Starting phenix.real_space_refine on Sat Feb 17 19:11:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9v_22112/02_2024/6x9v_22112.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9v_22112/02_2024/6x9v_22112.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9v_22112/02_2024/6x9v_22112.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9v_22112/02_2024/6x9v_22112.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9v_22112/02_2024/6x9v_22112.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x9v_22112/02_2024/6x9v_22112.pdb" } resolution = 3.5 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 "I PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19590 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3405 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 4 Chain: "B" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "H" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3405 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 4 Chain: "J" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "K" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "M" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "J" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "S" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3405 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 4 Chain: "T" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "U" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "V" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "T" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 10.52, per 1000 atoms: 0.54 Number of scatterers: 19590 At special positions: 0 Unit cell: (123.05, 125.35, 148.35, 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=2.07 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=2.13 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=2.08 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=2.07 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=2.13 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=2.08 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=2.07 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=2.13 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=2.08 Simple disulfide: pdb=" SG CYS T 598 " - pdb=" SG CYS T 604 " distance=2.03 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: 8.78 Conformation dependent library (CDL) restraints added in 3.4 seconds 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4332 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 48 sheets defined 20.6% alpha, 43.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.059A 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 334 through 354 removed outlier: 3.932A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.086A 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 387 through 390 Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.693A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 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: 4.059A 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 334 through 354 removed outlier: 3.932A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.086A 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 387 through 390 Processing helix chain 'I' and resid 476 through 484 removed outlier: 3.694A pdb=" N SER I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 536 through 542 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: 4.058A 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 334 through 354 removed outlier: 3.933A pdb=" N LYS S 351 " --> pdb=" O LYS S 347 " (cutoff:3.500A) removed outlier: 4.086A 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 387 through 390 Processing helix chain 'S' and resid 476 through 484 removed outlier: 3.693A pdb=" N SER S 481 " --> pdb=" O ASP S 477 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLU S 482 " --> pdb=" O ASN S 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 536 through 542 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: 3.727A 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 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: 6.356A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.598A 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: 6.318A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.632A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.915A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 11.993A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.860A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.826A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.971A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 12.284A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.320A 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 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: 6.293A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.471A 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: 6.004A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'H' and resid 11 through 12 Processing sheet with id= 14, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.589A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.499A 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: 6.589A 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: 3.727A 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 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: 6.356A pdb=" N ALA I 200 " --> pdb=" O ALA I 433 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N TYR I 435 " --> pdb=" O ALA I 200 " (cutoff:3.500A) removed outlier: 6.598A 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: 6.318A pdb=" N ILE I 358 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N PHE I 468 " --> pdb=" O ILE I 358 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLY I 441 " --> pdb=" O ASN I 300 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ASN I 300 " --> pdb=" O GLY I 441 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.632A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 11.915A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 