Starting phenix.real_space_refine on Wed Apr 10 13:12:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9t_22110/04_2024/6x9t_22110.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9t_22110/04_2024/6x9t_22110.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9t_22110/04_2024/6x9t_22110.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9t_22110/04_2024/6x9t_22110.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9t_22110/04_2024/6x9t_22110.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9t_22110/04_2024/6x9t_22110.pdb" } resolution = 3.2 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 "I PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 10.87, per 1000 atoms: 0.55 Number of scatterers: 19590 At special positions: 0 Unit cell: (122.57, 125.66, 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=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.15 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=2.17 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.15 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=2.16 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS S 228 " - pdb=" SG CYS S 239 " distance=2.15 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=2.17 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: 8.54 Conformation dependent library (CDL) restraints added in 3.3 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: 51 helices and 48 sheets defined 21.4% alpha, 43.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.141A 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: 4.070A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.207A 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: 3.752A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.390A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.558A 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: 4.141A 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: 4.069A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.207A 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: 3.752A pdb=" N SER I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 523 through 528 removed outlier: 4.390A pdb=" N GLY J 527 " --> pdb=" O GLY J 524 " (cutoff:3.500A) Processing helix chain 'J' and resid 536 through 542 removed outlier: 3.558A 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: 4.142A 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: 4.070A pdb=" N LYS S 351 " --> pdb=" O LYS S 347 " (cutoff:3.500A) removed outlier: 4.207A 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: 3.752A pdb=" N SER S 481 " --> pdb=" O ASP S 477 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLU S 482 " --> pdb=" O ASN S 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 523 through 528 removed outlier: 4.391A pdb=" N GLY T 527 " --> pdb=" O GLY T 524 " (cutoff:3.500A) Processing helix chain 'T' and resid 536 through 542 removed outlier: 3.557A 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: 3.807A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.900A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) 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: 6.406A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.526A 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: 6.525A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR A 467 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.486A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.903A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 11.876A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.885A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.843A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.991A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 12.141A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.343A 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: 6.591A 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: 6.311A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.572A 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: 6.807A pdb=" N MET H 34 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (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: 6.650A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.481A 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: 6.650A 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: 3.808A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'I' and resid 75 through 76 removed outlier: 6.900A pdb=" N CYS I 54 " --> pdb=" O VAL I 75 " (cutoff:3.500A) 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: 6.406A pdb=" N ALA I 200 " --> pdb=" O ALA I 433 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N TYR I 435 " --> pdb=" O ALA I 200 " (cutoff:3.500A) removed outlier: 6.526A 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: 6.525A pdb=" N ILE I 358 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N PHE I 468 " --> pdb=" O ILE I 358 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR I 467 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N GLY I 441 " --> pdb=" O ASN I 300 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ASN I 300 " --> pdb=" O GLY I 441 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.487A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 11.903A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 