_final: 0.8253 (mmp) outliers start: 32 outliers final: 18 residues processed: 250 average time/residue: 0.2703 time to fit residues: 99.1214 Evaluate side-chains 241 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 223 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 276 MET Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 484 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 121 optimal weight: 0.0970 chunk 183 optimal weight: 0.8980 chunk 168 optimal weight: 0.9990 chunk 145 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN B 323 GLN B 580 ASN C 323 GLN C 580 ASN D 323 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15276 Z= 0.164 Angle : 0.514 7.215 20800 Z= 0.283 Chirality : 0.041 0.339 2428 Planarity : 0.003 0.039 2556 Dihedral : 3.968 22.016 2268 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.88 % Favored : 95.90 % Rotamer: Outliers : 1.58 % Allowed : 16.97 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.11 % 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: 1.49 (0.20), residues: 1828 helix: 2.08 (0.16), residues: 1036 sheet: 0.96 (0.36), residues: 184 loop : -0.95 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 293 HIS 0.001 0.000 HIS B 379 PHE 0.036 0.001 PHE C 469 TYR 0.016 0.001 TYR B 527 ARG 0.003 0.000 ARG D 397 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 228 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 675 MET cc_start: 0.7904 (tpt) cc_final: 0.7634 (tpt) REVERT: B 675 MET cc_start: 0.7892 (tpt) cc_final: 0.7648 (tpt) REVERT: C 597 LEU cc_start: 0.7650 (mt) cc_final: 0.7210 (mt) REVERT: C 668 MET cc_start: 0.8523 (tpp) cc_final: 0.8243 (mmp) REVERT: D 597 LEU cc_start: 0.7657 (mt) cc_final: 0.7211 (mt) REVERT: D 668 MET cc_start: 0.8524 (tpp) cc_final: 0.8255 (mmp) outliers start: 24 outliers final: 18 residues processed: 241 average time/residue: 0.2584 time to fit residues: 92.8018 Evaluate side-chains 239 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 221 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 323 GLN Chi-restraints excluded: chain D residue 484 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 71.3046 > 50: distance: 44 - 152: 28.793 distance: 47 - 149: 34.083 distance: 61 - 139: 32.767 distance: 64 - 136: 27.175 distance: 80 - 120: 31.009 distance: 82 - 88: 26.528 distance: 83 - 117: 32.801 distance: 88 - 89: 7.215 distance: 89 - 90: 19.091 distance: 89 - 92: 38.344 distance: 90 - 91: 14.649 distance: 90 - 93: 21.522 distance: 93 - 94: 3.096 distance: 94 - 95: 20.234 distance: 94 - 97: 17.698 distance: 95 - 96: 10.158 distance: 95 - 101: 35.025 distance: 97 - 98: 27.922 distance: 98 - 99: 8.785 distance: 98 - 100: 7.730 distance: 101 - 102: 7.455 distance: 102 - 103: 17.164 distance: 102 - 105: 31.708 distance: 103 - 104: 11.419 distance: 103 - 109: 26.831 distance: 105 - 106: 19.933 distance: 105 - 107: 9.527 distance: 106 - 108: 9.282 distance: 109 - 110: 29.269 distance: 110 - 111: 29.957 distance: 110 - 113: 40.862 distance: 111 - 112: 7.279 distance: 111 - 117: 48.420 distance: 113 - 114: 10.981 distance: 114 - 115: 30.627 distance: 114 - 116: 9.220 distance: 117 - 118: 34.251 distance: 118 - 119: 6.230 distance: 118 - 121: 56.097 distance: 119 - 120: 41.638 distance: 119 - 125: 44.299 distance: 121 - 122: 36.119 distance: 122 - 123: 18.436 distance: 122 - 124: 4.706 distance: 125 - 126: 43.048 distance: 125 - 212: 28.525 distance: 126 - 127: 35.059 distance: 126 - 129: 29.375 distance: 127 - 128: 27.561 distance: 127 - 136: 22.635 distance: 128 - 209: 8.399 distance: 129 - 130: 52.689 distance: 130 - 131: 38.184 distance: 130 - 132: 3.133 distance: 131 - 133: 12.340 distance: 133 - 135: 28.472 distance: 134 - 135: 5.428 distance: 136 - 137: 45.540 distance: 137 - 138: 25.278 distance: 137 - 140: 50.971 distance: 138 - 139: 39.747 distance: 138 - 142: 39.415 distance: 140 - 141: 13.949 distance: 142 - 202: 36.375 distance: 143 - 144: 30.938 distance: 143 - 146: 43.383 distance: 144 - 145: 20.985 distance: 144 - 149: 33.108 distance: 145 - 199: 30.063 distance: 146 - 147: 41.335 distance: 146 - 148: 27.780 distance: 149 - 150: 37.132 distance: 150 - 151: 22.269 distance: 150 - 153: 31.869 distance: 151 - 152: 27.554 distance: 151 - 156: 32.877 distance: 153 - 154: 46.376 distance: 153 - 155: 25.234 distance: 156 - 157: 22.435 distance: 156 - 186: 33.046 distance: 157 - 158: 19.734 distance: 157 - 160: 31.736 distance: 158 - 159: 39.034 distance: 158 - 167: 35.087 distance: 159 - 183: 32.733 distance: 160 - 161: 43.089 distance: 162 - 163: 37.914 distance: 164 - 165: 33.436 distance: 164 - 166: 24.459