Starting phenix.real_space_refine on Sat Feb 17 19:10:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9r_22108/02_2024/6x9r_22108.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9r_22108/02_2024/6x9r_22108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9r_22108/02_2024/6x9r_22108.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9r_22108/02_2024/6x9r_22108.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9r_22108/02_2024/6x9r_22108.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9r_22108/02_2024/6x9r_22108.pdb" } resolution = 3.1 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= 0.000 sd= 0.006 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 126 5.16 5 C 12258 2.51 5 N 3273 2.21 5 O 3933 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19590 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3405 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 4 Chain: "B" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "H" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "C" 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: "D" 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: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" 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: "G" 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: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3405 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 4 Chain: "J" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "K" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "M" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "N" 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: "O" 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: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: "I" 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: "J" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "S" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3405 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 4 Chain: "T" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "U" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "V" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} 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: 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: "Y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: "0" 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: "S" 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: "T" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 10.43, per 1000 atoms: 0.53 Number of scatterers: 19590 At special positions: 0 Unit cell: (122.57, 126.69, 149.35, 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 126 16.00 O 3933 8.00 N 3273 7.00 C 12258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.06 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.17 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.15 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.06 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.02 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.04 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.17 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.02 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.02 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.15 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 119 " - pdb=" SG CYS S 205 " distance=2.06 Simple disulfide: pdb=" SG CYS S 126 " - pdb=" SG CYS S 196 " distance=2.03 Simple disulfide: pdb=" SG CYS S 131 " - pdb=" SG CYS S 157 " distance=2.02 Simple disulfide: pdb=" SG CYS S 218 " - pdb=" SG CYS S 247 " distance=2.04 Simple disulfide: pdb=" SG CYS S 228 " - pdb=" SG CYS S 239 " distance=2.16 Simple disulfide: pdb=" SG CYS S 296 " - pdb=" SG CYS S 331 " distance=2.03 Simple disulfide: pdb=" SG CYS S 378 " - pdb=" SG CYS S 445 " distance=2.02 Simple disulfide: pdb=" SG CYS S 385 " - pdb=" SG CYS S 418 " distance=2.02 Simple disulfide: pdb=" SG CYS S 501 " - pdb=" SG CYS T 605 " distance=2.15 Simple disulfide: pdb=" SG CYS T 598 " - pdb=" SG CYS T 604 " distance=2.02 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 92 " distance=2.04 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 88 " distance=2.03 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 ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA P 3 " - " MAN P 4 " " BMA Y 3 " - " MAN Y 4 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " 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 W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " NAG-ASN " NAG 0 1 " - " ASN S 448 " " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 137 " " NAG A 606 " - " ASN A 160 " " NAG A 609 " - " ASN A 234 " " NAG A 614 " - " ASN A 276 " " NAG A 615 " - " ASN A 295 " " NAG A 616 " - " ASN A 301 " " NAG A 617 " - " ASN A 332 " " NAG A 618 " - " ASN A 339 " " NAG A 619 " - " ASN A 355 " " NAG A 620 " - " ASN A 363 " " NAG A 623 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 625 " " NAG B 704 " - " ASN B 637 " " NAG C 1 " - " ASN A 156 " " NAG D 1 " - " ASN A 197 " " NAG E 1 " - " ASN A 262 " " NAG F 1 " - " ASN A 386 " " NAG G 1 " - " ASN A 448 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 133 " " NAG I 603 " - " ASN I 137 " " NAG I 606 " - " ASN I 160 " " NAG I 609 " - " ASN I 234 " " NAG I 614 " - " ASN I 276 " " NAG I 615 " - " ASN I 295 " " NAG I 616 " - " ASN I 301 " " NAG I 617 " - " ASN I 332 " " NAG I 618 " - " ASN I 339 " " NAG I 619 " - " ASN I 355 " " NAG I 620 " - " ASN I 363 " " NAG I 623 " - " ASN I 392 " " NAG J 701 " - " ASN J 611 " " NAG J 702 " - " ASN J 618 " " NAG J 703 " - " ASN J 625 " " NAG J 704 " - " ASN J 637 " " NAG N 1 " - " ASN I 156 " " NAG O 1 " - " ASN I 197 " " NAG P 1 " - " ASN I 262 " " NAG Q 1 " - " ASN I 386 " " NAG R 1 " - " ASN I 448 " " NAG S 601 " - " ASN S 88 " " NAG S 602 " - " ASN S 133 " " NAG S 603 " - " ASN S 137 " " NAG S 606 " - " ASN S 160 " " NAG S 609 " - " ASN S 234 " " NAG S 614 " - " ASN S 276 " " NAG S 615 " - " ASN S 295 " " NAG S 616 " - " ASN S 301 " " NAG S 617 " - " ASN S 332 " " NAG S 618 " - " ASN S 339 " " NAG S 619 " - " ASN S 355 " " NAG S 620 " - " ASN S 363 " " NAG S 623 " - " ASN S 392 " " NAG T 701 " - " ASN T 611 " " NAG T 702 " - " ASN T 618 " " NAG T 703 " - " ASN T 625 " " NAG T 704 " - " ASN T 637 " " NAG W 1 " - " ASN S 156 " " NAG X 1 " - " ASN S 197 " " NAG Y 1 " - " ASN S 262 " " NAG Z 1 " - " ASN S 386 " Time building additional restraints: 8.05 Conformation dependent library (CDL) restraints added in 3.2 seconds 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4332 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 48 sheets defined 20.6% alpha, 43.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.134A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 354 removed outlier: 4.048A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.756A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.519A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 660 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'I' and resid 98 through 115 removed outlier: 4.135A pdb=" N GLU I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 139 through 151 Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 334 through 354 removed outlier: 4.048A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 476 through 484 removed outlier: 3.755A pdb=" N SER I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 536 through 542 removed outlier: 3.520A pdb=" N GLN J 540 " --> pdb=" O THR J 536 " (cutoff:3.500A) Processing helix chain 'J' and resid 569 through 596 Processing helix chain 'J' and resid 618 through 625 Processing helix chain 'J' and resid 627 through 635 Processing helix chain 'J' and resid 638 through 660 Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'S' and resid 98 through 115 removed outlier: 4.134A pdb=" N GLU S 102 " --> pdb=" O ASN S 98 " (cutoff:3.500A) Processing helix chain 'S' and resid 122 through 126 Processing helix chain 'S' and resid 139 through 151 Processing helix chain 'S' and resid 195 through 198 Processing helix chain 'S' and resid 334 through 354 removed outlier: 4.048A pdb=" N LYS S 351 " --> pdb=" O LYS S 347 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N HIS S 352 " --> pdb=" O GLN S 348 " (cutoff:3.500A) Processing helix chain 'S' and resid 368 through 373 Processing helix chain 'S' and resid 476 through 484 removed outlier: 3.756A pdb=" N SER S 481 " --> pdb=" O ASP S 477 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU S 482 " --> pdb=" O ASN S 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 536 through 542 removed outlier: 3.519A pdb=" N GLN T 540 " --> pdb=" O THR T 536 " (cutoff:3.500A) Processing helix chain 'T' and resid 569 through 596 Processing helix chain 'T' and resid 618 through 625 Processing helix chain 'T' and resid 627 through 635 Processing helix chain 'T' and resid 638 through 660 Processing helix chain 'U' and resid 28 through 32 Processing helix chain 'U' and resid 61 through 64 Processing helix chain 'U' and resid 83 through 87 Processing helix chain 'V' and resid 79 through 83 Processing sheet with id= 1, first strand: chain 'A' and resid 494 through 498 Processing sheet with id= 2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.868A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id= 4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id= 5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id= 6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.450A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 393 through 394 removed outlier: 6.424A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 10.274A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 10.923A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.349A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.562A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.552A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 271 through 274 Processing sheet with id= 10, first strand: chain 'A' and resid 315 through 323A removed outlier: 6.234A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'H' and resid 3 through 8 Processing sheet with id= 12, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.060A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'H' and resid 11 through 12 Processing sheet with id= 14, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.566A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP L 35 " --> pdb=" O MET L 47 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.566A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'L' and resid 19 through 24 Processing sheet with id= 17, first strand: chain 'I' and resid 494 through 498 Processing sheet with id= 18, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.868A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'I' and resid 75 through 76 Processing sheet with id= 20, first strand: chain 'I' and resid 91 through 94 Processing sheet with id= 21, first strand: chain 'I' and resid 169 through 177 Processing sheet with id= 22, first strand: chain 'I' and resid 200 through 203 removed outlier: 6.451A pdb=" N ALA I 200 " --> pdb=" O ALA I 433 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N TYR I 435 " --> pdb=" O ALA I 200 