11.877A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 10.884A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 10.843A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 10.991A pdb=" N ASP I 457 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 12.141A pdb=" N ILE I 284 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 4.343A 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: 6.591A 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: 6.310A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ILE I 323 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 6.572A 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: 6.807A pdb=" N MET K 34 " --> pdb=" O LEU K 50 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (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: 6.649A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) removed outlier: 6.482A 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: 6.649A 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: 3.807A pdb=" N ILE S 225 " --> pdb=" O VAL S 245 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'S' and resid 75 through 76 removed outlier: 6.899A pdb=" N CYS S 54 " --> pdb=" O VAL S 75 " (cutoff:3.500A) 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: 6.406A pdb=" N ALA S 200 " --> pdb=" O ALA S 433 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N TYR S 435 " --> pdb=" O ALA S 200 " (cutoff:3.500A) removed outlier: 6.526A 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: 6.526A pdb=" N ILE S 358 " --> pdb=" O GLU S 466 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N PHE S 468 " --> pdb=" O ILE S 358 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG S 360 " --> pdb=" O PHE S 468 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR S 467 " --> pdb=" O ASP S 457 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N GLY S 441 " --> pdb=" O ASN S 300 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ASN S 300 " --> pdb=" O GLY S 441 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY S 451 " --> pdb=" O THR S 290 " (cutoff:3.500A) removed outlier: 10.487A pdb=" N THR S 290 " --> pdb=" O GLY S 451 " (cutoff:3.500A) removed outlier: 11.903A pdb=" N ILE S 453 " --> pdb=" O PHE S 288 " (cutoff:3.500A) removed outlier: 11.876A pdb=" N PHE S 288 " --> pdb=" O ILE S 453 " (cutoff:3.500A) removed outlier: 10.885A pdb=" N THR S 455 " --> pdb=" O VAL S 286 " (cutoff:3.500A) removed outlier: 10.843A pdb=" N VAL S 286 " --> pdb=" O THR S 455 " (cutoff:3.500A) removed outlier: 10.991A pdb=" N ASP S 457 " --> pdb=" O ILE S 284 " (cutoff:3.500A) removed outlier: 12.141A pdb=" N ILE S 284 " --> pdb=" O ASP S 457 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA S 329 " --> pdb=" O CYS S 418 " (cutoff:3.500A) removed outlier: 4.342A 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: 6.591A 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: 6.311A pdb=" N GLN S 315 " --> pdb=" O ILE S 309 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N THR S 303 " --> pdb=" O GLY S 321 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ILE S 323 " --> pdb=" O ASN S 301 " (cutoff:3.500A) removed outlier: 6.573A 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: 6.807A pdb=" N MET U 34 " --> pdb=" O LEU U 50 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU U 50 " --> pdb=" O MET U 34 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP U 36 " --> pdb=" O VAL U 48 " (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: 6.650A pdb=" N VAL V 11 " --> pdb=" O THR V 105 " (cutoff:3.500A) removed outlier: 6.481A 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: 6.650A 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. 1944 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: 7.16 Time building geometry restraints manager: 9.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3489 1.31 - 1.44: 5380 1.44 - 1.56: 10847 1.56 - 1.69: 84 1.69 - 1.82: 174 Bond restraints: 19974 Sorted by residual: bond pdb=" C1 NAG Y 2 " pdb=" O5 NAG Y 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.06e+01 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" C1 NAG 0 2 " pdb=" O5 NAG 0 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" C1 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.02e+01 ... (remaining 19969 not shown) Histogram of bond angle deviations from ideal: 96.15 - 103.75: 263 103.75 - 111.34: 8312 111.34 - 118.94: 8195 118.94 - 126.54: 10049 126.54 - 134.13: 274 Bond angle restraints: 27093 Sorted by residual: angle pdb=" N PRO M 7 " pdb=" CA PRO M 7 " pdb=" C PRO M 7 " ideal model delta sigma weight residual 110.70 122.92 -12.22 1.22e+00 6.72e-01 1.00e+02 angle pdb=" N PRO L 7 " pdb=" CA PRO L 7 " pdb=" C PRO L 7 " ideal model delta sigma weight residual 110.70 122.92 -12.22 1.22e+00 6.72e-01 1.00e+02 angle pdb=" N PRO V 7 " pdb=" CA PRO V 7 " pdb=" C PRO V 7 " ideal model delta sigma weight residual 110.70 122.88 -12.18 1.22e+00 6.72e-01 9.96e+01 angle pdb=" C ASP V 50 " pdb=" N VAL V 51 " pdb=" CA VAL V 51 " ideal model delta sigma weight residual 123.16 114.80 8.36 1.06e+00 8.90e-01 6.21e+01 angle pdb=" C ASP L 50 " pdb=" N VAL L 51 " pdb=" CA VAL L 51 " ideal model delta sigma weight residual 123.16 114.83 8.33 1.06e+00 8.90e-01 6.18e+01 ... (remaining 27088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.85: 