11.994A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 10.860A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 10.826A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 10.970A pdb=" N ASP I 457 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 12.285A pdb=" N ILE I 284 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 4.320A 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 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: 6.292A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE I 323 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 6.471A 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: 6.004A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'K' and resid 11 through 12 Processing sheet with id= 30, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.589A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) removed outlier: 6.499A 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: 6.589A 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: 3.727A 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 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: 6.357A pdb=" N ALA S 200 " --> pdb=" O ALA S 433 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N TYR S 435 " --> pdb=" O ALA S 200 " (cutoff:3.500A) removed outlier: 6.598A 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: 6.318A pdb=" N ILE S 358 " --> pdb=" O GLU S 466 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N PHE S 468 " --> pdb=" O ILE S 358 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ARG S 360 " --> pdb=" O PHE S 468 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLY S 441 " --> pdb=" O ASN S 300 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ASN S 300 " --> pdb=" O GLY S 441 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY S 451 " --> pdb=" O THR S 290 " (cutoff:3.500A) removed outlier: 10.632A pdb=" N THR S 290 " --> pdb=" O GLY S 451 " (cutoff:3.500A) removed outlier: 11.915A pdb=" N ILE S 453 " --> pdb=" O PHE S 288 " (cutoff:3.500A) removed outlier: 11.993A pdb=" N PHE S 288 " --> pdb=" O ILE S 453 " (cutoff:3.500A) removed outlier: 10.860A pdb=" N THR S 455 " --> pdb=" O VAL S 286 " (cutoff:3.500A) removed outlier: 10.826A pdb=" N VAL S 286 " --> pdb=" O THR S 455 " (cutoff:3.500A) removed outlier: 10.971A pdb=" N ASP S 457 " --> pdb=" O ILE S 284 " (cutoff:3.500A) removed outlier: 12.284A pdb=" N ILE S 284 " --> pdb=" O ASP S 457 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA S 329 " --> pdb=" O CYS S 418 " (cutoff:3.500A) removed outlier: 4.320A 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 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: 6.293A pdb=" N GLN S 315 " --> pdb=" O ILE S 309 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N THR S 303 " --> pdb=" O GLY S 321 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ILE S 323 " --> pdb=" O ASN S 301 " (cutoff:3.500A) removed outlier: 6.471A 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: 6.005A pdb=" N ARG U 38 " --> pdb=" O TRP U 47 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TRP U 47 " --> pdb=" O ARG U 38 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'U' and resid 11 through 12 Processing sheet with id= 46, first strand: chain 'V' and resid 11 through 13 removed outlier: 6.590A pdb=" N VAL V 11 " --> pdb=" O THR V 105 " (cutoff:3.500A) removed outlier: 6.498A 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: 6.590A 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 24 768 hydrogen bonds defined for protein. 1980 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: 8.35 Time building geometry restraints manager: 9.24 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: 3619 1.31 - 1.44: 5416 1.44 - 1.56: 10679 1.56 - 1.69: 86 1.69 - 1.82: 174 Bond restraints: 19974 Sorted by residual: bond pdb=" CD ARG U 71 " pdb=" NE ARG U 71 " ideal model delta sigma weight residual 1.458 1.358 0.100 1.40e-02 5.10e+03 5.10e+01 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.549 -0.143 2.00e-02 2.50e+03 5.10e+01 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.549 -0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" CD ARG K 71 " pdb=" NE ARG K 71 " ideal model delta sigma weight residual 1.458 1.358 0.100 1.40e-02 5.10e+03 5.08e+01 bond pdb=" C1 NAG X 2 " pdb=" O5 NAG X 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.07e+01 ... (remaining 19969 not shown) Histogram of bond angle deviations from ideal: 97.27 - 104.61: 363 104.61 - 111.96: 9662 111.96 - 119.31: 7322 119.31 - 126.66: 9479 126.66 - 134.00: 267 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 110.70 122.59 -11.89 1.22e+00 6.72e-01 9.50e+01 angle pdb=" N PRO L 7 " pdb=" CA PRO L 7 " pdb=" C PRO L 7 " ideal model delta sigma weight residual 110.70 122.58 -11.88 1.22e+00 6.72e-01 9.47e+01 angle pdb=" N PRO V 7 " pdb=" CA PRO V 7 " pdb=" C PRO V 7 " ideal model delta sigma weight residual 110.70 122.57 -11.87 1.22e+00 6.72e-01 9.46e+01 angle pdb=" C CYS I 239 " pdb=" N PRO I 240 " pdb=" CA PRO I 240 " ideal model delta sigma weight residual 120.98 129.17 -8.19 1.07e+00 8.73e-01 5.85e+01 angle pdb=" C CYS S 239 " pdb=" N PRO S 240 " pdb=" CA PRO S 240 " ideal model delta sigma weight residual 120.98 129.16 -8.18 1.07e+00 8.73e-01 5.85e+01 ... (remaining 27088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.78: 12615 21.78 - 43.55: 297 43.55 - 65.33: 84 65.33 - 87.11: 30 87.11 - 108.89: 12 Dihedral angle restraints: 13038 sinusoidal: 6291 harmonic: 6747 Sorted by residual: 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 93.00 163.47 -70.47 1 1.00e+01 1.00e-02 6.39e+01 dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 163.46 -70.46 1 1.00e+01 1.00e-02 6.39e+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 93.00 163.46 -70.46 1 1.00e+01 1.00e-02 6.39e+01 ... (remaining 13035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 2434 0.108 - 0.215: 724 0.215 - 0.323: 105 0.323 - 0.430: 13 0.430 - 0.538: 3 Chirality restraints: 3279 Sorted by residual: 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 -2.62 0.22 2.00e-02 2.50e+03 1.17e+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 -2.61 0.21 2.00e-02 2.50e+03 1.13e+02 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 -2.61 0.21 2.00e-02 2.50e+03 1.13e+02 ... (remaining 3276 not shown) Planarity restraints: 3405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 702 " 0.237 2.00e-02 2.50e+03 1.96e-01 4.79e+02 pdb=" C7 NAG B 702 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG B 702 " 0.167 2.00e-02 2.50e+03 pdb=" N2 NAG B 702 " -0.321 2.00e-02 2.50e+03 pdb=" O7 NAG B 702 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 702 " -0.237 2.00e-02 2.50e+03 1.96e-01 4.78e+02 pdb=" C7 NAG J 702 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG J 702 " -0.167 2.00e-02 2.50e+03 pdb=" N2 NAG J 702 " 0.321 2.00e-02 2.50e+03 pdb=" O7 NAG J 702 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 702 " 0.237 2.00e-02 2.50e+03 1.95e-01 4.78e+02 pdb=" C7 NAG T 702 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG T 702 " 0.167 2.00e-02 2.50e+03 pdb=" N2 NAG T 702 " -0.320 2.00e-02 2.50e+03 pdb=" O7 NAG T 702 " -0.018 2.00e-02 2.50e+03 ... (remaining 3402 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 4611 2.77 - 3.30: 17084 3.30 - 3.83: 32577 3.83 - 4.37: 38969 4.37 - 4.90: 64839 Nonbonded interactions: 158080 Sorted by model distance: nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.233 2.440 nonbonded pdb=" OG1 THR S 37 " pdb=" OG1 THR S 499 " model vdw 2.233 2.440 nonbonded pdb=" OG1 THR I 37 " pdb=" OG1 THR I 499 " model vdw 2.234 2.440 nonbonded pdb=" N ASP K 84 " pdb=" OD1 ASP K 84 " model vdw 2.327 2.520 nonbonded pdb=" N ASP H 84 " pdb=" OD1 ASP H 84 " model vdw 2.327 2.520 ... (remaining 158075 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 group one per residue 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: 2.230 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: 0.040 Extract box with map and model: 6.350 Check model and map are aligned: 0.320 Set scattering table: 0.180 Process input model: 55.690 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 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 : 0.026 0.148 19974 Z= 1.693 Angle : 1.735 11.889 27093 Z= 1.132 Chirality : 0.101 0.538 3279 Planarity : 0.011 0.196 3339 Dihedral : 11.128 108.886 8598 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.39 % Favored : 96.35 % Rotamer: Outliers : 0.29 % Allowed : 0.44 % Favored : 99.27 % 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: 0.76 (0.17), residues: 2304 helix: 0.06 (0.25), residues: 378 sheet: 0.89 (0.19), residues: 690 loop : 0.59 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.012 TRP I 427 HIS 0.011 0.002 HIS U 82A PHE 0.032 0.006 PHE A 383 TYR 0.058 0.008 TYR S 40 ARG 0.011 0.001 ARG U 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 498 time to evaluate : 2.213 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: A 46 LYS cc_start: 0.8454 (mmtp) cc_final: 0.8219 (mmtp) REVERT: A 108 ILE cc_start: 0.8727 (pp) cc_final: 0.8437 (mm) REVERT: A 492 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7926 (mt-10) REVERT: B 625 ASN cc_start: 0.7934 (m110) cc_final: 0.7708 (m-40) REVERT: L 45 LYS cc_start: 0.8776 (tttt) cc_final: 0.8489 (ttmm) REVERT: L 60 ASP cc_start: 0.8345 (p0) cc_final: 0.8074 (t0) REVERT: L 105 THR cc_start: 0.7867 (m) cc_final: 0.7658 (p) REVERT: J 625 ASN cc_start: 0.7995 (m110) cc_final: 0.7728 (m-40) REVERT: K 72 ASP cc_start: 0.7636 (t0) cc_final: 0.7288 (t70) REVERT: M 45 LYS cc_start: 0.8166 (tttt) cc_final: 0.7868 (ttmm) REVERT: M 94 ARG cc_start: 0.6206 (mmt180) cc_final: 0.5072 (ttm-80) REVERT: M 95 THR cc_start: 0.7841 (m) cc_final: 0.7545 (p) REVERT: S 161 MET cc_start: 0.8423 (tpp) cc_final: 0.8000 (tpp) REVERT: V 45 LYS cc_start: 0.8913 (tttt) cc_final: 0.8548 (ttmm) REVERT: V 94 ARG cc_start: 0.5748 (mmt180) cc_final: 0.5334 (mmt-90) outliers start: 6 outliers final: 3 residues processed: 503 average time/residue: 0.3396 time to fit residues: 252.3375 Evaluate side-chains 262 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 259 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain S residue 355 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 4.9990 chunk 175 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 93 optimal weight: 8.9990 chunk 181 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 chunk 209 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN A 352 HIS A 428 GLN L 37 GLN ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 352 HIS I 432 GLN J 630 GLN J 653 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN ** S 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 352 HIS S 428 GLN S 432 GLN T 630 GLN V 37 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2736 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= 0.265 Angle : 0.701 9.081 27093 Z= 0.371 Chirality : 0.048 0.260 3279 Planarity : 0.005 0.065 3339 Dihedral : 7.590 57.011 4341 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.86 % Favored : 96.88 % Rotamer: Outliers : 1.81 % Allowed : 8.65 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.17), residues: 2304 helix: 1.34 (0.27), residues: 387 sheet: 0.47 (0.20), residues: 639 loop : 0.06 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 479 HIS 0.010 0.001 HIS S 72 PHE 0.024 0.002 PHE U 102 TYR 0.017 0.002 TYR K 100G ARG 0.007 0.001 ARG S 151 *********************** 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 368 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 331 time to evaluate : 2.153 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 492 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7963 (mt-10) REVERT: B 601 LYS cc_start: 0.9030 (mttp) cc_final: 0.8823 (mttt) REVERT: H 72 ASP cc_start: 0.7688 (t70) cc_final: 0.7380 (t70) REVERT: H 111 VAL cc_start: 0.8513 (t) cc_final: 0.8107 (m) REVERT: I 161 MET cc_start: 0.8508 (tpp) cc_final: 0.8278 (tpp) REVERT: I 271 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7954 (mtp) REVERT: I 323 ILE cc_start: 0.8588 (mt) cc_final: 0.8364 (mt) REVERT: J 648 GLU cc_start: 0.8470 (tp30) cc_final: 0.8027 (tt0) REVERT: K 28 THR cc_start: 0.8586 (m) cc_final: 0.8377 (p) REVERT: M 45 LYS cc_start: 0.8365 (tttt) cc_final: 0.8151 (ttmm) REVERT: M 94 ARG cc_start: 0.5891 (mmt180) cc_final: 0.5056 (mmt-90) REVERT: S 161 MET cc_start: 0.8399 (tpp) cc_final: 0.8038 (tpt) REVERT: T 625 ASN cc_start: 0.7071 (m110) cc_final: 0.6784 (m-40) REVERT: T 633 LYS cc_start: 0.8773 (mttt) cc_final: 0.8511 (mttp) REVERT: V 45 LYS cc_start: 0.8702 (tttt) cc_final: 0.8348 (ttmm) REVERT: V 94 ARG cc_start: 0.6047 (mmt180) cc_final: 0.5211 (mmt-90) outliers start: 37 outliers final: 26 residues processed: 353 average time/residue: 0.3008 time to fit residues: 161.6011 Evaluate side-chains 287 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 260 time to evaluate : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 188 ASN Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain J residue 637 ASN Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 56 SER Chi-restraints excluded: chain S residue 136 ASN Chi-restraints excluded: chain S residue 140 ASP Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain V residue 5 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 116 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 174 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 210 optimal weight: 7.9990 chunk 227 optimal weight: 10.0000 chunk 187 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 168 optimal weight: 0.9980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 39 HIS ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 19974 Z= 0.423 Angle : 0.726 10.418 27093 Z= 0.378 Chirality : 0.049 0.241 3279 Planarity : 0.005 0.047 3339 Dihedral : 6.572 58.065 4335 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.25 % Favored : 95.49 % Rotamer: Outliers : 3.76 % Allowed : 9.58 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.17), residues: 2304 helix: 1.38 (0.26), residues: 378 sheet: -0.03 (0.20), residues: 684 loop : -0.34 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP S 112 HIS 0.007 0.002 HIS I 105 PHE 0.019 0.003 PHE S 376 TYR 0.017 0.002 TYR L 49 ARG 0.012 0.001 ARG A 151 *********************** 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 354 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 277 time to evaluate : 2.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8491 (mmtp) cc_final: 0.7965 (mmtt) REVERT: A 161 MET cc_start: 0.8659 (tpt) cc_final: 0.8346 (tpt) REVERT: A 428 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7445 (mm110) REVERT: A 492 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7914 (mt-10) REVERT: I 161 MET cc_start: 0.8499 (tpp) cc_final: 0.8243 (tpp) REVERT: I 271 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8031 (mtp) REVERT: M 45 LYS cc_start: 0.8845 (tttt) cc_final: 0.8546 (ttmm) REVERT: M 94 ARG cc_start: 0.5984 (mmt180) cc_final: 0.5433 (mmt-90) REVERT: S 161 MET cc_start: 0.8382 (tpp) cc_final: 0.7837 (tpt) REVERT: T 625 ASN cc_start: 0.7539 (m110) cc_final: 0.7298 (m-40) REVERT: U 72 ASP cc_start: 0.7668 (t70) cc_final: 0.7322 (t70) REVERT: U 73 ASN cc_start: 0.8681 (OUTLIER) cc_final: 0.8388 (m110) REVERT: V 45 LYS cc_start: 0.8749 (tttt) cc_final: 0.8489 (ttmm) REVERT: V 70 THR cc_start: 0.8252 (m) cc_final: 0.7816 (p) REVERT: V 94 ARG cc_start: 0.6021 (mmt180) cc_final: 0.5417 (mmt180) REVERT: V 95 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8497 (pm20) outliers start: 77 outliers final: 57 residues processed: 324 average time/residue: 0.3154 time to fit residues: 155.4274 Evaluate side-chains 306 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 245 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 185 ASN Chi-restraints excluded: chain I residue 188 ASN Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 377 ASN Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 95 GLN Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain S residue 115 SER Chi-restraints excluded: chain S residue 136 ASN Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 225 ILE Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain S residue 377 ASN Chi-restraints excluded: chain S residue 420 ILE Chi-restraints excluded: chain S residue 434 MET Chi-restraints excluded: chain S residue 439 ILE Chi-restraints excluded: chain T residue 595 ILE Chi-restraints excluded: chain T residue 627 THR Chi-restraints excluded: chain T residue 637 ASN Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 73 ASN Chi-restraints excluded: chain U residue 77 THR Chi-restraints excluded: chain U residue 94 THR Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 95 GLN Chi-restraints excluded: chain V residue 102 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 109 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 141 optimal weight: 0.5980 chunk 210 optimal weight: 7.9990 chunk 223 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 199 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19974 Z= 0.184 Angle : 0.561 8.229 27093 Z= 0.291 Chirality : 0.044 0.235 3279 Planarity : 0.004 0.049 3339 Dihedral : 5.710 59.515 4335 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.43 % Favored : 96.35 % Rotamer: Outliers : 2.59 % Allowed : 11.83 % Favored : 85.58 % 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: 0.19 (0.17), residues: 2304 helix: 1.81 (0.27), residues: 384 sheet: 0.07 (0.19), residues: 696 loop : -0.33 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 112 HIS 0.004 0.001 HIS S 374 PHE 0.013 0.001 PHE I 53 TYR 0.017 0.001 TYR L 49 ARG 0.005 0.000 ARG I 151 *********************** 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 334 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 281 time to evaluate : 2.