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'I' and resid 393 through 394 removed outlier: 6.423A pdb=" N ILE I 358 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N PHE I 468 " --> pdb=" O ILE I 358 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) removed outlier: 10.274A pdb=" N VAL I 442 " --> pdb=" O CYS I 296 " (cutoff:3.500A) removed outlier: 10.923A pdb=" N CYS I 296 " --> pdb=" O VAL I 442 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N ARG I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.349A pdb=" N ILE I 294 " --> pdb=" O ARG I 444 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N VAL I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 10.563A pdb=" N VAL I 292 " --> pdb=" O VAL I 446 " (cutoff:3.500A) removed outlier: 9.256A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR I 450 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'I' and resid 259 through 261 removed outlier: 6.552A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'I' and resid 271 through 274 Processing sheet with id= 26, first strand: chain 'I' and resid 315 through 323A removed outlier: 6.234A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ILE I 323 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASN I 301 " --> pdb=" O ILE I 323 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'K' and resid 3 through 8 Processing sheet with id= 28, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.059A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'K' and resid 11 through 12 Processing sheet with id= 30, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.566A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP M 35 " --> pdb=" O MET M 47 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.566A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'M' and resid 19 through 24 Processing sheet with id= 33, first strand: chain 'S' and resid 494 through 498 Processing sheet with id= 34, first strand: chain 'S' and resid 45 through 47 removed outlier: 3.869A pdb=" N ILE S 225 " --> pdb=" O VAL S 245 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL S 242 " --> pdb=" O LEU S 86 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'S' and resid 75 through 76 Processing sheet with id= 36, first strand: chain 'S' and resid 91 through 94 Processing sheet with id= 37, first strand: chain 'S' and resid 169 through 177 Processing sheet with id= 38, first strand: chain 'S' and resid 200 through 203 removed outlier: 6.450A pdb=" N ALA S 200 " --> pdb=" O ALA S 433 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N TYR S 435 " --> pdb=" O ALA S 200 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR S 202 " --> pdb=" O TYR S 435 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'S' and resid 393 through 394 removed outlier: 6.424A pdb=" N ILE S 358 " --> pdb=" O GLU S 466 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE S 468 " --> pdb=" O ILE S 358 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG S 360 " --> pdb=" O PHE S 468 " (cutoff:3.500A) removed outlier: 10.274A pdb=" N VAL S 442 " --> pdb=" O CYS S 296 " (cutoff:3.500A) removed outlier: 10.922A pdb=" N CYS S 296 " --> pdb=" O VAL S 442 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N ARG S 444 " --> pdb=" O ILE S 294 " (cutoff:3.500A) removed outlier: 11.349A pdb=" N ILE S 294 " --> pdb=" O ARG S 444 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N VAL S 446 " --> pdb=" O VAL S 292 " (cutoff:3.500A) removed outlier: 10.562A pdb=" N VAL S 292 " --> pdb=" O VAL S 446 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N ASN S 448 " --> pdb=" O THR S 290 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N THR S 290 " --> pdb=" O ASN S 448 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR S 450 " --> pdb=" O PHE S 288 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA S 329 " --> pdb=" O CYS S 418 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE S 382 " --> pdb=" O LYS S 421 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'S' and resid 259 through 261 removed outlier: 6.552A pdb=" N LEU S 260 " --> pdb=" O THR S 450 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'S' and resid 271 through 274 Processing sheet with id= 42, first strand: chain 'S' and resid 315 through 323A removed outlier: 6.233A pdb=" N GLN S 315 " --> pdb=" O ILE S 309 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N THR S 303 " --> pdb=" O GLY S 321 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ILE S 323 " --> pdb=" O ASN S 301 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASN S 301 " --> pdb=" O ILE S 323 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'U' and resid 3 through 8 Processing sheet with id= 44, first strand: chain 'U' and resid 11 through 12 removed outlier: 6.060A pdb=" N ARG U 38 " --> pdb=" O TRP U 47 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N TRP U 47 " --> pdb=" O ARG U 38 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'U' and resid 11 through 12 Processing sheet with id= 46, first strand: chain 'V' and resid 11 through 13 removed outlier: 6.566A pdb=" N VAL V 11 " --> pdb=" O THR V 105 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP V 35 " --> pdb=" O MET V 47 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'V' and resid 11 through 13 removed outlier: 6.566A pdb=" N VAL V 11 " --> pdb=" O THR V 105 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'V' and resid 19 through 24 756 hydrogen bonds defined for protein. 1935 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: 7.14 Time building geometry restraints manager: 8.