12606 21.85 - 43.70: 300 43.70 - 65.55: 90 65.55 - 87.39: 30 87.39 - 109.24: 12 Dihedral angle restraints: 13038 sinusoidal: 6291 harmonic: 6747 Sorted by residual: 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 93.00 160.22 -67.22 1 1.00e+01 1.00e-02 5.88e+01 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 93.00 160.22 -67.22 1 1.00e+01 1.00e-02 5.88e+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 93.00 160.20 -67.20 1 1.00e+01 1.00e-02 5.88e+01 ... (remaining 13035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 2335 0.100 - 0.201: 788 0.201 - 0.301: 132 0.301 - 0.401: 21 0.401 - 0.502: 3 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 1.56e+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 -2.65 0.25 2.00e-02 2.50e+03 1.55e+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 -2.65 0.25 2.00e-02 2.50e+03 1.54e+02 ... (remaining 3276 not shown) Planarity restraints: 3405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 702 " 0.152 2.00e-02 2.50e+03 1.26e-01 1.99e+02 pdb=" C7 NAG B 702 " -0.040 2.00e-02 2.50e+03 pdb=" C8 NAG B 702 " 0.112 2.00e-02 2.50e+03 pdb=" N2 NAG B 702 " -0.206 2.00e-02 2.50e+03 pdb=" O7 NAG B 702 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 702 " -0.152 2.00e-02 2.50e+03 1.26e-01 1.99e+02 pdb=" C7 NAG J 702 " 0.041 2.00e-02 2.50e+03 pdb=" C8 NAG J 702 " -0.112 2.00e-02 2.50e+03 pdb=" N2 NAG J 702 " 0.205 2.00e-02 2.50e+03 pdb=" O7 NAG J 702 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 702 " 0.152 2.00e-02 2.50e+03 1.26e-01 1.99e+02 pdb=" C7 NAG T 702 " -0.040 2.00e-02 2.50e+03 pdb=" C8 NAG T 702 " 0.112 2.00e-02 2.50e+03 pdb=" N2 NAG T 702 " -0.206 2.00e-02 2.50e+03 pdb=" O7 NAG T 702 " -0.017 2.00e-02 2.50e+03 ... (remaining 3402 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4745 2.78 - 3.31: 16764 3.31 - 3.84: 31952 3.84 - 4.37: 38180 4.37 - 4.90: 64656 Nonbonded interactions: 156297 Sorted by model distance: nonbonded pdb=" OG1 THR I 37 " pdb=" OG1 THR I 499 " model vdw 2.251 2.440 nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.251 2.440 nonbonded pdb=" OG1 THR S 37 " pdb=" OG1 THR S 499 " model vdw 2.252 2.440 nonbonded pdb=" N ASN I 355 " pdb=" OD1 ASN I 355 " model vdw 2.272 2.520 nonbonded pdb=" N ASN A 355 " pdb=" OD1 ASN A 355 " model vdw 2.273 2.520 ... (remaining 156292 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: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.290 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 54.280 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 0.166 19974 Z= 1.612 Angle : 1.706 12.224 27093 Z= 1.115 Chirality : 0.101 0.502 3279 Planarity : 0.010 0.126 3339 Dihedral : 11.430 109.243 8598 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.26 % 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: 0.44 (0.17), residues: 2304 helix: -0.19 (0.24), residues: 384 sheet: 0.72 (0.20), residues: 666 loop : 0.35 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.010 TRP I 427 HIS 0.006 0.002 HIS A 216 PHE 0.033 0.006 PHE I 383 TYR 0.054 0.007 TYR L 36 ARG 0.008 0.001 ARG K 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 498 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 489 time to evaluate : 2.231 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7783 (mm-30) REVERT: A 136 ASN cc_start: 0.7204 (m-40) cc_final: 0.6895 (p0) REVERT: A 502 LYS cc_start: 0.6423 (mmtp) cc_final: 0.5930 (mmtp) REVERT: B 632 ASP cc_start: 0.8593 (t70) cc_final: 0.8277 (t0) REVERT: L 54 ARG cc_start: 0.8602 (ptp90) cc_final: 0.8386 (ptp90) REVERT: L 94 ARG cc_start: 0.6210 (mmt180) cc_final: 0.5150 (ttm110) REVERT: I 136 ASN cc_start: 0.7034 (m-40) cc_final: 0.6819 (p0) REVERT: I 268 GLU cc_start: 0.7341 (mt-10) cc_final: 0.7106 (mt-10) REVERT: I 502 LYS cc_start: 0.6416 (mmtp) cc_final: 0.5344 (mmtp) REVERT: J 616 ASN cc_start: 0.8275 (t0) cc_final: 0.7673 (p0) REVERT: J 633 LYS cc_start: 0.8670 (mttt) cc_final: 0.8468 (mtmm) REVERT: M 54 ARG cc_start: 0.8631 (ptp90) cc_final: 0.8421 (ptt-90) REVERT: M 94 ARG cc_start: 0.6113 (mmt180) cc_final: 0.4630 (mtp180) REVERT: S 49 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7918 (mm-30) REVERT: S 136 ASN cc_start: 0.7371 (m-40) cc_final: 0.6698 (p0) REVERT: S 207 LYS cc_start: 0.7673 (pttt) cc_final: 0.7441 (mmtm) REVERT: S 502 LYS cc_start: 0.6464 (mmtp) cc_final: 0.5547 (mmtm) REVERT: V 94 ARG cc_start: 0.6106 (mmt180) cc_final: 0.5128 (mmt180) outliers start: 9 outliers final: 8 residues processed: 497 average time/residue: 0.3678 time to fit residues: 263.6323 Evaluate side-chains 279 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 271 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 637 ASN Chi-restraints excluded: chain S residue 355 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: 2.9990 chunk 175 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 181 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 209 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 103 GLN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 246 GLN ** S 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19974 Z= 0.229 Angle : 0.646 7.513 27093 Z= 0.346 Chirality : 0.046 0.260 3279 Planarity : 0.004 0.037 3339 Dihedral : 8.684 66.780 4351 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.21 % Favored : 96.40 % Rotamer: Outliers : 