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8469 (mmtp) cc_final: 0.7762 (mmtt) REVERT: A 161 MET cc_start: 0.8608 (tpt) cc_final: 0.8242 (tpt) REVERT: A 492 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7824 (mt-10) REVERT: B 655 LYS cc_start: 0.8785 (tptp) cc_final: 0.8413 (tptt) REVERT: H 39 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8183 (tt0) REVERT: L 95 GLN cc_start: 0.8631 (mp10) cc_final: 0.8397 (mp10) REVERT: I 161 MET cc_start: 0.8493 (tpp) cc_final: 0.8250 (tpp) REVERT: I 271 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7944 (mtp) REVERT: J 624 ASP cc_start: 0.8579 (m-30) cc_final: 0.8256 (m-30) REVERT: M 45 LYS cc_start: 0.8886 (tttt) cc_final: 0.8643 (ttmm) REVERT: S 102 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7429 (mm-30) REVERT: S 161 MET cc_start: 0.8254 (tpp) cc_final: 0.7877 (tpt) REVERT: S 217 TYR cc_start: 0.8653 (m-80) cc_final: 0.8374 (m-80) REVERT: T 625 ASN cc_start: 0.7580 (m110) cc_final: 0.7332 (m-40) REVERT: V 45 LYS cc_start: 0.8753 (tttt) cc_final: 0.8479 (ttmm) REVERT: V 94 ARG cc_start: 0.6079 (mmt180) cc_final: 0.5614 (mmt-90) outliers start: 53 outliers final: 35 residues processed: 313 average time/residue: 0.3146 time to fit residues: 151.1017 Evaluate side-chains 286 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 248 time to evaluate : 2.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 188 ASN Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 377 ASN Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain S residue 69 TRP Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 136 ASN Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain S residue 420 ILE Chi-restraints excluded: chain S residue 434 MET Chi-restraints excluded: chain T residue 595 ILE Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain V residue 102 THR Chi-restraints excluded: chain V residue 105 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 10.0000 chunk 126 optimal weight: 0.5980 chunk 3 optimal weight: 10.0000 chunk 166 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 chunk 190 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 114 optimal weight: 0.0030 chunk 200 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 overall best weight: 1.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19974 Z= 0.238 Angle : 0.561 9.164 27093 Z= 0.291 Chirality : 0.044 0.217 3279 Planarity : 0.004 0.049 3339 Dihedral : 5.329 53.852 4335 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.38 % Favored : 95.40 % Rotamer: Outliers : 2.93 % Allowed : 12.22 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.17), residues: 2304 helix: 1.96 (0.26), residues: 384 sheet: 0.08 (0.20), residues: 681 loop : -0.33 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 112 HIS 0.004 0.001 HIS A 105 PHE 0.012 0.001 PHE K 29 TYR 0.021 0.001 TYR L 91 ARG 0.004 0.000 ARG K 53 *********************** 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 313 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 253 time to evaluate : 2.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8504 (mmtp) cc_final: 0.7654 (mmtt) REVERT: A 102 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7778 (mm-30) REVERT: A 161 MET cc_start: 0.8542 (tpt) cc_final: 0.8276 (tpt) REVERT: A 492 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7725 (mt-10) REVERT: B 648 GLU cc_start: 0.8329 (tp30) cc_final: 0.8109 (tt0) REVERT: B 655 LYS cc_start: 0.8755 (tptp) cc_final: 0.8435 (tptt) REVERT: H 39 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8101 (tt0) REVERT: L 42 LYS cc_start: 0.8545 (mtmt) cc_final: 0.8317 (mtmm) REVERT: I 271 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.8052 (mtp) REVERT: M 45 LYS cc_start: 0.8934 (tttt) cc_final: 0.8656 (ttmm) REVERT: S 102 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7549 (mm-30) REVERT: T 625 ASN cc_start: 0.7514 (m110) cc_final: 0.7307 (m-40) REVERT: V 45 LYS cc_start: 0.8793 (tttt) cc_final: 0.8536 (ttmm) REVERT: V 70 THR cc_start: 0.8206 (m) cc_final: 0.7703 (p) REVERT: V 94 ARG cc_start: 0.5985 (mmt180) cc_final: 0.5514 (mmt-90) REVERT: V 95 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8520 (pm20) outliers start: 60 outliers final: 45 residues processed: 291 average time/residue: 0.3060 time to fit residues: 137.6932 Evaluate side-chains 294 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 244 time to evaluate : 2.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 185 ASN Chi-restraints excluded: chain I residue 188 ASN Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 377 ASN Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 636 SER Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 136 ASN Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain S residue 420 ILE Chi-restraints excluded: chain S residue 434 MET Chi-restraints excluded: chain T residue 595 ILE Chi-restraints excluded: chain T residue 599 SER Chi-restraints excluded: chain T residue 627 THR Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 61 ASP Chi-restraints excluded: chain U residue 76 ASN Chi-restraints excluded: chain V residue 31 ASN Chi-restraints excluded: chain V residue 95 GLN Chi-restraints excluded: chain V residue 102 THR Chi-restraints excluded: chain V residue 105 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 75 optimal weight: 5.9990 chunk 201 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 223 optimal weight: 9.9990 chunk 185 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.060 19974 Z= 0.685 Angle : 0.824 12.110 27093 Z= 0.420 Chirality : 0.053 0.284 3279 Planarity : 0.006 0.054 3339 Dihedral : 6.335 45.530 4335 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.69 % Favored : 94.14 % Rotamer: Outliers : 4.25 % Allowed : 12.27 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.17), residues: 2304 helix: 1.10 (0.25), residues: 378 sheet: -0.23 (0.20), residues: 666 loop : -0.78 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP S 427 HIS 0.008 0.002 HIS I 105 PHE 0.024 0.003 PHE A 468 TYR 0.018 0.003 TYR M 86 ARG 0.007 0.001 ARG K 53 *********************** 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 308 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 221 time to evaluate : 2.