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3667 1.31 - 1.44: 5372 1.44 - 1.57: 10724 1.57 - 1.69: 40 1.69 - 1.82: 171 Bond restraints: 19974 Sorted by residual: bond pdb=" C1 NAG A 603 " pdb=" O5 NAG A 603 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C1 NAG I 603 " pdb=" O5 NAG I 603 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.90e+01 bond pdb=" C1 NAG S 603 " pdb=" O5 NAG S 603 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" C1 NAG X 2 " pdb=" O5 NAG X 2 " ideal model delta sigma weight residual 1.406 1.545 -0.139 2.00e-02 2.50e+03 4.85e+01 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.545 -0.139 2.00e-02 2.50e+03 4.84e+01 ... (remaining 19969 not shown) Histogram of bond angle deviations from ideal: 96.07 - 103.68: 258 103.68 - 111.29: 8321 111.29 - 118.90: 8219 118.90 - 126.50: 10006 126.50 - 134.11: 289 Bond angle restraints: 27093 Sorted by residual: angle pdb=" N PRO V 7 " pdb=" CA PRO V 7 " pdb=" C PRO V 7 " ideal model delta sigma weight residual 110.70 124.03 -13.33 1.22e+00 6.72e-01 1.19e+02 angle pdb=" N PRO M 7 " pdb=" CA PRO M 7 " pdb=" C PRO M 7 " ideal model delta sigma weight residual 110.70 124.02 -13.32 1.22e+00 6.72e-01 1.19e+02 angle pdb=" N PRO L 7 " pdb=" CA PRO L 7 " pdb=" C PRO L 7 " ideal model delta sigma weight residual 110.70 123.99 -13.29 1.22e+00 6.72e-01 1.19e+02 angle pdb=" N GLY M 100 " pdb=" CA GLY M 100 " pdb=" C GLY M 100 " ideal model delta sigma weight residual 112.85 100.34 12.51 1.61e+00 3.86e-01 6.04e+01 angle pdb=" C ASP M 50 " pdb=" N VAL M 51 " pdb=" CA VAL M 51 " ideal model delta sigma weight residual 123.16 114.93 8.23 1.06e+00 8.90e-01 6.03e+01 ... (remaining 27088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.78: 12574 21.78 - 43.55: 329 43.55 - 65.33: 93 65.33 - 87.11: 27 87.11 - 108.88: 15 Dihedral angle restraints: 13038 sinusoidal: 6291 harmonic: 6747 Sorted by residual: dihedral pdb=" CB CYS S 228 " pdb=" SG CYS S 228 " pdb=" SG CYS S 239 " pdb=" CB CYS S 239 " ideal model delta sinusoidal sigma weight residual 93.00 161.95 -68.95 1 1.00e+01 1.00e-02 6.15e+01 dihedral pdb=" CB CYS I 228 " pdb=" SG CYS I 228 " pdb=" SG CYS I 239 " pdb=" CB CYS I 239 " ideal model delta sinusoidal sigma weight residual 93.00 161.95 -68.95 1 1.00e+01 1.00e-02 6.15e+01 dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 161.95 -68.95 1 1.00e+01 1.00e-02 6.15e+01 ... (remaining 13035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 2322 0.098 - 0.196: 769 0.196 - 0.294: 164 0.294 - 0.392: 18 0.392 - 0.491: 6 Chirality restraints: 3279 Sorted by residual: chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.50e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.49e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.48e+02 ... (remaining 3276 not shown) Planarity restraints: 3405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 702 " 0.222 2.00e-02 2.50e+03 1.84e-01 4.21e+02 pdb=" C7 NAG T 702 " -0.060 2.00e-02 2.50e+03 pdb=" C8 NAG T 702 " 0.158 2.00e-02 2.50e+03 pdb=" N2 NAG T 702 " -0.300 2.00e-02 2.50e+03 pdb=" O7 NAG T 702 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 702 " 0.222 2.00e-02 2.50e+03 1.83e-01 4.20e+02 pdb=" C7 NAG B 702 " -0.060 2.00e-02 2.50e+03 pdb=" C8 NAG B 702 " 0.158 2.00e-02 2.50e+03 pdb=" N2 NAG B 702 " -0.300 2.00e-02 2.50e+03 pdb=" O7 NAG B 702 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 702 " -0.221 2.00e-02 2.50e+03 1.83e-01 4.20e+02 pdb=" C7 NAG J 702 " 0.060 2.00e-02 2.50e+03 pdb=" C8 NAG J 702 " -0.158 2.00e-02 2.50e+03 pdb=" N2 NAG J 702 " 0.300 2.00e-02 2.50e+03 pdb=" O7 NAG J 702 " 0.019 2.00e-02 2.50e+03 ... (remaining 3402 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4132 2.76 - 3.30: 16799 3.30 - 3.83: 32205 3.83 - 4.37: 38499 4.37 - 4.90: 65142 Nonbonded interactions: 156777 Sorted by model distance: nonbonded pdb=" OG1 THR I 37 " pdb=" OG1 THR I 499 " model vdw 2.228 2.440 nonbonded pdb=" OG1 THR S 37 " pdb=" OG1 THR S 499 " model vdw 2.229 2.440 nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.229 2.440 nonbonded pdb=" N ASN A 355 " pdb=" OD1 ASN A 355 " model vdw 2.283 2.520 nonbonded pdb=" N ASN S 355 " pdb=" OD1 ASN S 355 " model vdw 2.283 2.520 ... (remaining 156772 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 '0' selection = chain 'C' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'W' selection = chain 'X' selection = chain 'Z' } ncs_group { reference = chain 'A' selection = chain 'I' selection = chain 'S' } ncs_group { reference = chain 'B' selection = chain 'J' selection = chain 'T' } ncs_group { reference = chain 'E' selection = chain 'P' selection = chain 'Y' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'U' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'V' } 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 5.830 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 52.930 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.210 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:3.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 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 : 0.025 0.150 19974 Z= 1.615 Angle : 1.719 13.332 27093 Z= 1.125 Chirality : 0.100 0.491 3279 Planarity : 0.011 0.184 3339 Dihedral : 11.452 108.883 8598 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 0.93 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.30 % Favored : 96.35 % Rotamer: Outliers : 0.44 % Allowed : 0.15 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.17), residues: 2304 helix: -0.32 (0.24), residues: 393 sheet: 0.83 (0.20), residues: 630 loop : 0.48 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.012 TRP A 427 HIS 0.008 0.002 HIS U 82A PHE 0.035 0.006 PHE A 383 TYR 0.047 0.007 TYR V 36 ARG 0.008 0.001 ARG U 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 495 time to evaluate : 2.