1.42 % Allowed : 6.30 % Favored : 92.28 % 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: 0.71 (0.17), residues: 2304 helix: 1.59 (0.28), residues: 381 sheet: 0.60 (0.20), residues: 675 loop : 0.14 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 479 HIS 0.005 0.001 HIS U 82A PHE 0.018 0.002 PHE A 383 TYR 0.023 0.002 TYR S 173 ARG 0.008 0.001 ARG A 444 *********************** 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 348 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 319 time to evaluate : 2.236 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 49 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7567 (mm-30) REVERT: A 136 ASN cc_start: 0.7283 (m-40) cc_final: 0.7010 (p0) REVERT: A 502 LYS cc_start: 0.6367 (mmtp) cc_final: 0.5308 (ttpt) REVERT: B 632 ASP cc_start: 0.8286 (t70) cc_final: 0.8024 (t0) REVERT: L 67 SER cc_start: 0.8919 (p) cc_final: 0.8683 (m) REVERT: L 94 ARG cc_start: 0.6113 (mmt180) cc_final: 0.5044 (ttm110) REVERT: I 161 MET cc_start: 0.8375 (tpp) cc_final: 0.8098 (tpp) REVERT: I 268 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7150 (mt-10) REVERT: I 428 GLN cc_start: 0.7169 (mp10) cc_final: 0.6950 (mp10) REVERT: I 502 LYS cc_start: 0.6743 (mmtp) cc_final: 0.5375 (tttp) REVERT: J 616 ASN cc_start: 0.7971 (t0) cc_final: 0.7650 (p0) REVERT: M 94 ARG cc_start: 0.5812 (mmt180) cc_final: 0.4674 (mtp180) REVERT: S 49 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7949 (mm-30) REVERT: S 82 GLN cc_start: 0.7249 (mm110) cc_final: 0.7035 (tp40) REVERT: S 136 ASN cc_start: 0.7311 (m-40) cc_final: 0.6663 (p0) REVERT: S 502 LYS cc_start: 0.6794 (mmtp) cc_final: 0.5400 (mmtp) REVERT: V 94 ARG cc_start: 0.5588 (mmt180) cc_final: 0.4703 (mmt180) outliers start: 29 outliers final: 16 residues processed: 338 average time/residue: 0.3698 time to fit residues: 183.9579 Evaluate side-chains 284 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 268 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 174 SER Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain T residue 618 ASN Chi-restraints excluded: chain U residue 2 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 116 optimal weight: 0.0370 chunk 65 optimal weight: 0.0270 chunk 174 optimal weight: 4.9990 chunk 142 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 210 optimal weight: 8.9990 chunk 227 optimal weight: 10.0000 chunk 187 optimal weight: 4.9990 chunk 208 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 103 GLN K 82AHIS S 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 19974 Z= 0.170 Angle : 0.569 8.705 27093 Z= 0.298 Chirality : 0.044 0.275 3279 Planarity : 0.004 0.060 3339 Dihedral : 7.139 54.499 4345 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.65 % Favored : 96.09 % Rotamer: Outliers : 1.27 % Allowed : 8.75 % Favored : 89.98 % 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: 0.70 (0.18), residues: 2304 helix: 1.81 (0.28), residues: 396 sheet: 0.62 (0.20), residues: 669 loop : 0.00 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 112 HIS 0.005 0.001 HIS I 105 PHE 0.013 0.002 PHE S 53 TYR 0.019 0.001 TYR A 173 ARG 0.006 0.000 ARG S 419 *********************** 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 306 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 280 time to evaluate : 2.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7648 (mm-30) REVERT: A 121 LYS cc_start: 0.8404 (mtpp) cc_final: 0.8177 (mptt) REVERT: A 136 ASN cc_start: 0.7325 (m-40) cc_final: 0.7110 (p0) REVERT: A 502 LYS cc_start: 0.6476 (mmtp) cc_final: 0.5383 (ttpt) REVERT: B 632 ASP cc_start: 0.8235 (t70) cc_final: 0.7973 (t0) REVERT: L 42 LYS cc_start: 0.8236 (mppt) cc_final: 0.7874 (mptt) REVERT: L 67 SER cc_start: 0.8958 (p) cc_final: 0.8713 (m) REVERT: L 94 ARG cc_start: 0.5842 (mmt180) cc_final: 0.4536 (mtp180) REVERT: I 161 MET cc_start: 0.8349 (tpp) cc_final: 0.8049 (tpp) REVERT: I 268 GLU cc_start: 0.7343 (mt-10) cc_final: 0.7126 (mt-10) REVERT: I 502 LYS cc_start: 0.6728 (mmtp) cc_final: 0.5411 (tttp) REVERT: M 94 ARG cc_start: 0.5757 (mmt180) cc_final: 0.4441 (mtp180) REVERT: S 49 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7962 (mm-30) REVERT: S 82 GLN cc_start: 0.7318 (mm110) cc_final: 0.7084 (tp40) REVERT: S 502 LYS cc_start: 0.6711 (mmtp) cc_final: 0.5659 (mmtm) REVERT: V 94 ARG cc_start: 0.5768 (mmt180) cc_final: 0.4652 (mtp180) outliers start: 26 outliers final: 19 residues processed: 292 average time/residue: 0.3577 time to fit residues: 158.4049 Evaluate side-chains 287 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 268 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain S residue 355 ASN 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 2 VAL Chi-restraints excluded: chain V residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 0.9990 chunk 158 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 210 optimal weight: 10.0000 chunk 223 optimal weight: 0.0970 chunk 110 optimal weight: 0.8980 chunk 199 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 ASN I 103 GLN I 246 GLN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 246 GLN ** S 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19974 Z= 0.206 Angle : 0.555 8.467 27093 Z= 0.290 Chirality : 0.045 0.274 3279 Planarity : 0.004 0.041 3339 Dihedral : 5.997 59.943 4343 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.86 % Favored : 95.88 % Rotamer: Outliers : 1.76 % Allowed : 9.38 % Favored : 88.86 % 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: 0.64 (0.18), residues: 2304 helix: 1.87 (0.28), residues: 396 sheet: 0.65 (0.20), residues: 669 loop : -0.12 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 35 HIS 0.005 0.001 HIS A 105 PHE 0.013 0.002 PHE I 383 TYR 0.018 0.001 TYR V 49 ARG 0.003 0.000 ARG V 61 *********************** 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 325 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 289 time to evaluate : 2.