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8537 (mmtp) cc_final: 0.7728 (mmtt) REVERT: A 102 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8066 (mm-30) REVERT: A 492 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7768 (mt-10) REVERT: H 39 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8303 (tt0) REVERT: H 72 ASP cc_start: 0.7836 (t70) cc_final: 0.7613 (t0) REVERT: L 42 LYS cc_start: 0.8640 (mtmt) cc_final: 0.8383 (mtmm) REVERT: L 70 THR cc_start: 0.8433 (m) cc_final: 0.8121 (p) REVERT: L 95 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8543 (mp10) REVERT: I 217 TYR cc_start: 0.8713 (m-80) cc_final: 0.8504 (m-80) REVERT: I 271 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7894 (mmp) REVERT: K 59 TYR cc_start: 0.9090 (m-80) cc_final: 0.8845 (m-80) REVERT: M 45 LYS cc_start: 0.9109 (tttt) cc_final: 0.8776 (ttmm) REVERT: S 102 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7996 (mm-30) REVERT: S 161 MET cc_start: 0.8297 (tpt) cc_final: 0.7855 (tpt) REVERT: S 217 TYR cc_start: 0.8708 (m-80) cc_final: 0.8280 (m-80) REVERT: V 45 LYS cc_start: 0.8911 (tttt) cc_final: 0.8635 (ttmm) REVERT: V 94 ARG cc_start: 0.6350 (mmt180) cc_final: 0.5722 (mmt-90) REVERT: V 95 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8546 (pm20) outliers start: 87 outliers final: 71 residues processed: 282 average time/residue: 0.3287 time to fit residues: 146.0148 Evaluate side-chains 286 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 209 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 185 ASN Chi-restraints excluded: chain I residue 188 ASN Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 377 ASN Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 56 SER Chi-restraints excluded: chain M residue 95 GLN Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 136 ASN Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 420 ILE Chi-restraints excluded: chain S residue 434 MET Chi-restraints excluded: chain S residue 446 VAL Chi-restraints excluded: chain T residue 535 MET Chi-restraints excluded: chain T residue 595 ILE Chi-restraints excluded: chain T residue 599 SER Chi-restraints excluded: chain T residue 627 THR Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 61 ASP Chi-restraints excluded: chain U residue 76 ASN Chi-restraints excluded: chain U residue 94 THR Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 31 ASN Chi-restraints excluded: chain V residue 56 SER Chi-restraints excluded: chain V residue 95 GLN Chi-restraints excluded: chain V residue 102 THR Chi-restraints excluded: chain V residue 105 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 163 optimal weight: 8.9990 chunk 126 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 222 optimal weight: 6.9990 chunk 139 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19974 Z= 0.251 Angle : 0.591 9.060 27093 Z= 0.305 Chirality : 0.045 0.210 3279 Planarity : 0.004 0.050 3339 Dihedral : 5.624 48.215 4335 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.60 % Favored : 95.23 % Rotamer: Outliers : 3.23 % Allowed : 14.13 % Favored : 82.65 % 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: -0.17 (0.17), residues: 2304 helix: 2.04 (0.26), residues: 366 sheet: -0.10 (0.20), residues: 687 loop : -0.75 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 112 HIS 0.004 0.001 HIS S 105 PHE 0.012 0.001 PHE K 29 TYR 0.016 0.001 TYR L 91 ARG 0.004 0.000 ARG K 53 *********************** 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: 66 poor density : 246 time to evaluate : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8539 (mmtp) cc_final: 0.7723 (mmtt) REVERT: A 102 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7944 (mm-30) REVERT: A 161 MET cc_start: 0.8614 (tpt) cc_final: 0.8240 (tpt) REVERT: A 492 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7732 (mt-10) REVERT: H 39 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.7967 (tt0) REVERT: L 24 THR cc_start: 0.9205 (OUTLIER) cc_final: 0.8903 (p) REVERT: L 42 LYS cc_start: 0.8711 (mtmt) cc_final: 0.8461 (mtmm) REVERT: L 70 THR cc_start: 0.8259 (m) cc_final: 0.7811 (p) REVERT: L 95 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8264 (mp10) REVERT: I 217 TYR cc_start: 0.8516 (m-80) cc_final: 0.8297 (m-80) REVERT: I 271 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.7995 (mmp) REVERT: I 318 TYR cc_start: 0.8641 (m-80) cc_final: 0.8380 (m-80) REVERT: J 651 ASN cc_start: 0.9053 (OUTLIER) cc_final: 0.8661 (m-40) REVERT: M 45 LYS cc_start: 0.9060 (tttt) cc_final: 0.8748 (ttmm) REVERT: S 102 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7784 (mm-30) REVERT: S 161 MET cc_start: 0.8255 (tpt) cc_final: 0.7796 (tpt) REVERT: V 45 LYS cc_start: 0.8832 (tttt) cc_final: 0.8564 (ttmm) REVERT: V 94 ARG cc_start: 0.6186 (mmt180) cc_final: 0.5441 (mmt-90) REVERT: V 95 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8500 (pm20) outliers start: 66 outliers final: 48 residues processed: 285 average time/residue: 0.2932 time to fit residues: 130.2159 Evaluate side-chains 292 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 236 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 95 GLN Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 188 ASN Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 377 ASN Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain J residue 651 ASN Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain M residue 56 SER Chi-restraints excluded: chain M residue 95 GLN Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 136 ASN Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 420 ILE Chi-restraints excluded: chain S residue 434 MET Chi-restraints excluded: chain S residue 446 VAL Chi-restraints excluded: chain T residue 595 ILE Chi-restraints excluded: chain T residue 627 THR Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 61 ASP Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 31 ASN Chi-restraints excluded: chain V residue 95 GLN Chi-restraints excluded: chain V residue 97 ILE Chi-restraints excluded: chain V residue 102 THR Chi-restraints excluded: chain V residue 105 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 137 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 175 optimal weight: 0.9990 chunk 202 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19974 Z= 0.178 Angle : 0.540 10.472 27093 Z= 0.279 Chirality : 0.044 0.270 3279 Planarity : 0.004 0.049 3339 Dihedral : 5.080 50.859 4335 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.56 % Favored : 95.31 % Rotamer: Outliers : 2.88 % Allowed : 14.81 % Favored : 82.31 % 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: 0.04 (0.18), residues: 2304 helix: 2.07 (0.26), residues: 384 sheet: 0.08 (0.20), residues: 702 loop : -0.65 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 96 HIS 0.003 0.001 HIS I 105 PHE 0.011 0.001 PHE K 29 TYR 0.025 0.001 TYR M 91 ARG 0.006 0.000 ARG I 476 *********************** 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 315 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 256 time to evaluate : 2.