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8724 (mmtp) cc_final: 0.8521 (mmtp) REVERT: A 150 MET cc_start: 0.8053 (mmm) cc_final: 0.7749 (mmm) REVERT: A 318 TYR cc_start: 0.8763 (m-80) cc_final: 0.8518 (m-80) REVERT: A 492 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8421 (mt-10) REVERT: A 502 LYS cc_start: 0.6886 (mmtp) cc_final: 0.5918 (mmtm) REVERT: L 94 ARG cc_start: 0.5936 (mmt180) cc_final: 0.4510 (mmt180) REVERT: I 150 MET cc_start: 0.7869 (mmm) cc_final: 0.7137 (mmt) REVERT: I 502 LYS cc_start: 0.6375 (mmtp) cc_final: 0.5553 (mmtm) REVERT: J 624 ASP cc_start: 0.8293 (m-30) cc_final: 0.8037 (m-30) REVERT: M 94 ARG cc_start: 0.6375 (mmt180) cc_final: 0.4685 (mtp180) REVERT: S 46 LYS cc_start: 0.8803 (mmtp) cc_final: 0.8563 (mmtp) REVERT: S 502 LYS cc_start: 0.6176 (mmtp) cc_final: 0.5680 (mmtp) REVERT: V 47 MET cc_start: 0.8171 (mmm) cc_final: 0.7801 (mmt) REVERT: V 94 ARG cc_start: 0.6002 (mmt180) cc_final: 0.5111 (mmt180) outliers start: 9 outliers final: 7 residues processed: 500 average time/residue: 0.3783 time to fit residues: 270.7303 Evaluate side-chains 278 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 271 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 637 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 209 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN L 79 GLN J 607 ASN M 79 GLN S 103 GLN T 607 ASN U 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19974 Z= 0.223 Angle : 0.661 8.810 27093 Z= 0.357 Chirality : 0.046 0.303 3279 Planarity : 0.004 0.035 3339 Dihedral : 8.939 65.796 4349 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.60 % Favored : 96.14 % Rotamer: Outliers : 1.91 % Allowed : 6.11 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.17), residues: 2304 helix: 1.59 (0.28), residues: 384 sheet: 0.50 (0.20), residues: 660 loop : 0.08 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 479 HIS 0.004 0.001 HIS H 82A PHE 0.018 0.002 PHE I 383 TYR 0.013 0.001 TYR L 96 ARG 0.009 0.001 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 339 time to evaluate : 2.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9393 (ptm) cc_final: 0.9068 (ptm) REVERT: A 117 LYS cc_start: 0.8087 (mtpt) cc_final: 0.7724 (mttp) REVERT: A 150 MET cc_start: 0.7948 (mmm) cc_final: 0.7628 (mmm) REVERT: A 502 LYS cc_start: 0.6788 (mmtp) cc_final: 0.5593 (mmtm) REVERT: I 426 MET cc_start: 0.8880 (mmt) cc_final: 0.8618 (tpt) REVERT: I 502 LYS cc_start: 0.6444 (mmtp) cc_final: 0.5400 (mmtm) REVERT: J 624 ASP cc_start: 0.8042 (m-30) cc_final: 0.7675 (m-30) REVERT: M 94 ARG cc_start: 0.6045 (mmt180) cc_final: 0.4506 (mmt180) REVERT: S 46 LYS cc_start: 0.8647 (mmtp) cc_final: 0.8258 (mmtp) REVERT: S 502 LYS cc_start: 0.6299 (mmtp) cc_final: 0.5742 (mmtp) REVERT: T 607 ASN cc_start: 0.8619 (OUTLIER) cc_final: 0.8402 (t0) REVERT: U 25 SER cc_start: 0.8494 (p) cc_final: 0.8120 (m) REVERT: V 45 LYS cc_start: 0.8810 (tttt) cc_final: 0.8606 (tttt) REVERT: V 47 MET cc_start: 0.8172 (mmm) cc_final: 0.7755 (mmt) REVERT: V 94 ARG cc_start: 0.5644 (mmt180) cc_final: 0.4520 (mtp180) outliers start: 39 outliers final: 25 residues processed: 366 average time/residue: 0.3815 time to fit residues: 204.8271 Evaluate side-chains 297 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 271 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 607 ASN Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 655 LYS Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 213 ILE Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain T residue 607 ASN Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 655 LYS Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 11 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 116 optimal weight: 2.9990 chunk 65 optimal weight: 0.0170 chunk 174 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 210 optimal weight: 2.9990 chunk 227 optimal weight: 10.0000 chunk 187 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN I 377 ASN J 651 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19974 Z= 0.289 Angle : 0.626 10.702 27093 Z= 0.330 Chirality : 0.047 0.513 3279 Planarity : 0.004 0.051 3339 Dihedral : 7.981 59.891 4347 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.56 % Favored : 95.31 % Rotamer: Outliers : 2.49 % Allowed : 7.72 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.45 (0.17), residues: 2304 helix: 1.53 (0.28), residues: 405 sheet: 0.58 (0.20), residues: 636 loop : -0.21 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 96 HIS 0.006 0.001 HIS I 105 PHE 0.018 0.002 PHE S 383 TYR 0.010 0.001 TYR M 49 ARG 0.008 0.001 ARG I 444 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 281 time to evaluate : 2.