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ASN cc_start: 0.7285 (m-40) cc_final: 0.7084 (p0) REVERT: A 502 LYS cc_start: 0.6664 (mmtp) cc_final: 0.5586 (mmtp) REVERT: B 632 ASP cc_start: 0.8242 (t70) cc_final: 0.7971 (t0) REVERT: L 94 ARG cc_start: 0.5940 (mmt180) cc_final: 0.4581 (mtp180) REVERT: I 161 MET cc_start: 0.8376 (tpp) cc_final: 0.8050 (tpp) REVERT: I 268 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7193 (mt-10) REVERT: I 502 LYS cc_start: 0.6662 (mmtp) cc_final: 0.5276 (tttp) REVERT: M 94 ARG cc_start: 0.5679 (mmt180) cc_final: 0.4355 (mtp180) REVERT: S 49 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7955 (mm-30) REVERT: S 82 GLN cc_start: 0.7477 (mm110) cc_final: 0.7234 (tp40) REVERT: S 136 ASN cc_start: 0.7324 (m-40) cc_final: 0.6777 (p0) REVERT: S 502 LYS cc_start: 0.6552 (mmtp) cc_final: 0.5779 (mmtt) REVERT: U 100 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8971 (pt0) REVERT: V 94 ARG cc_start: 0.5901 (mmt180) cc_final: 0.4687 (mtp180) outliers start: 36 outliers final: 27 residues processed: 305 average time/residue: 0.3612 time to fit residues: 165.2191 Evaluate side-chains 295 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 267 time to evaluate : 2.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain I residue 67 ASN Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 636 SER Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain S residue 355 ASN 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 2 VAL Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain U residue 100 GLN Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 8.9990 chunk 126 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 166 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 190 optimal weight: 8.9990 chunk 154 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 200 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 103 GLN I 246 GLN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 246 GLN ** S 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 607 ASN V 69 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19974 Z= 0.172 Angle : 0.521 6.448 27093 Z= 0.272 Chirality : 0.044 0.270 3279 Planarity : 0.004 0.044 3339 Dihedral : 5.634 58.918 4343 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.95 % Favored : 95.88 % Rotamer: Outliers : 1.91 % Allowed : 9.78 % Favored : 88.32 % 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: 0.64 (0.18), residues: 2304 helix: 1.97 (0.28), residues: 396 sheet: 0.65 (0.20), residues: 669 loop : -0.16 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 112 HIS 0.006 0.001 HIS I 66 PHE 0.012 0.001 PHE S 53 TYR 0.014 0.001 TYR M 49 ARG 0.008 0.000 ARG S 444 *********************** 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 315 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 276 time to evaluate : 2.313 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 502 LYS cc_start: 0.6612 (mmtp) cc_final: 0.5342 (mmtp) REVERT: B 632 ASP cc_start: 0.8206 (t70) cc_final: 0.7939 (t0) REVERT: L 42 LYS cc_start: 0.8207 (mppt) cc_final: 0.7730 (mptt) REVERT: L 94 ARG cc_start: 0.5994 (mmt180) cc_final: 0.4613 (mtp180) REVERT: I 161 MET cc_start: 0.8372 (tpp) cc_final: 0.8058 (tpp) REVERT: I 268 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7244 (mt-10) REVERT: I 371 VAL cc_start: 0.8787 (t) cc_final: 0.8550 (m) REVERT: I 502 LYS cc_start: 0.6707 (mmtp) cc_final: 0.5390 (tttp) REVERT: M 94 ARG cc_start: 0.5700 (mmt180) cc_final: 0.4360 (mtp180) REVERT: S 47 ASP cc_start: 0.8502 (m-30) cc_final: 0.8280 (m-30) REVERT: S 49 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7903 (mm-30) REVERT: S 82 GLN cc_start: 0.7452 (mm110) cc_final: 0.7202 (tp40) REVERT: S 136 ASN cc_start: 0.7332 (m-40) cc_final: 0.6756 (p0) REVERT: S 502 LYS cc_start: 0.6327 (mmtp) cc_final: 0.5332 (mmtp) REVERT: V 94 ARG cc_start: 0.5878 (mmt180) cc_final: 0.4642 (mtp180) outliers start: 39 outliers final: 30 residues processed: 291 average time/residue: 0.3436 time to fit residues: 149.0151 Evaluate side-chains 295 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 265 time to evaluate : 2.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain I residue 82 GLN Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain J residue 618 ASN Chi-restraints excluded: chain J residue 636 SER Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 445 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 U residue 2 VAL Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 102 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 75 optimal weight: 0.5980 chunk 201 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 223 optimal weight: 5.9990 chunk 185 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 18 optimal weight: 0.0010 chunk 73 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 overall best weight: 2.