Starting phenix.real_space_refine on Sat Aug 10 12:12:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tjr_41309/08_2024/8tjr_41309.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tjr_41309/08_2024/8tjr_41309.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tjr_41309/08_2024/8tjr_41309.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tjr_41309/08_2024/8tjr_41309.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tjr_41309/08_2024/8tjr_41309.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tjr_41309/08_2024/8tjr_41309.cif" } resolution = 3.29 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= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 13531 atoms to isotropic. 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 124 5.16 5 C 11422 2.51 5 N 3075 2.21 5 O 3662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 101": "OD1" <-> "OD2" Residue "J GLU 102": "OE1" <-> "OE2" Residue "A GLU 49": "OE1" <-> "OE2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 584": "OE1" <-> "OE2" Residue "D ASP 632": "OD1" <-> "OD2" Residue "D TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 390": "OE1" <-> "OE2" Residue "E ASP 624": "OD1" <-> "OD2" Residue "E GLU 647": "OE1" <-> "OE2" Residue "H ASP 31": "OD1" <-> "OD2" Residue "H TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 277": "OE1" <-> "OE2" Residue "C TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 624": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 18283 Number of models: 1 Model: "" Number of chains: 25 Chain: "J" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 893 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "K" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 855 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "A" Number of atoms: 3551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3551 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 3 Chain: "D" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "B" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3559 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 3 Chain: "E" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "H" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 893 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "L" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 855 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "C" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3559 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Chain: "F" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "P" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 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 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "E" 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: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "F" 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: 9.84, per 1000 atoms: 0.54 Number of scatterers: 18283 At special positions: 0 Unit cell: (127.828, 152.011, 145.965, 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 124 16.00 O 3662 8.00 N 3075 7.00 C 11422 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 98 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 93 " distance=2.04 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 214 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 210 " - pdb=" SG CYS A 442 " distance=2.05 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 256 " distance=2.03 Simple disulfide: pdb=" SG CYS A 237 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS A 305 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 427 " distance=2.03 Simple disulfide: pdb=" SG CYS A 510 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 214 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 210 " - pdb=" SG CYS B 442 " distance=2.03 Simple disulfide: pdb=" SG CYS B 227 " - pdb=" SG CYS B 256 " distance=2.03 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 305 " - pdb=" SG CYS B 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 454 " distance=2.03 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 427 " distance=2.03 Simple disulfide: pdb=" SG CYS B 510 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 210 " - pdb=" SG CYS C 442 " distance=2.03 Simple disulfide: pdb=" SG CYS C 227 " - pdb=" SG CYS C 256 " distance=2.04 Simple disulfide: pdb=" SG CYS C 237 " - pdb=" SG CYS C 248 " distance=2.03 Simple disulfide: pdb=" SG CYS C 305 " - pdb=" SG CYS C 340 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 427 " distance=2.03 Simple disulfide: pdb=" SG CYS C 510 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 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 ALPHA1-2 " MAN P 4 " - " MAN P 5 " " MAN U 4 " - " MAN U 5 " " MAN X 4 " - " MAN X 5 " ALPHA1-3 " BMA P 3 " - " MAN P 4 " " BMA U 3 " - " MAN U 4 " " BMA X 3 " - " MAN X 4 " ALPHA1-6 " BMA P 3 " - " MAN P 6 " " BMA U 3 " - " MAN U 6 " " BMA X 3 " - " MAN X 6 " BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " NAG-ASN " NAG A 601 " - " ASN A 243 " " NAG A 602 " - " ASN A 285 " " NAG A 603 " - " ASN A 348 " " NAG A 604 " - " ASN A 364 " " NAG A 605 " - " ASN A 372 " " NAG A 606 " - " ASN A 395 " " NAG A 607 " - " ASN A 401 " " NAG A 608 " - " ASN A 457 " " NAG A 609 " - " ASN A 156 " " NAG A 610 " - " ASN A 160 " " NAG A 611 " - " ASN A 304 " " NAG A 612 " - " ASN A 310 " " NAG A 613 " - " ASN A 88 " " NAG B 601 " - " ASN B 243 " " NAG B 602 " - " ASN B 285 " " NAG B 603 " - " ASN B 348 " " NAG B 604 " - " ASN B 364 " " NAG B 605 " - " ASN B 372 " " NAG B 606 " - " ASN B 395 " " NAG B 607 " - " ASN B 401 " " NAG B 608 " - " ASN B 457 " " NAG B 609 " - " ASN B 156 " " NAG B 610 " - " ASN B 160 " " NAG B 611 " - " ASN B 304 " " NAG B 612 " - " ASN B 310 " " NAG B 613 " - " ASN B 88 " " NAG C 601 " - " ASN C 243 " " NAG C 602 " - " ASN C 285 " " NAG C 603 " - " ASN C 348 " " NAG C 604 " - " ASN C 364 " " NAG C 605 " - " ASN C 372 " " NAG C 606 " - " ASN C 395 " " NAG C 607 " - " ASN C 401 " " NAG C 608 " - " ASN C 457 " " NAG C 609 " - " ASN C 156 " " NAG C 610 " - " ASN C 160 " " NAG C 611 " - " ASN C 304 " " NAG C 612 " - " ASN C 310 " " NAG C 613 " - " ASN C 88 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 637 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 618 " " NAG E 703 " - " ASN E 637 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 637 " Time building additional restraints: 8.33 Conformation dependent library (CDL) restraints added in 3.3 seconds 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4070 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 35 sheets defined 16.6% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.81 Creating SS restraints... Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.603A pdb=" N ASP J 31 " --> pdb=" O THR J 28 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 28 through 32' Processing helix chain 'J' and resid 89 through 93 removed outlier: 4.208A pdb=" N THR J 93 " --> pdb=" O THR J 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.230A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 4.086A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 126' Processing helix chain 'A' and resid 344 through 363 removed outlier: 4.241A pdb=" N LYS A 360 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N HIS A 361 " --> pdb=" O GLN A 357 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.508A pdb=" N THR A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 490 removed outlier: 3.762A pdb=" N TRP A 488 " --> pdb=" O MET A 484 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A 490 " --> pdb=" O ASP A 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 527 removed outlier: 3.528A pdb=" N ALA D 526 " --> pdb=" O LEU D 523 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 523 through 527' Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 543 removed outlier: 3.972A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 596 removed outlier: 4.128A pdb=" N VAL D 580 " --> pdb=" O LEU D 576 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU D 581 " --> pdb=" O GLN D 577 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY D 594 " --> pdb=" O GLN D 590 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 622 Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.518A pdb=" N ASP D 632 " --> pdb=" O TRP D 628 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 660 removed outlier: 3.552A pdb=" N GLU D 657 " --> pdb=" O GLN D 653 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN D 658 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP D 659 " --> pdb=" O LYS D 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 98 removed outlier: 3.710A pdb=" N LYS B 97 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN B 98 " --> pdb=" O MET B 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 94 through 98' Processing helix chain 'B' and resid 99 through 114 removed outlier: 3.958A pdb=" N MET B 104 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS B 105 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.873A pdb=" N LEU B 125 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N CYS B 126 " --> pdb=" O THR B 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 122 through 126' Processing helix chain 'B' and resid 344 through 353 removed outlier: 3.658A pdb=" N ASN B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 358 Processing helix chain 'B' and resid 358 through 363 removed outlier: 3.807A pdb=" N PHE B 362 " --> pdb=" O LEU B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 489 removed outlier: 3.765A pdb=" N TRP B 488 " --> pdb=" O MET B 484 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 removed outlier: 3.530A pdb=" N SER E 534 " --> pdb=" O MET E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 542 removed outlier: 4.261A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 546 removed outlier: 3.893A pdb=" N SER E 546 " --> pdb=" O ASN E 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 543 through 546' Processing helix chain 'E' and resid 573 through 595 removed outlier: 3.713A pdb=" N ARG E 588 " --> pdb=" O GLU E 584 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP E 589 " --> pdb=" O ARG E 585 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 632 Processing helix chain 'E' and resid 638 through 643 removed outlier: 3.785A pdb=" N ILE E 642 " --> pdb=" O TYR E 638 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 655 removed outlier: 3.724A pdb=" N LYS E 655 " --> pdb=" O ASN E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 657 through 662 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.507A pdb=" N ASP H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'C' and resid 98 through 115 removed outlier: 4.017A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS C 105 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.845A pdb=" N LEU C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 126' Processing helix chain 'C' and resid 344 through 362 removed outlier: 3.690A pdb=" N LYS C 356 " --> pdb=" O GLY C 352 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN C 357 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS C 360 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N HIS C 361 " --> pdb=" O GLN C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 487 removed outlier: 3.660A pdb=" N ASP C 486 " --> pdb=" O ASP C 483 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.907A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 596 removed outlier: 4.214A pdb=" N GLY F 594 " --> pdb=" O GLN F 590 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.568A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 651 through 664 Processing sheet with id=AA1, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.965A pdb=" N LYS J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER J 25 " --> pdb=" O LYS J 3 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU J 18 " --> pdb=" O MET J 85 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU J 20 " --> pdb=" O LEU J 83 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU J 83 " --> pdb=" O LEU J 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.543A pdb=" N VAL J 108 " --> pdb=" O TYR J 96 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL J 110 " --> pdb=" O ALA J 94 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA J 94 " --> pdb=" O VAL J 110 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ILE J 34 " --> pdb=" O LEU J 50 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LEU J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 5 through 6 Processing sheet with id=AA4, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.568A pdb=" N LEU K 11 " --> pdb=" O GLU K 110 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR K 107 " --> pdb=" O TYR K 91 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER K 90 " --> pdb=" O LEU K 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 67 through 68 Processing sheet with id=AA6, first strand: chain 'A' and resid 503 through 508 removed outlier: 4.740A pdb=" N VAL A 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.916A pdb=" N ILE A 234 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 66 through 67 removed outlier: 7.180A pdb=" N HIS A 66 " --> pdb=" O SER A 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.779A pdb=" N GLU A 91 " --> pdb=" O CYS A 248 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 169 through 177 removed outlier: 3.559A pdb=" N LYS A 198 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 268 through 270 removed outlier: 5.737A pdb=" N LEU A 269 " --> pdb=" O THR A 459 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 303 " --> pdb=" O SER A 456 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 301 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N GLN A 302 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER A 343 " --> pdb=" O GLN A 302 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS A 339 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 390 " --> pdb=" O CYS A 387 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 280 through 282 removed outlier: 6.472A pdb=" N ARG A 369 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 