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.8080 (mtpt) cc_final: 0.7718 (mttp) REVERT: A 150 MET cc_start: 0.8064 (mmm) cc_final: 0.7711 (mmm) REVERT: A 502 LYS cc_start: 0.6937 (mmtp) cc_final: 0.5645 (mmtm) REVERT: H 25 SER cc_start: 0.8556 (p) cc_final: 0.8259 (m) REVERT: I 502 LYS cc_start: 0.6659 (mmtp) cc_final: 0.5322 (mmtp) REVERT: J 624 ASP cc_start: 0.8219 (m-30) cc_final: 0.7700 (m-30) REVERT: S 46 LYS cc_start: 0.8622 (mmtp) cc_final: 0.8395 (mmtp) REVERT: S 395 TRP cc_start: 0.6740 (m-10) cc_final: 0.6325 (m-10) REVERT: S 502 LYS cc_start: 0.6748 (mmtp) cc_final: 0.5970 (mmtp) REVERT: U 25 SER cc_start: 0.8695 (p) cc_final: 0.8391 (m) REVERT: V 47 MET cc_start: 0.8122 (mmm) cc_final: 0.7721 (mmt) REVERT: V 94 ARG cc_start: 0.5803 (mmt180) cc_final: 0.4453 (mtp180) outliers start: 51 outliers final: 37 residues processed: 310 average time/residue: 0.3600 time to fit residues: 163.4408 Evaluate side-chains 299 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 262 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 377 ASN Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain S residue 95 MET Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 213 ILE Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 636 SER Chi-restraints excluded: chain T residue 655 LYS Chi-restraints excluded: chain U residue 94 THR Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 11 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 210 optimal weight: 1.9990 chunk 223 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 199 optimal weight: 0.0670 chunk 60 optimal weight: 1.9990 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 377 ASN J 651 ASN S 377 ASN T 607 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19974 Z= 0.192 Angle : 0.560 10.183 27093 Z= 0.294 Chirality : 0.046 0.429 3279 Planarity : 0.004 0.054 3339 Dihedral : 7.117 58.652 4347 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.21 % Favored : 95.66 % Rotamer: Outliers : 2.35 % Allowed : 8.85 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.51 (0.18), residues: 2304 helix: 1.78 (0.28), residues: 402 sheet: 0.58 (0.19), residues: 726 loop : -0.27 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 623 HIS 0.004 0.001 HIS S 105 PHE 0.015 0.002 PHE S 53 TYR 0.011 0.001 TYR M 49 ARG 0.005 0.000 ARG T 542 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 292 time to evaluate : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8749 (mmtt) cc_final: 0.8283 (mmtt) REVERT: A 117 LYS cc_start: 0.8097 (mtpt) cc_final: 0.7737 (mttp) REVERT: A 502 LYS cc_start: 0.6940 (mmtp) cc_final: 0.5608 (mmtm) REVERT: H 25 SER cc_start: 0.8638 (p) cc_final: 0.8303 (m) REVERT: H 43 LYS cc_start: 0.8446 (mmtm) cc_final: 0.8178 (mmmm) REVERT: I 502 LYS cc_start: 0.6650 (mmtp) cc_final: 0.5320 (mmtp) REVERT: J 624 ASP cc_start: 0.8073 (m-30) cc_final: 0.7815 (m-30) REVERT: S 395 TRP cc_start: 0.6727 (m-10) cc_final: 0.6435 (m-10) REVERT: S 502 LYS cc_start: 0.6741 (mmtp) cc_final: 0.5837 (mmtp) REVERT: U 25 SER cc_start: 0.8741 (p) cc_final: 0.8463 (m) REVERT: V 47 MET cc_start: 0.8112 (mmm) cc_final: 0.7718 (mmt) REVERT: V 94 ARG cc_start: 0.5825 (mmt180) cc_final: 0.4428 (mtp180) outliers start: 48 outliers final: 34 residues processed: 318 average time/residue: 0.3555 time to fit residues: 166.3905 Evaluate side-chains 304 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 270 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 213 ILE Chi-restraints excluded: chain S residue 325 ASP Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 377 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 655 LYS Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 5 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 6.9990 chunk 126 optimal weight: 0.6980 chunk 3 optimal weight: 8.9990 chunk 166 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN J 651 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 19974 Z= 0.306 Angle : 0.600 10.406 27093 Z= 0.311 Chirality : 0.047 0.573 3279 Planarity : 0.004 0.057 3339 Dihedral : 7.444 109.949 4347 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.03 % Favored : 94.84 % Rotamer: Outliers : 2.88 % Allowed : 9.19 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.36 (0.18), residues: 2304 helix: 1.91 (0.27), residues: 384 sheet: 0.46 (0.19), residues: 726 loop : -0.42 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 427 HIS 0.006 0.001 HIS A 105 PHE 0.021 0.002 PHE S 383 TYR 0.013 0.001 TYR M 49 ARG 0.004 0.001 ARG S 480 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 274 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8628 (mmtt) cc_final: 0.8417 (mmtt) REVERT: A 117 LYS cc_start: 0.8107 (mtpt) cc_final: 0.7735 (mttp) REVERT: A 502 LYS cc_start: 0.6985 (mmtp) cc_final: 0.5674 (mmtm) REVERT: H 25 SER cc_start: 0.8733 (p) cc_final: 0.8432 (m) REVERT: I 502 LYS cc_start: 0.6804 (mmtp) cc_final: 0.5407 (mmtp) REVERT: J 624 ASP cc_start: 0.8360 (m-30) cc_final: 0.7964 (m-30) REVERT: S 395 TRP cc_start: 0.6825 (m-10) cc_final: 0.6569 (m-10) REVERT: S 502 LYS cc_start: 0.6872 (mmtp) cc_final: 0.6028 (mmtp) REVERT: U 25 SER cc_start: 0.8817 (p) cc_final: 0.8583 (m) REVERT: V 47 MET cc_start: 0.8080 (mmm) cc_final: 0.7703 (mmt) REVERT: V 94 ARG cc_start: 0.5897 (mmt180) cc_final: 0.4635 (mmt180) outliers start: 59 outliers final: 46 residues processed: 308 average time/residue: 0.3583 time to fit residues: 161.3241 Evaluate side-chains 309 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 263 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 95 MET Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 213 ILE Chi-restraints excluded: chain S residue 325 ASP Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 615 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain U residue 21 SER Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 11 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 75 optimal weight: 8.9990 chunk 201 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 223 optimal weight: 6.9990 chunk 185 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN L 79 GLN J 651 ASN M 79 GLN S 377 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 19974 Z= 0.400 Angle : 0.654 8.413 27093 Z= 0.338 Chirality : 0.050 0.587 3279 Planarity : 0.004 0.057 3339 Dihedral : 7.627 103.254 4347 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.51 % Favored : 94.36 % Rotamer: Outliers : 3.32 % Allowed : 9.29 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.08 (0.17), residues: 2304 helix: 1.41 (0.27), residues: 405 sheet: 0.28 (0.18), residues: 735 loop : -0.54 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 427 HIS 0.006 0.001 HIS I 105 PHE 0.022 0.002 PHE S 383 TYR 0.015 0.002 TYR M 49 ARG 0.005 0.001 ARG A 480 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 269 time to evaluate : 2.