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8556 (mmtp) cc_final: 0.7749 (mmtt) REVERT: A 102 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7859 (mm-30) REVERT: A 161 MET cc_start: 0.8595 (tpt) cc_final: 0.8304 (tpt) REVERT: A 492 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7894 (mt-10) REVERT: B 655 LYS cc_start: 0.8705 (tptp) cc_final: 0.8383 (tptt) REVERT: H 39 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8004 (tt0) REVERT: H 72 ASP cc_start: 0.7580 (t70) cc_final: 0.7158 (t70) REVERT: L 42 LYS cc_start: 0.8656 (mtmt) cc_final: 0.8421 (mtmm) REVERT: I 161 MET cc_start: 0.8679 (tpt) cc_final: 0.8440 (tpt) REVERT: I 217 TYR cc_start: 0.8418 (m-80) cc_final: 0.8179 (m-80) REVERT: I 271 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.8059 (mmp) REVERT: I 318 TYR cc_start: 0.8594 (m-80) cc_final: 0.8338 (m-80) REVERT: M 45 LYS cc_start: 0.9019 (tttt) cc_final: 0.8746 (ttmm) REVERT: S 102 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7746 (mm-30) REVERT: S 161 MET cc_start: 0.8269 (tpt) cc_final: 0.7807 (tpt) REVERT: S 428 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7769 (mm110) REVERT: T 636 SER cc_start: 0.9038 (t) cc_final: 0.8767 (p) REVERT: V 45 LYS cc_start: 0.8837 (tttt) cc_final: 0.8572 (ttmm) REVERT: V 78 LEU cc_start: 0.7758 (tt) cc_final: 0.7531 (tt) REVERT: V 79 GLN cc_start: 0.8660 (mt0) cc_final: 0.8155 (mp10) REVERT: V 94 ARG cc_start: 0.6207 (mmt180) cc_final: 0.5572 (mmt180) REVERT: V 95 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8482 (pm20) outliers start: 59 outliers final: 45 residues processed: 290 average time/residue: 0.3205 time to fit residues: 144.8725 Evaluate side-chains 294 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 243 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 188 ASN Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 377 ASN Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 105 GLN Chi-restraints excluded: chain M residue 56 SER Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain S residue 47 ASP Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 136 ASN Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 418 CYS Chi-restraints excluded: chain S residue 420 ILE Chi-restraints excluded: chain S residue 428 GLN Chi-restraints excluded: chain S residue 446 VAL Chi-restraints excluded: chain T residue 595 ILE Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 61 ASP Chi-restraints excluded: chain U residue 76 ASN Chi-restraints excluded: chain U residue 97 MET Chi-restraints excluded: chain V residue 56 SER Chi-restraints excluded: chain V residue 95 GLN Chi-restraints excluded: chain V residue 97 ILE Chi-restraints excluded: chain V residue 102 THR Chi-restraints excluded: chain V residue 105 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 213 optimal weight: 8.9990 chunk 194 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 162 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 196 optimal weight: 0.8980 chunk 206 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 19974 Z= 0.294 Angle : 0.578 9.677 27093 Z= 0.298 Chirality : 0.045 0.263 3279 Planarity : 0.004 0.049 3339 Dihedral : 5.159 50.402 4335 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.77 % Favored : 95.10 % Rotamer: Outliers : 3.13 % Allowed : 14.81 % Favored : 82.06 % 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: -0.02 (0.18), residues: 2304 helix: 2.09 (0.26), residues: 375 sheet: 0.07 (0.20), residues: 669 loop : -0.70 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP T 571 HIS 0.004 0.001 HIS S 105 PHE 0.014 0.001 PHE K 29 TYR 0.013 0.001 TYR K 100G ARG 0.003 0.000 ARG K 53 *********************** 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 306 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 242 time to evaluate : 2.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8537 (mmtp) cc_final: 0.7694 (mmtt) REVERT: A 102 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7967 (mm-30) REVERT: A 161 MET cc_start: 0.8639 (tpt) cc_final: 0.8182 (tpt) REVERT: A 492 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7736 (mt-10) REVERT: H 39 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8014 (tt0) REVERT: L 24 THR cc_start: 0.9185 (OUTLIER) cc_final: 0.8917 (p) REVERT: L 42 LYS cc_start: 0.8659 (mtmt) cc_final: 0.8432 (mtmm) REVERT: I 161 MET cc_start: 0.8694 (tpt) cc_final: 0.8412 (tpt) REVERT: I 217 TYR cc_start: 0.8441 (m-80) cc_final: 0.8215 (m-80) REVERT: I 271 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.8079 (mmp) REVERT: I 318 TYR cc_start: 0.8622 (m-80) cc_final: 0.8345 (m-80) REVERT: M 45 LYS cc_start: 0.9007 (tttt) cc_final: 0.8686 (ttmm) REVERT: S 102 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7840 (mm-30) REVERT: S 161 MET cc_start: 0.8302 (tpt) cc_final: 0.7816 (tpt) REVERT: S 428 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7887 (mm110) REVERT: T 636 SER cc_start: 0.9065 (t) cc_final: 0.8816 (p) REVERT: V 45 LYS cc_start: 0.8839 (tttt) cc_final: 0.8569 (ttmm) REVERT: V 79 GLN cc_start: 0.8652 (mt0) cc_final: 0.8022 (mp10) REVERT: V 95 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8478 (pm20) outliers start: 64 outliers final: 54 residues processed: 288 average time/residue: 0.3014 time to fit residues: 135.6634 Evaluate side-chains 298 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 