368 " --> pdb=" O TRP A 404 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 402 " --> pdb=" O PHE A 370 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 313 through 321 removed outlier: 6.667A pdb=" N GLN A 324 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 432 through 433 removed outlier: 4.188A pdb=" N ILE A 433 " --> pdb=" O MET A 443 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 503 through 508 removed outlier: 4.563A pdb=" N VAL B 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 45 through 47 removed outlier: 4.231A pdb=" N ILE B 234 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL B 251 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 91 through 93 Processing sheet with id=AB9, first strand: chain 'B' and resid 169 through 177 removed outlier: 3.698A pdb=" N LYS B 198 " --> pdb=" O CYS B 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 268 through 270 removed outlier: 5.861A pdb=" N LEU B 269 " --> pdb=" O THR B 459 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLY B 450 " --> pdb=" O ASN B 309 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASN B 309 " --> pdb=" O GLY B 450 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE B 452 " --> pdb=" O ARG B 307 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLY B 460 " --> pdb=" O THR B 299 " (cutoff:3.500A) removed outlier: 10.674A pdb=" N THR B 299 " --> pdb=" O GLY B 460 " (cutoff:3.500A) removed outlier: 12.030A pdb=" N ILE B 462 " --> pdb=" O PHE B 297 " (cutoff:3.500A) removed outlier: 12.248A pdb=" N PHE B 297 " --> pdb=" O ILE B 462 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N THR B 464 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 11.157A pdb=" N VAL B 295 " --> pdb=" O THR B 464 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N GLN B 302 " --> pdb=" O SER B 343 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N SER B 343 " --> pdb=" O GLN B 302 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS B 339 " --> pdb=" O THR B 306 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 430 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE B 391 " --> pdb=" O LYS B 430 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 390 " --> pdb=" O CYS B 387 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 280 through 282 removed outlier: 11.157A pdb=" N VAL B 295 " --> pdb=" O THR B 464 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N THR B 464 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 12.248A pdb=" N PHE B 297 " --> pdb=" O ILE B 462 " (cutoff:3.500A) removed outlier: 12.030A pdb=" N ILE B 462 " --> pdb=" O PHE B 297 " (cutoff:3.500A) removed outlier: 10.674A pdb=" N THR B 299 " --> pdb=" O GLY B 460 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLY B 460 " --> pdb=" O THR B 299 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE B 452 " --> pdb=" O ARG B 307 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASN B 309 " --> pdb=" O GLY B 450 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLY B 450 " --> pdb=" O ASN B 309 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 368 " --> pdb=" O TRP B 404 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 313 through 321 removed outlier: 6.628A pdb=" N GLN B 324 " --> pdb=" O ILE B 318 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 432 through 433 Processing sheet with id=AC5, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.825A pdb=" N LYS H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER H 25 " --> pdb=" O LYS H 3 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.608A pdb=" N VAL H 12 " --> pdb=" O THR H 111 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL H 108 " --> pdb=" O TYR H 96 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE H 34 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.535A pdb=" N LEU L 78 " --> pdb=" O MET L 21 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.878A pdb=" N GLU L 110 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY L 89 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU L 38 " --> pdb=" O HIS L 54 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N HIS L 54 " --> pdb=" O LEU L 38 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 503 through 508 removed outlier: 4.999A pdb=" N VAL C 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.528A pdb=" N ILE C 234 " --> pdb=" O VAL C 254 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.747A pdb=" N GLU C 91 " --> pdb=" O CYS C 248 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 129 through 131 removed outlier: 3.654A pdb=" N LYS C 198 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 154 through 159 Processing sheet with id=AD5, first strand: chain 'C' and resid 211 