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.8114 (mtpt) cc_final: 0.7789 (mmmt) REVERT: A 502 LYS cc_start: 0.7050 (mmtp) cc_final: 0.5712 (mmtt) REVERT: H 25 SER cc_start: 0.8835 (p) cc_final: 0.8577 (m) REVERT: H 43 LYS cc_start: 0.8682 (mmtm) cc_final: 0.8467 (mmmm) REVERT: H 100 LEU cc_start: 0.9556 (OUTLIER) cc_final: 0.9277 (mt) REVERT: I 502 LYS cc_start: 0.6839 (mmtp) cc_final: 0.5994 (mmtt) REVERT: J 624 ASP cc_start: 0.8168 (m-30) cc_final: 0.7914 (m-30) REVERT: K 100 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9022 (mp) REVERT: M 79 GLN cc_start: 0.7994 (mp-120) cc_final: 0.7747 (mt0) REVERT: S 395 TRP cc_start: 0.6864 (m-10) cc_final: 0.6620 (m-10) REVERT: S 502 LYS cc_start: 0.6922 (mmtp) cc_final: 0.6024 (mmtp) REVERT: V 47 MET cc_start: 0.8049 (mmm) cc_final: 0.7680 (mmt) REVERT: V 94 ARG cc_start: 0.6074 (mmt180) cc_final: 0.4330 (mmt180) outliers start: 68 outliers final: 52 residues processed: 311 average time/residue: 0.3745 time to fit residues: 169.0651 Evaluate side-chains 316 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 262 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 213 ILE Chi-restraints excluded: chain S residue 325 ASP Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 615 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 639 THR Chi-restraints excluded: chain T residue 655 LYS Chi-restraints excluded: chain U residue 21 SER Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 11 VAL Chi-restraints excluded: chain V residue 20 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 127 optimal weight: 0.7980 chunk 163 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 222 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN J 651 ASN ** S 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19974 Z= 0.243 Angle : 0.588 13.063 27093 Z= 0.305 Chirality : 0.050 1.041 3279 Planarity : 0.004 0.054 3339 Dihedral : 7.382 113.746 4347 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.43 % Favored : 94.44 % Rotamer: Outliers : 3.13 % Allowed : 10.02 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.21 (0.18), residues: 2304 helix: 1.66 (0.27), residues: 402 sheet: 0.35 (0.19), residues: 726 loop : -0.49 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 427 HIS 0.004 0.001 HIS A 105 PHE 0.015 0.002 PHE A 383 TYR 0.014 0.001 TYR M 49 ARG 0.004 0.000 ARG J 585 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 274 time to evaluate : 2.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.8101 (mtpt) cc_final: 0.7795 (mmmt) REVERT: A 502 LYS cc_start: 0.6997 (mmtp) cc_final: 0.5676 (mmtp) REVERT: H 100 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9268 (mt) REVERT: I 502 LYS cc_start: 0.6867 (mmtp) cc_final: 0.5544 (mmtm) REVERT: K 100 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9084 (mp) REVERT: S 502 LYS cc_start: 0.6884 (mmtp) cc_final: 0.5617 (mmtm) REVERT: V 47 MET cc_start: 0.8020 (mmm) cc_final: 0.7643 (mmt) outliers start: 64 outliers final: 48 residues processed: 312 average time/residue: 0.3664 time to fit residues: 167.7241 Evaluate side-chains 312 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 262 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 213 ILE Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 615 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 655 LYS Chi-restraints excluded: chain U residue 21 SER Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 11 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 137 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 132 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 43 optimal weight: 0.3980 chunk 141 optimal weight: 9.9990 chunk 151 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 202 optimal weight: 0.1980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN J 651 ASN M 79 GLN V 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19974 Z= 0.232 Angle : 0.560 7.480 27093 Z= 0.292 Chirality : 0.046 0.709 3279 Planarity : 0.004 0.054 3339 Dihedral : 7.014 111.082 4345 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.38 % Favored : 94.49 % Rotamer: Outliers : 2.59 % Allowed : 10.46 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.27 (0.18), residues: 2304 helix: 1.81 (0.27), residues: 402 sheet: 0.38 (0.19), residues: 726 loop : -0.49 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 427 HIS 0.004 0.001 HIS A 105 PHE 0.014 0.002 PHE A 383 TYR 0.016 0.001 TYR M 49 ARG 0.004 0.000 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 261 time to evaluate : 2.