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 69 ASN I 67 ASN I 103 GLN I 246 GLN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 67 ASN S 246 GLN ** S 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 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 0.046 19974 Z= 0.314 Angle : 0.597 7.471 27093 Z= 0.310 Chirality : 0.046 0.273 3279 Planarity : 0.004 0.047 3339 Dihedral : 5.706 56.017 4343 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.69 % Favored : 95.18 % Rotamer: Outliers : 1.96 % Allowed : 10.51 % Favored : 87.54 % 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: 0.43 (0.18), residues: 2304 helix: 1.77 (0.28), residues: 396 sheet: 0.51 (0.20), residues: 669 loop : -0.28 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 35 HIS 0.005 0.001 HIS I 105 PHE 0.018 0.002 PHE H 29 TYR 0.022 0.002 TYR M 49 ARG 0.005 0.001 ARG S 444 *********************** 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 314 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 274 time to evaluate : 2.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 LYS cc_start: 0.6875 (mmtp) cc_final: 0.5644 (mmtp) REVERT: B 632 ASP cc_start: 0.8350 (t70) cc_final: 0.8074 (t0) REVERT: L 17 GLN cc_start: 0.6683 (mt0) cc_final: 0.6370 (mt0) REVERT: L 42 LYS cc_start: 0.8220 (mppt) cc_final: 0.7736 (mptt) REVERT: L 94 ARG cc_start: 0.6129 (mmt180) cc_final: 0.4641 (mtp180) REVERT: I 161 MET cc_start: 0.8448 (tpp) cc_final: 0.8081 (tpp) REVERT: I 502 LYS cc_start: 0.6839 (mmtp) cc_final: 0.5281 (tttm) REVERT: M 94 ARG cc_start: 0.5755 (mmt180) cc_final: 0.4323 (mtp180) REVERT: S 49 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7896 (mm-30) REVERT: S 82 GLN cc_start: 0.7512 (mm110) cc_final: 0.7241 (tp40) REVERT: S 136 ASN cc_start: 0.7488 (m-40) cc_final: 0.6880 (p0) REVERT: S 502 LYS cc_start: 0.6782 (mmtp) cc_final: 0.6279 (mmtt) REVERT: V 94 ARG cc_start: 0.5869 (mmt180) cc_final: 0.4768 (mmt180) outliers start: 40 outliers final: 30 residues processed: 296 average time/residue: 0.3390 time to fit residues: 150.4909 Evaluate side-chains 288 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 258 time to evaluate : 2.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain I residue 67 ASN Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain J residue 636 SER Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain S residue 67 ASN Chi-restraints excluded: chain S residue 355 ASN 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 2 VAL Chi-restraints excluded: chain U residue 79 SER Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 127 optimal weight: 0.7980 chunk 163 optimal weight: 3.9990 chunk 126 optimal weight: 0.0970 chunk 188 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 222 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN I 103 GLN I 246 GLN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 246 GLN ** S 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 607 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19974 Z= 0.246 Angle : 0.561 7.192 27093 Z= 0.291 Chirality : 0.045 0.263 3279 Planarity : 0.004 0.046 3339 Dihedral : 5.400 46.058 4339 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.69 % Favored : 95.18 % Rotamer: Outliers : 2.25 % Allowed : 10.22 % Favored : 87.54 % 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: 0.37 (0.18), residues: 2304 helix: 1.74 (0.28), residues: 399 sheet: 0.48 (0.20), residues: 669 loop : -0.34 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 112 HIS 0.004 0.001 HIS I 105 PHE 0.015 0.002 PHE K 29 TYR 0.018 0.001 TYR M 49 ARG 0.005 0.000 ARG S 444 *********************** 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 312 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 266 time to evaluate : 2.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 502 LYS cc_start: 0.6850 (mmtp) cc_final: 0.5697 (mmtt) REVERT: B 632 ASP cc_start: 0.8335 (t70) cc_final: 0.8058 (t0) REVERT: L 17 GLN cc_start: 0.6876 (mt0) cc_final: 0.6495 (mt0) REVERT: L 42 LYS cc_start: 0.8230 (mppt) cc_final: 0.7740 (mptt) REVERT: L 94 ARG cc_start: 0.6119 (mmt180) cc_final: 0.4712 (mtp180) REVERT: I 161 MET cc_start: 0.8406 (tpp) cc_final: 0.8022 (tpp) REVERT: I 371 VAL cc_start: 0.8714 (t) cc_final: 0.8509 (m) REVERT: I 502 LYS cc_start: 0.6715 (mmtp) cc_final: 0.5234 (tttm) REVERT: M 94 ARG cc_start: 0.5749 (mmt180) cc_final: 0.4309 (mtp180) REVERT: S 49 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7864 (mm-30) REVERT: S 82 GLN cc_start: 0.7383 (mm110) cc_final: 0.7119 (tp40) REVERT: S 136 ASN cc_start: 0.7502 (m-40) cc_final: 0.6868 (p0) REVERT: S 161 MET cc_start: 0.8418 (tpp) cc_final: 0.8137 (tpp) REVERT: S 502 LYS cc_start: 0.6647 (mmtp) cc_final: 0.6179 (mmtt) REVERT: V 94 ARG cc_start: 0.5898 (mmt180) cc_final: 0.4789 (mmt180) outliers start: 46 outliers final: 34 residues processed: 287 average time/residue: 0.3483 time to fit residues: 149.2997 Evaluate side-chains 293 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 259 time to evaluate : 2.