237 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 188 ASN Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 358 ILE Chi-restraints excluded: chain I residue 377 ASN Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain M residue 56 SER Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 136 ASN Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 225 ILE Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 418 CYS Chi-restraints excluded: chain S residue 420 ILE Chi-restraints excluded: chain S residue 428 GLN Chi-restraints excluded: chain S residue 446 VAL Chi-restraints excluded: chain T residue 595 ILE Chi-restraints excluded: chain T residue 627 THR Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 61 ASP Chi-restraints excluded: chain U residue 76 ASN Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 31 ASN Chi-restraints excluded: chain V residue 56 SER Chi-restraints excluded: chain V residue 95 GLN Chi-restraints excluded: chain V residue 97 ILE Chi-restraints excluded: chain V residue 102 THR Chi-restraints excluded: chain V residue 105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 219 optimal weight: 0.9990 chunk 133 optimal weight: 0.0000 chunk 104 optimal weight: 5.9990 chunk 152 optimal weight: 7.9990 chunk 230 optimal weight: 1.9990 chunk 211 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.5255 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= 0.218 Angle : 0.549 10.714 27093 Z= 0.283 Chirality : 0.044 0.216 3279 Planarity : 0.004 0.049 3339 Dihedral : 4.950 51.484 4335 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.56 % Favored : 95.31 % Rotamer: Outliers : 2.74 % Allowed : 15.25 % Favored : 82.01 % 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: 0.05 (0.18), residues: 2304 helix: 2.36 (0.26), residues: 366 sheet: 0.14 (0.20), residues: 666 loop : -0.72 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 112 HIS 0.003 0.001 HIS S 105 PHE 0.012 0.001 PHE K 29 TYR 0.023 0.001 TYR M 91 ARG 0.003 0.000 ARG I 151 ********************** 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 314 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 258 time to evaluate : 2.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8538 (mmtp) cc_final: 0.7683 (mmtt) REVERT: A 102 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7876 (mm-30) REVERT: A 161 MET cc_start: 0.8618 (tpt) cc_final: 0.8219 (tpt) REVERT: A 492 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7965 (mt-10) REVERT: B 655 LYS cc_start: 0.8719 (tptp) cc_final: 0.8392 (tptt) REVERT: H 39 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.7908 (tt0) REVERT: L 24 THR cc_start: 0.9145 (OUTLIER) cc_final: 0.8905 (p) REVERT: I 161 MET cc_start: 0.8697 (tpt) cc_final: 0.8463 (tpt) REVERT: I 217 TYR cc_start: 0.8449 (m-80) cc_final: 0.8204 (m-80) REVERT: I 271 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.8105 (mmp) REVERT: M 45 LYS cc_start: 0.8989 (tttt) cc_final: 0.8678 (ttmm) REVERT: S 102 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7802 (mm-30) REVERT: S 161 MET cc_start: 0.8291 (tpt) cc_final: 0.7765 (tpt) REVERT: S 428 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7970 (mm110) REVERT: T 636 SER cc_start: 0.9070 (t) cc_final: 0.8773 (p) REVERT: V 45 LYS cc_start: 0.8842 (tttt) cc_final: 0.8587 (ttmm) REVERT: V 79 GLN cc_start: 0.8651 (mt0) cc_final: 0.8043 (mp10) REVERT: V 95 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8477 (pm20) outliers start: 56 outliers final: 48 residues processed: 294 average time/residue: 0.3002 time to fit residues: 137.3472 Evaluate side-chains 305 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 250 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 188 ASN Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 355 ASN Chi-restraints excluded: chain I residue 358 ILE Chi-restraints excluded: chain I residue 377 ASN Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 612 SER Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain M residue 56 SER Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain S residue 102 GLU Chi-restraints excluded: chain S residue 136 ASN Chi-restraints excluded: chain S residue 185 ASN Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 418 CYS Chi-restraints excluded: chain S residue 420 ILE Chi-restraints excluded: chain S residue 428 GLN Chi-restraints excluded: chain S residue 446 VAL Chi-restraints excluded: chain T residue 595 ILE Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 61 ASP Chi-restraints excluded: chain V residue 26 THR Chi-restraints excluded: chain V residue 31 ASN Chi-restraints excluded: chain V residue 56 SER Chi-restraints excluded: chain V residue 95 GLN Chi-restraints excluded: chain V residue 97 ILE Chi-restraints excluded: chain V residue 102 THR Chi-restraints excluded: chain V residue 105 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: 6.9990 chunk 168 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 188 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.103700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.084200 restraints weight = 35151.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.086916 restraints weight = 21012.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.088723 restraints weight = 15025.889| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 19974 Z= 0.302 Angle : 0.588 10.282 27093 Z= 0.302 Chirality : 0.045 0.204 3279 Planarity : 0.004 0.048 3339 Dihedral : 5.121 50.590 4335 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.03 % Favored : 94.84 % Rotamer: Outliers : 3.03 % Allowed : 15.15 % Favored : 81.82 % 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: -0.06 (0.17), residues: 2304 helix: 2.20 (0.26), residues: 366 sheet: 0.09 (0.20), residues: 666 loop : -0.78 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP T 571 HIS 0.004 0.001 HIS I 105 PHE 0.015 0.002 PHE A 382 TYR 0.012 0.001 TYR K 100G ARG 0.004 0.000 ARG K 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3719.92 seconds wall clock time: 69 minutes 14.56 seconds (4154.56 seconds total)