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.8078 (mtpt) cc_final: 0.7788 (mmmt) REVERT: A 502 LYS cc_start: 0.6983 (mmtp) cc_final: 0.5659 (mmtp) REVERT: I 502 LYS cc_start: 0.6799 (mmtp) cc_final: 0.5411 (mmtm) REVERT: K 100 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9068 (mp) REVERT: S 502 LYS cc_start: 0.6875 (mmtp) cc_final: 0.5726 (mmtm) REVERT: V 47 MET cc_start: 0.8003 (mmm) cc_final: 0.7688 (mmt) outliers start: 53 outliers final: 46 residues processed: 294 average time/residue: 0.3629 time to fit residues: 155.5807 Evaluate side-chains 300 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 253 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 213 ILE Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain U residue 21 SER Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 11 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 213 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 187 optimal weight: 3.9990 chunk 196 optimal weight: 0.6980 chunk 206 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN J 651 ASN M 17 GLN V 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 19974 Z= 0.302 Angle : 0.586 7.373 27093 Z= 0.304 Chirality : 0.047 0.490 3279 Planarity : 0.004 0.054 3339 Dihedral : 6.963 110.908 4345 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.51 % Favored : 94.36 % Rotamer: Outliers : 2.74 % Allowed : 10.65 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.12 (0.18), residues: 2304 helix: 1.66 (0.27), residues: 405 sheet: 0.24 (0.19), residues: 750 loop : -0.56 (0.19), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 427 HIS 0.005 0.001 HIS A 105 PHE 0.017 0.002 PHE A 383 TYR 0.015 0.001 TYR M 49 ARG 0.010 0.001 ARG M 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 265 time to evaluate : 2.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.8086 (mtpt) cc_final: 0.7825 (mmmt) REVERT: A 502 LYS cc_start: 0.6974 (mmtp) cc_final: 0.5585 (mmtp) REVERT: I 502 LYS cc_start: 0.6884 (mmtp) cc_final: 0.5965 (mmtt) REVERT: K 100 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.8986 (mp) REVERT: S 502 LYS cc_start: 0.6892 (mmtp) cc_final: 0.5532 (mmtm) REVERT: V 47 MET cc_start: 0.8003 (mmm) cc_final: 0.7689 (mmt) outliers start: 56 outliers final: 49 residues processed: 302 average time/residue: 0.3565 time to fit residues: 157.7910 Evaluate side-chains 305 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 255 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 213 ILE Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 615 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 639 THR Chi-restraints excluded: chain U residue 21 SER Chi-restraints excluded: chain U residue 25 SER Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 11 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 219 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 230 optimal weight: 2.9990 chunk 211 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 141 optimal weight: 10.0000 chunk 112 optimal weight: 0.7980 chunk 145 optimal weight: 7.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN J 607 ASN J 651 ASN V 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 19974 Z= 0.366 Angle : 0.630 11.176 27093 Z= 0.325 Chirality : 0.048 0.435 3279 Planarity : 0.004 0.054 3339 Dihedral : 7.553 116.318 4345 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.64 % Favored : 94.23 % Rotamer: Outliers : 2.64 % Allowed : 10.61 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.04 (0.18), residues: 2304 helix: 1.41 (0.27), residues: 402 sheet: 0.29 (0.19), residues: 726 loop : -0.59 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 427 HIS 0.006 0.001 HIS A 72 PHE 0.019 0.002 PHE A 383 TYR 0.015 0.002 TYR M 49 ARG 0.009 0.001 ARG M 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 261 time to evaluate : 2.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.8083 (mtpt) cc_final: 0.7830 (mmmt) REVERT: A 502 LYS cc_start: 0.7011 (mmtp) cc_final: 0.5621 (mmtp) REVERT: I 502 LYS cc_start: 0.6996 (mmtp) cc_final: 0.5679 (mmtm) REVERT: K 100 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9020 (mp) REVERT: S 502 LYS cc_start: 0.6933 (mmtp) cc_final: 0.5940 (mmtt) REVERT: V 47 MET cc_start: 0.8002 (mmm) cc_final: 0.7701 (mmt) outliers start: 54 outliers final: 49 residues processed: 298 average time/residue: 0.3577 time to fit residues: 157.0320 Evaluate side-chains 305 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 255 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 375 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 111 LEU Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain S residue 167 ASP Chi-restraints excluded: chain S residue 213 ILE Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain S residue 426 MET Chi-restraints excluded: chain S residue 445 CYS Chi-restraints excluded: chain T residue 612 SER Chi-restraints excluded: chain T residue 615 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain T residue 639 THR Chi-restraints excluded: chain U residue 21 SER Chi-restraints excluded: chain U residue 25 SER Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 11 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 50 optimal weight: 0.5980 chunk 183 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 161 optimal weight: 6.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 ASN J 651 ASN V 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.119517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.089257 restraints weight = 27449.366| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.50 r_work: 0.2767 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19974 Z= 0.258 Angle : 0.574 10.036 27093 Z= 0.297 Chirality : 0.046 0.392 3279 Planarity : 0.004 0.053 3339 Dihedral : 7.585 112.699 4345 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.25 % Favored : 94.62 % Rotamer: Outliers : 2.44 % Allowed : 10.85 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.18 (0.18), residues: 2304 helix: 1.96 (0.27), residues: 381 sheet: 0.32 (0.19), residues: 726 loop : -0.59 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 427 HIS 0.004 0.001 HIS S 105 PHE 0.015 0.001 PHE A 383 TYR 0.015 0.001 TYR M 49 ARG 0.009 0.000 ARG M 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4430.17 seconds wall clock time: 81 minutes 17.01 seconds (4877.01 seconds total)