through 212 removed outlier: 6.429A pdb=" N THR C 211 " --> pdb=" O TYR C 444 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 268 through 270 removed outlier: 5.747A pdb=" N LEU C 269 " --> pdb=" O THR C 459 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N GLY C 450 " --> pdb=" O ASN C 309 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ASN C 309 " --> pdb=" O GLY C 450 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE C 452 " --> pdb=" O ARG C 307 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG C 307 " --> pdb=" O ILE C 452 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 301 " --> pdb=" O ILE C 458 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLN C 302 " --> pdb=" O SER C 343 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER C 343 " --> pdb=" O GLN C 302 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS C 339 " --> pdb=" O THR C 306 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ALA C 338 " --> pdb=" O CYS C 427 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS C 430 " --> pdb=" O PHE C 391 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE C 391 " --> pdb=" O LYS C 430 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 280 through 282 removed outlier: 3.597A pdb=" N MET C 280 " --> pdb=" O GLN C 296 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ARG C 369 " --> pdb=" O PHE C 477 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE C 368 " --> pdb=" O TRP C 404 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER C 402 " --> pdb=" O PHE C 370 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 313 through 321 removed outlier: 6.411A pdb=" N GLN C 324 " --> pdb=" O ILE C 318 " (cutoff:3.500A) 484 hydrogen bonds defined for protein. 1344 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: 5.43 Time building geometry restraints manager: 9.20 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: 5786 1.34 - 1.47: 4538 1.47 - 1.59: 8147 1.59 - 1.72: 0 1.72 - 1.84: 168 Bond restraints: 18639 Sorted by residual: bond pdb=" C1 NAG F 702 " pdb=" O5 NAG F 702 " ideal model delta sigma weight residual 1.406 1.490 -0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" N VAL K 63 " pdb=" CA VAL K 63 " ideal model delta sigma weight residual 1.462 1.494 -0.032 8.70e-03 1.32e+04 1.36e+01 bond pdb=" N VAL K 56 " pdb=" CA VAL K 56 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.25e-02 6.40e+03 1.12e+01 bond pdb=" N GLU D 621 " pdb=" CA GLU D 621 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.18e-02 7.18e+03 9.77e+00 bond pdb=" N VAL A 254 " pdb=" CA VAL A 254 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.14e-02 7.69e+03 9.74e+00 ... (remaining 18634 not shown) Histogram of bond angle deviations from ideal: 99.17 - 106.19: 454 106.19 - 113.22: 10635 113.22 - 120.24: 6155 120.24 - 127.27: 7822 127.27 - 134.30: 227 Bond angle restraints: 25293 Sorted by residual: angle pdb=" CA VAL F 570 " pdb=" C VAL F 570 " pdb=" O VAL F 570 " ideal model delta sigma weight residual 121.58 117.35 4.23 1.00e+00 1.00e+00 1.79e+01 angle pdb=" CA ASP K 55 " pdb=" C ASP K 55 " pdb=" O ASP K 55 " ideal model delta sigma weight residual 122.03 117.18 4.85 1.17e+00 7.31e-01 1.72e+01 angle pdb=" N GLN D 640 " pdb=" CA GLN D 640 " pdb=" C GLN D 640 " ideal model delta sigma weight residual 114.56 109.36 5.20 1.27e+00 6.20e-01 1.67e+01 angle pdb=" C TYR J 56 " pdb=" N THR J 57 " pdb=" CA THR J 57 " ideal model delta sigma weight residual 121.54 128.68 -7.14 1.91e+00 2.74e-01 1.40e+01 angle pdb=" C TYR H 56 " pdb=" N THR H 57 " pdb=" CA THR H 57 " ideal model delta sigma weight residual 121.54 128.40 -6.86 1.91e+00 2.74e-01 1.29e+01 ... (remaining 25288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.45: 11464 25.45 - 50.89: 625 50.89 - 76.34: 85 76.34 - 101.79: 36 101.79 - 127.24: 9 Dihedral angle restraints: 12219 sinusoidal: 5907 harmonic: 6312 Sorted by residual: dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual -86.00 -0.17 -85.83 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual -86.00 -9.99 -76.01 1 1.00e+01 1.00e-02 7.28e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 214 " pdb=" CB CYS A 214 " ideal model delta sinusoidal sigma weight residual -86.00 -156.80 70.80 1 1.00e+01 1.00e-02 6.44e+01 ... (remaining 12216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 2922 0.111 - 0.223: 124 0.223 - 0.334: 8 0.334 - 0.446: 1 0.446 - 0.557: 1 Chirality restraints: 3056 Sorted by residual: chirality pdb=" C1 NAG F 703 " pdb=" ND2 ASN F 637 " pdb=" C2 NAG F 703 " pdb=" O5 NAG F 703 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.77e+00 chirality pdb=" C1 NAG D 702 " pdb=" ND2 ASN D 618 " pdb=" C2 NAG D 702 " pdb=" O5 NAG D 702 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" C5 