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain J residue 636 SER Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain S residue 67 ASN Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 357 THR Chi-restraints excluded: chain S residue 445 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 U residue 2 VAL Chi-restraints excluded: chain U residue 79 SER Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 137 optimal weight: 0.5980 chunk 88 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 67 optimal weight: 0.0670 chunk 43 optimal weight: 0.2980 chunk 141 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 103 GLN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 246 GLN ** S 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 607 ASN V 69 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19974 Z= 0.224 Angle : 0.549 6.906 27093 Z= 0.285 Chirality : 0.045 0.260 3279 Planarity : 0.004 0.047 3339 Dihedral : 5.192 46.489 4339 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.90 % Favored : 95.05 % Rotamer: Outliers : 2.10 % Allowed : 10.51 % Favored : 87.39 % 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: 0.38 (0.18), residues: 2304 helix: 1.79 (0.27), residues: 399 sheet: 0.48 (0.20), residues: 669 loop : -0.35 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 112 HIS 0.004 0.001 HIS I 105 PHE 0.014 0.001 PHE K 29 TYR 0.016 0.001 TYR M 49 ARG 0.005 0.000 ARG S 444 *********************** 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 311 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 268 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8192 (tpp) cc_final: 0.7817 (tpp) REVERT: A 213 ILE cc_start: 0.8887 (tp) cc_final: 0.8579 (mm) REVERT: A 502 LYS cc_start: 0.6821 (mmtp) cc_final: 0.5607 (mmtp) REVERT: B 632 ASP cc_start: 0.8369 (t70) cc_final: 0.8110 (t0) REVERT: L 17 GLN cc_start: 0.6787 (mt0) cc_final: 0.6413 (mt0) REVERT: L 42 LYS cc_start: 0.8238 (mppt) cc_final: 0.7737 (mptt) REVERT: L 94 ARG cc_start: 0.6109 (mmt180) cc_final: 0.4726 (mtp180) REVERT: I 161 MET cc_start: 0.8407 (tpp) cc_final: 0.8023 (tpp) REVERT: I 268 GLU cc_start: 0.7312 (mt-10) cc_final: 0.7106 (mt-10) REVERT: I 318 TYR cc_start: 0.8791 (m-80) cc_final: 0.8565 (m-80) REVERT: I 502 LYS cc_start: 0.6839 (mmtp) cc_final: 0.5359 (tttm) REVERT: M 94 ARG cc_start: 0.5741 (mmt180) cc_final: 0.4302 (mtp180) REVERT: S 49 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7891 (mm-30) REVERT: S 82 GLN cc_start: 0.7394 (mm110) cc_final: 0.7124 (tp40) REVERT: S 136 ASN cc_start: 0.7526 (m-40) cc_final: 0.6888 (p0) REVERT: S 161 MET cc_start: 0.8418 (tpp) cc_final: 0.8074 (tpp) REVERT: S 502 LYS cc_start: 0.6678 (mmtp) cc_final: 0.5671 (mmtm) REVERT: T 632 ASP cc_start: 0.7994 (t70) cc_final: 0.7789 (t0) REVERT: V 94 ARG cc_start: 0.5889 (mmt180) cc_final: 0.4745 (mmt180) outliers start: 43 outliers final: 32 residues processed: 291 average time/residue: 0.3483 time to fit residues: 151.4367 Evaluate side-chains 294 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 262 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain S residue 67 ASN Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 357 THR Chi-restraints excluded: chain S residue 445 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 U residue 2 VAL Chi-restraints excluded: chain U residue 79 SER Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain V residue 67 SER Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 213 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 162 optimal weight: 0.6980 chunk 63 optimal weight: 7.9990 chunk 187 optimal weight: 4.9990 chunk 196 optimal weight: 0.9980 chunk 206 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 ASN I 103 GLN I 246 GLN S 246 GLN ** S 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 607 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19974 Z= 0.161 Angle : 0.516 6.525 27093 Z= 0.269 Chirality : 0.043 0.257 3279 Planarity : 0.004 0.045 3339 Dihedral : 4.864 47.180 4339 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.56 % Allowed : 11.29 % Favored : 87.15 % 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 (0.18), residues: 2304 helix: 2.27 (0.28), residues: 381 sheet: 0.55 (0.20), residues: 675 loop : -0.34 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 112 HIS 0.004 0.001 HIS I 105 PHE 0.012 0.001 PHE S 53 TYR 0.012 0.001 TYR M 49 ARG 0.008 0.000 ARG T 542 *********************** 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 299 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 267 time to evaluate : 2.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ILE cc_start: 0.8844 (tp) cc_final: 0.8518 (mm) REVERT: A 492 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8159 (mm-30) REVERT: A 502 LYS cc_start: 0.6762 (mmtp) cc_final: 0.5538 (mmtp) REVERT: B 632 ASP cc_start: 0.8367 (t70) cc_final: 0.8068 (t0) REVERT: L 17 GLN cc_start: 0.6819 (mt0) cc_final: 0.6429 (mt0) REVERT: L 27 ASP cc_start: 0.7942 (m-30) cc_final: 0.7728 (m-30) REVERT: L 42 LYS cc_start: 0.8227 (mppt) cc_final: 0.7730 (mptt) REVERT: L 94 ARG cc_start: 0.6038 (mmt180) cc_final: 0.4594 (mtp180) REVERT: I 161 MET cc_start: 0.8371 (tpp) cc_final: 0.7988 (tpp) REVERT: I 268 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7136 (mt-10) REVERT: I 318 TYR cc_start: 0.8765 (m-80) cc_final: 0.8543 (m-80) REVERT: I 502 LYS cc_start: 0.6779 (mmtp) cc_final: 0.5354 (tttp) REVERT: M 94 ARG cc_start: 0.5694 (mmt180) cc_final: 0.4284 (mtp180) REVERT: S 49 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7870 (mm-30) REVERT: S 82 GLN cc_start: 0.7406 (mm110) cc_final: 0.7153 (tp40) REVERT: S 136 ASN cc_start: 0.7433 (m-40) cc_final: 0.6825 (p0) REVERT: S 161 MET cc_start: 0.8381 (tpp) cc_final: 0.8069 (tpp) REVERT: S 502 LYS cc_start: 0.6648 (mmtp) cc_final: 0.5696 (mmtp) REVERT: V 94 ARG cc_start: 0.5796 (mmt180) cc_final: 0.4597 (mtp180) outliers start: 32 outliers final: 21 residues processed: 283 average time/residue: 0.3545 time to fit residues: 149.0295 Evaluate side-chains 284 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 263 time to evaluate : 2.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 TRP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain S residue 213 ILE Chi-restraints excluded: chain S residue 355 ASN 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 2 VAL Chi-restraints excluded: chain U residue 79 SER Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 219 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 152 optimal weight: 0.9990 chunk 230 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 145 optimal weight: 6.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 ASN I 103 GLN I 246 GLN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 246 GLN ** S 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19974 Z= 0.197 Angle : 0.526 7.445 27093 Z= 0.272 Chirality : 0.044 0.259 3279 Planarity : 0.004 0.046 3339 Dihedral : 4.801 47.670 4339 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.52 % Allowed : 11.24 % Favored : 87.24 % 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: 0.52 (0.18), residues: 2304 helix: 2.26 (0.28), residues: 381 sheet: 0.57 (0.20), residues: 675 loop : -0.35 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 112 HIS 0.004 0.001 HIS I 105 PHE 0.013 0.001 PHE K 29 TYR 0.015 0.001 TYR V 49 ARG 0.006 0.000 ARG T 542 ********************** 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 299 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 268 time to evaluate : 2.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ILE cc_start: 0.8860 (tp) cc_final: 0.8546 (mm) REVERT: A 492 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8178 (mm-30) REVERT: A 502 LYS cc_start: 0.6823 (mmtp) cc_final: 0.5565 (mmtp) REVERT: B 632 ASP cc_start: 0.8365 (t70) cc_final: 0.8095 (t0) REVERT: L 17 GLN cc_start: 0.6992 (mt0) cc_final: 0.6621 (mt0) REVERT: L 27 ASP cc_start: 0.7964 (m-30) cc_final: 0.7755 (m-30) REVERT: L 42 LYS cc_start: 0.8254 (mppt) cc_final: 0.7767 (mptt) REVERT: L 94 ARG cc_start: 0.6073 (mmt180) cc_final: 0.4600 (mtp180) REVERT: I 68 VAL cc_start: 0.8721 (t) cc_final: 0.8511 (t) REVERT: I 161 MET cc_start: 0.8405 (tpp) cc_final: 0.8030 (tpp) REVERT: I 268 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7177 (mt-10) REVERT: I 318 TYR cc_start: 0.8771 (m-80) cc_final: 0.8553 (m-80) REVERT: I 502 LYS cc_start: 0.6844 (mmtp) cc_final: 0.5376 (tttp) REVERT: J 616 ASN cc_start: 0.8113 (t0) cc_final: 0.7725 (p0) REVERT: M 94 ARG cc_start: 0.5679 (mmt180) cc_final: 0.4254 (mtp180) REVERT: S 49 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7865 (mm-30) REVERT: S 82 GLN cc_start: 0.7398 (mm110) cc_final: 0.7126 (tp40) REVERT: S 136 ASN cc_start: 0.7466 (m-40) cc_final: 0.6830 (p0) REVERT: S 161 MET cc_start: 0.8387 (tpp) cc_final: 0.8066 (tpp) REVERT: S 271 MET cc_start: 0.8261 (mmt) cc_final: 0.7883 (mmt) REVERT: S 502 LYS cc_start: 0.6652 (mmtp) cc_final: 0.6237 (mmtt) REVERT: V 94 ARG cc_start: 0.5803 (mmt180) cc_final: 0.4585 (mtp180) outliers start: 31 outliers final: 23 residues processed: 284 average time/residue: 0.3549 time to fit residues: 149.2917 Evaluate side-chains 286 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 263 time to evaluate : 2.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain I residue 35 TRP Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 357 THR 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 2 VAL Chi-restraints excluded: chain U residue 79 SER Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 2.9990 chunk 56 optimal weight: 0.0010 chunk 168 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 50 optimal weight: 0.1980 chunk 183 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 overall best weight: 1.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 ASN I 103 GLN I 246 GLN S 246 GLN ** S 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.123072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.096297 restraints weight = 25972.084| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.18 r_work: 0.2947 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19974 Z= 0.179 Angle : 0.515 6.794 27093 Z= 0.267 Chirality : 0.044 0.256 3279 Planarity : 0.004 0.046 3339 Dihedral : 4.691 47.983 4339 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.42 % Allowed : 11.58 % Favored : 87.00 % 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: 0.55 (0.18), residues: 2304 helix: 2.31 (0.28), residues: 381 sheet: 0.63 (0.20), residues: 660 loop : -0.36 (0.18), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 112 HIS 0.003 0.001 HIS I 105 PHE 0.012 0.001 PHE S 53 TYR 0.013 0.001 TYR M 49 ARG 0.006 0.000 ARG T 542 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4467.54 seconds wall clock time: 82 minutes 30.49 seconds (4950.49 seconds total)