BMA U 3 " pdb=" C4 BMA U 3 " pdb=" C6 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.59 0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 3053 not shown) Planarity restraints: 3180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR L 14 " -0.069 5.00e-02 4.00e+02 1.05e-01 1.78e+01 pdb=" N PRO L 15 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO L 15 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO L 15 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 611 " -0.000 2.00e-02 2.50e+03 3.29e-02 1.35e+01 pdb=" CG ASN E 611 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN E 611 " -0.040 2.00e-02 2.50e+03 pdb=" ND2 ASN E 611 " 0.034 2.00e-02 2.50e+03 pdb=" C1 NAG E 701 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 304 " 0.001 2.00e-02 2.50e+03 2.38e-02 7.09e+00 pdb=" CG ASN B 304 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN B 304 " 0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN B 304 " -0.032 2.00e-02 2.50e+03 pdb=" C1 NAG B 611 " 0.026 2.00e-02 2.50e+03 ... (remaining 3177 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1080 2.74 - 3.28: 15716 3.28 - 3.82: 26835 3.82 - 4.36: 32230 4.36 - 4.90: 57608 Nonbonded interactions: 133469 Sorted by model distance: nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 508 " model vdw 2.196 3.040 nonbonded pdb=" OH TYR C 61 " pdb=" O CYS C 74 " model vdw 2.219 3.040 nonbonded pdb=" O LEU C 378 " pdb=" OG1 THR C 382 " model vdw 2.251 3.040 nonbonded pdb=" OD2 ASP A 466 " pdb=" OG1 THR A 476 " model vdw 2.275 3.040 nonbonded pdb=" O LEU A 378 " pdb=" OG1 THR A 382 " model vdw 2.284 3.040 ... (remaining 133464 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 32 through 140 or resid 150 through 514 or resid 601 throu \ gh 613)) selection = (chain 'C' and (resid 32 through 140 or resid 150 through 514 or resid 601 throu \ gh 613)) } ncs_group { reference = chain 'D' selection = (chain 'E' and (resid 519 through 664 or resid 701 through 703)) selection = (chain 'F' and (resid 519 through 664 or resid 701 through 703)) } ncs_group { reference = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'P' selection = chain 'U' selection = chain 'X' } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' } 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: 18.190 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 53.420 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6228 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 18639 Z= 0.325 Angle : 0.766 10.487 25293 Z= 0.418 Chirality : 0.053 0.557 3056 Planarity : 0.005 0.105 3132 Dihedral : 15.514 127.236 8029 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.10 % Allowed : 0.67 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % 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: -2.10 (0.17), residues: 2154 helix: -2.48 (0.24), residues: 370 sheet: -0.38 (0.22), residues: 616 loop : -1.57 (0.16), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 488 HIS 0.003 0.001 HIS B 225 PHE 0.010 0.001 PHE B 53 TYR 0.011 0.001 TYR D 586 ARG 0.014 0.000 ARG F 542 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 304 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 7 THR cc_start: 0.2942 (OUTLIER) cc_final: 0.2636 (m) REVERT: A 114 GLN cc_start: 0.8303 (tt0) cc_final: 0.7997 (tt0) REVERT: A 341 ASN cc_start: 0.7022 (p0) cc_final: 0.6502 (p0) REVERT: D 655 LYS cc_start: 0.8205 (ttmt) cc_final: 0.7853 (ttpt) REVERT: B 365 ASN cc_start: 0.8523 (m-40) cc_final: 0.7608 (p0) REVERT: E 636 SER cc_start: 0.7612 (t) cc_final: 0.7230 (p) REVERT: E 647 GLU cc_start: 0.8113 (tt0) cc_final: 0.7840 (tt0) REVERT: E 655 LYS cc_start: 0.7533 (pttp) cc_final: 0.7095 (tttt) REVERT: E 660 LEU cc_start: 0.7580 (tp) cc_final: 0.7354 (tt) REVERT: C 199 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7467 (mm-30) REVERT: C 241 LYS cc_start: 0.7971 (tppt) cc_final: 0.7770 (mtmm) REVERT: C 276 GLU cc_start: 0.8012 (mp0) cc_final: 0.7725 (mp0) REVERT: C 367 ILE cc_start: 0.7681 (mm) cc_final: 0.7438 (mm) REVERT: C 513 ARG cc_start: 0.7529 (mtt180) cc_final: 0.6879 (mmt90) REVERT: F 621 GLU cc_start: 0.7364 (pt0) cc_final: 0.7121 (pt0) REVERT: F 653 GLN cc_start: 0.7556 (tp40) cc_final: 0.7337 (tp40) outliers start: 2 outliers final: 0 residues processed: 306 average time/residue: 0.3297 time to fit residues: 150.1278 Evaluate side-chains 217 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 216 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 7 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 0.8980 chunk 164 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 197 optimal weight: 0.2980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 47 GLN A 137 ASN C 302 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6339 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18639 Z= 0.205 Angle : 0.610 10.349 25293 Z= 0.306 Chirality : 0.047 0.517 3056 Planarity : 0.004 0.084 3132 Dihedral : 11.641 109.288 3967 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.45 % Allowed : 7.11 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % 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: -1.73 (0.17), residues: 2154 helix: -1.83 (0.26), residues: 376 sheet: -0.08 (0.21), residues: 643 loop : -1.53 (0.17), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 571 HIS 0.003 0.001 HIS B 383 PHE 0.013 0.001 PHE A 391 TYR 0.010 0.001 TYR H 103 ARG 0.006 0.000 ARG A 513 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 231 time to evaluate : 1.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8339 (tt0) cc_final: 0.8044 (tt0) REVERT: A 151 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.6930 (mmt-90) REVERT: D 542 ARG cc_start: 0.8422 (mtp85) cc_final: 0.8206 (mtt90) REVERT: D 611 ASN cc_start: 0.4120 (t0) cc_final: 0.3804 (t0) REVERT: D 655 LYS cc_start: 0.8126 (ttmt) cc_final: 0.7852 (ttpt) REVERT: E 513 VAL cc_start: 0.8720 (m) cc_final: 0.8510 (m) REVERT: E 620 SER cc_start: 0.8476 (m) cc_final: 0.7959 (p) REVERT: E 625 ASN cc_start: 0.8386 (m-40) cc_final: 0.8079 (m110) REVERT: E 636 SER cc_start: 0.7894 (t) cc_final: 0.7423 (p) REVERT: E 655 LYS cc_start: 0.7713 (pttp) cc_final: 0.7211 (tttt) REVERT: E 660 LEU cc_start: 0.7415 (tp) cc_final: 0.7206 (tt) REVERT: C 100 MET cc_start: 0.8418 (mtp) cc_final: 0.8024 (mtp) REVERT: C 241 LYS cc_start: 0.8004 (tppt) cc_final: 0.7787 (mtmm) REVERT: C 367 ILE cc_start: 0.7680 (mm) cc_final: 0.7399 (mm) REVERT: C 513 ARG cc_start: 0.7605 (mtt180) cc_final: 0.7010 (mmt90) REVERT: F 621 GLU cc_start: 0.7361 (pt0) cc_final: 0.7127 (pt0) outliers start: 28 outliers final: 14 residues processed: 241 average time/residue: 0.3061 time to fit residues: 111.5327 Evaluate side-chains 221 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 206 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 655 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 109 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 164 optimal weight: 8.9990 chunk 134 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 197 optimal weight: 0.0870 chunk 213 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 61 ASN B 67 ASN E 656 ASN L 98 GLN C 271 ASN C 487 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 18639 Z= 0.326 Angle : 0.685 9.512 25293 Z= 0.342 Chirality : 0.049 0.508 3056 Planarity : 0.005 0.075 3132 Dihedral : 10.041 105.016 3966 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.34 % Allowed : 9.96 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.77 (0.18), residues: 2154 helix: -1.63 (0.27), residues: 374 sheet: -0.28 (0.20), residues: 691 loop : -1.58 (0.17), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 614 HIS 0.004 0.001 HIS B 383 PHE 0.018 0.002 PHE K 76 TYR 0.012 0.002 TYR F 638 ARG 0.008 0.001 ARG F 542 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 234 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 7 THR cc_start: 0.2798 (OUTLIER) cc_final: 0.2583 (m) REVERT: A 114 GLN cc_start: 0.8233 (tt0) cc_final: 0.8033 (tt0) REVERT: D 621 GLU cc_start: 0.8138 (pt0) cc_final: 0.7213 (pm20) REVERT: B 280 MET cc_start: 0.8089 (mmt) cc_final: 0.7736 (mmt) REVERT: E 543 ASN cc_start: 0.8589 (t0) cc_final: 0.8362 (t0) REVERT: E 620 SER cc_start: 0.8591 (m) cc_final: 0.8124 (p) REVERT: E 625 ASN cc_start: 0.8555 (m-40) cc_final: 0.8190 (m110) REVERT: E 636 SER cc_start: 0.8319 (t) cc_final: 0.7863 (p) REVERT: E 655 LYS cc_start: 0.7904 (pttp) cc_final: 0.7236 (tttt) REVERT: E 660 LEU cc_start: 0.7448 (tp) cc_final: 0.7237 (tt) REVERT: C 178 ARG cc_start: 0.8873 (tmm-80) cc_final: 0.8654 (tmm-80) REVERT: C 241 LYS cc_start: 0.8062 (tppt) cc_final: 0.7827 (mtmm) REVERT: C 367 ILE cc_start: 0.7680 (mm) cc_final: 0.7405 (mm) REVERT: F 543 ASN cc_start: 0.8702 (m-40) cc_final: 0.8424 (m-40) outliers start: 45 outliers final: 30 residues processed: 263 average time/residue: 0.3261 time to fit residues: 126.5403 Evaluate side-chains 242 residues out of total 1927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 211 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 61 ASN Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 98 CYS Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 656 ASN Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain F residue 655 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 195 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 198 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 187 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: