Starting phenix.real_space_refine on Thu Mar 5 06:07:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x9u_22111/03_2026/6x9u_22111.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x9u_22111/03_2026/6x9u_22111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x9u_22111/03_2026/6x9u_22111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x9u_22111/03_2026/6x9u_22111.map" model { file = "/net/cci-nas-00/data/ceres_data/6x9u_22111/03_2026/6x9u_22111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x9u_22111/03_2026/6x9u_22111.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 4.53, per 1000 atoms: 0.23 Number of scatterers: 19590 At special positions: 0 Unit cell: (124.63, 122.57, 150.38, 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=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.12 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=2.13 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.02 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.04 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.12 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=2.14 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS S 126 " - pdb=" SG CYS S 196 " distance=2.03 Simple disulfide: pdb=" SG CYS S 131 " - pdb=" SG CYS S 157 " distance=2.02 Simple disulfide: pdb=" SG CYS S 218 " - pdb=" SG CYS S 247 " distance=2.04 Simple disulfide: pdb=" SG CYS S 228 " - pdb=" SG CYS S 239 " distance=2.12 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=2.13 Simple disulfide: pdb=" SG CYS T 598 " - pdb=" SG CYS T 604 " distance=2.02 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 92 " distance=2.05 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 - 3.00 Amino acid : True - 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: 1.94 Conformation dependent library (CDL) restraints added in 866.1 milliseconds 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4332 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 48 sheets defined 21.4% alpha, 43.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.093A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 354 removed outlier: 4.108A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.796A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.472A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.557A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 660 removed outlier: 3.531A pdb=" N GLN B 658 " --> pdb=" O GLU B 654 " (cutoff:3.500A) 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: 4.093A pdb=" N GLU I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 139 through 151 Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 334 through 354 removed outlier: 4.109A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 476 through 484 removed outlier: 3.796A pdb=" N SER I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 523 through 528 removed outlier: 4.473A pdb=" N GLY J 527 " --> pdb=" O GLY J 524 " (cutoff:3.500A) Processing helix chain 'J' and resid 536 through 542 removed outlier: 3.556A pdb=" N GLN J 540 " --> pdb=" O THR J 536 " (cutoff:3.500A) Processing helix chain 'J' and resid 569 through 596 Processing helix chain 'J' and resid 618 through 625 Processing helix chain 'J' and resid 627 through 635 Processing helix chain 'J' and resid 638 through 660 removed outlier: 3.531A pdb=" N GLN J 658 " --> pdb=" O GLU J 654 " (cutoff:3.500A) 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: 4.093A pdb=" N GLU S 102 " --> pdb=" O ASN S 98 " (cutoff:3.500A) Processing helix chain 'S' and resid 122 through 126 Processing helix chain 'S' and resid 139 through 151 Processing helix chain 'S' and resid 195 through 198 Processing helix chain 'S' and resid 334 through 354 removed outlier: 4.108A pdb=" N LYS S 351 " --> pdb=" O LYS S 347 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N HIS S 352 " --> pdb=" O GLN S 348 " (cutoff:3.500A) Processing helix chain 'S' and resid 368 through 373 Processing helix chain 'S' and resid 476 through 484 removed outlier: 3.796A pdb=" N SER S 481 " --> pdb=" O ASP S 477 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLU S 482 " --> pdb=" O ASN S 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 523 through 528 removed outlier: 4.472A pdb=" N GLY T 527 " --> pdb=" O GLY T 524 " (cutoff:3.500A) Processing helix chain 'T' and resid 536 through 542 removed outlier: 3.556A pdb=" N GLN T 540 " --> pdb=" O THR T 536 " (cutoff:3.500A) Processing helix chain 'T' and resid 569 through 596 Processing helix chain 'T' and resid 618 through 625 Processing helix chain 'T' and resid 627 through 635 Processing helix chain 'T' and resid 638 through 660 removed outlier: 3.531A pdb=" N GLN T 658 " --> pdb=" O GLU T 654 " (cutoff:3.500A) 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: 3.815A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.900A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.423A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.527A 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: 6.531A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.607A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.917A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 11.942A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.880A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.898A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.998A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 12.167A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.752A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'A' and resid 271 through 274 Processing sheet with id=10, first strand: chain 'A' and resid 315 through 323A removed outlier: 6.267A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.649A 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: 6.089A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.553A 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 removed outlier: 6.846A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.551A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.494A 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: 6.551A 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: 3.815A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'I' and resid 75 through 76 removed outlier: 6.900A pdb=" N CYS I 54 " --> pdb=" O VAL I 75 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=21, first strand: chain 'I' and resid 169 through 177 Processing sheet with id=22, first strand: chain 'I' and resid 200 through 203 removed outlier: 6.423A pdb=" N ALA I 200 " --> pdb=" O ALA I 433 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N TYR I 435 " --> pdb=" O ALA I 200 " (cutoff:3.500A) removed outlier: 6.527A 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: 6.530A pdb=" N ILE I 358 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N PHE I 468 " --> pdb=" O ILE I 358 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLY I 441 " --> pdb=" O ASN I 300 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ASN I 300 " --> pdb=" O GLY I 441 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE I 443 " --> pdb=" O ARG I 298 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.607A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 11.917A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 11.941A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 10.880A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 10.898A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 10.998A pdb=" N ASP I 457 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 12.167A pdb=" N ILE I 284 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'I' and resid 259 through 261 removed outlier: 3.752A pdb=" N GLY I 451 " --> pdb=" O LEU I 260 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'I' and resid 271 through 274 Processing sheet with id=26, first strand: chain 'I' and resid 315 through 323A removed outlier: 6.268A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ILE I 323 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 6.649A 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: 6.089A 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 removed outlier: 6.847A pdb=" N CYS K 92 " --> pdb=" O TRP K 103 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TRP K 103 " --> pdb=" O CYS K 92 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N THR K 94 " --> pdb=" O ASP K 101 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.551A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) removed outlier: 6.495A 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: 6.551A 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: 3.815A pdb=" N ILE S 225 " --> pdb=" O VAL S 245 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'S' and resid 75 through 76 removed outlier: 6.900A pdb=" N CYS S 54 " --> pdb=" O VAL S 75 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'S' and resid 91 through 94 Processing sheet with id=37, first strand: chain 'S' and resid 169 through 177 Processing sheet with id=38, first strand: chain 'S' and resid 200 through 203 removed outlier: 6.424A pdb=" N ALA S 200 " --> pdb=" O ALA S 433 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N TYR S 435 " --> pdb=" O ALA S 200 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR S 202 " --> pdb=" O TYR S 435 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'S' and resid 393 through 394 removed outlier: 6.531A pdb=" N ILE S 358 " --> pdb=" O GLU S 466 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N PHE S 468 " --> pdb=" O ILE S 358 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG S 360 " --> pdb=" O PHE S 468 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLY S 441 " --> pdb=" O ASN S 300 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ASN S 300 " --> pdb=" O GLY S 441 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE S 443 " --> pdb=" O ARG S 298 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLY S 451 " --> pdb=" O THR S 290 " (cutoff:3.500A) removed outlier: 10.607A pdb=" N THR S 290 " --> pdb=" O GLY S 451 " (cutoff:3.500A) removed outlier: 11.917A pdb=" N ILE S 453 " --> pdb=" O PHE S 288 " (cutoff:3.500A) removed outlier: 11.941A pdb=" N PHE S 288 " --> pdb=" O ILE S 453 " (cutoff:3.500A) removed outlier: 10.881A pdb=" N THR S 455 " --> pdb=" O VAL S 286 " (cutoff:3.500A) removed outlier: 10.898A pdb=" N VAL S 286 " --> pdb=" O THR S 455 " (cutoff:3.500A) removed outlier: 10.998A pdb=" N ASP S 457 " --> pdb=" O ILE S 284 " (cutoff:3.500A) removed outlier: 12.167A pdb=" N ILE S 284 " --> pdb=" O ASP S 457 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA S 329 " --> pdb=" O CYS S 418 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE S 382 " --> pdb=" O LYS S 421 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'S' and resid 259 through 261 removed outlier: 3.752A pdb=" N GLY S 451 " --> pdb=" O LEU S 260 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'S' and resid 271 through 274 Processing sheet with id=42, first strand: chain 'S' and resid 315 through 323A removed outlier: 6.267A pdb=" N GLN S 315 " --> pdb=" O ILE S 309 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N THR S 303 " --> pdb=" O GLY S 321 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ILE S 323 " --> pdb=" O ASN S 301 " (cutoff:3.500A) removed outlier: 6.650A 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: 6.089A 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 removed outlier: 6.846A pdb=" N CYS U 92 " --> pdb=" O TRP U 103 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TRP U 103 " --> pdb=" O CYS U 92 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR U 94 " --> pdb=" O ASP U 101 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'V' and resid 11 through 13 removed outlier: 6.551A pdb=" N VAL V 11 " --> pdb=" O THR V 105 " (cutoff:3.500A) removed outlier: 6.494A 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: 6.551A 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 24 753 hydrogen bonds defined for protein. 1926 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: 3.78 Time building geometry restraints manager: 2.46 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: 3539 1.31 - 1.44: 5489 1.44 - 1.57: 10739 1.57 - 1.70: 33 1.70 - 1.82: 174 Bond restraints: 19974 Sorted by residual: bond pdb=" C1 NAG 0 2 " pdb=" O5 NAG 0 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 G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.05e+01 bond pdb=" C1 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.406 1.548 -0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.545 -0.139 2.00e-02 2.50e+03 4.84e+01 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.545 -0.139 2.00e-02 2.50e+03 4.81e+01 ... (remaining 19969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 23975 2.56 - 5.12: 2763 5.12 - 7.68: 325 7.68 - 10.24: 27 10.24 - 12.80: 3 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 110.70 123.50 -12.80 1.22e+00 6.72e-01 1.10e+02 angle pdb=" N PRO L 7 " pdb=" CA PRO L 7 " pdb=" C PRO L 7 " ideal model delta sigma weight residual 110.70 123.50 -12.80 1.22e+00 6.72e-01 1.10e+02 angle pdb=" N PRO V 7 " pdb=" CA PRO V 7 " pdb=" C PRO V 7 " ideal model delta sigma weight residual 110.70 123.47 -12.77 1.22e+00 6.72e-01 1.10e+02 angle pdb=" C ASP L 50 " pdb=" N VAL L 51 " pdb=" CA VAL L 51 " ideal model delta sigma weight residual 123.16 114.73 8.43 1.06e+00 8.90e-01 6.33e+01 angle pdb=" C ASP M 50 " pdb=" N VAL M 51 " pdb=" CA VAL M 51 " ideal model delta sigma weight residual 123.16 114.73 8.43 1.06e+00 8.90e-01 6.32e+01 ... (remaining 27088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.83: 12609 21.83 - 43.66: 282 43.66 - 65.48: 102 65.48 - 87.31: 30 87.31 - 109.14: 15 Dihedral angle restraints: 13038 sinusoidal: 6291 harmonic: 6747 Sorted by residual: dihedral pdb=" CB CYS S 228 " pdb=" SG CYS S 228 " pdb=" SG CYS S 239 " pdb=" CB CYS S 239 " ideal model delta sinusoidal sigma weight residual 93.00 161.54 -68.54 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" CB CYS I 228 " pdb=" SG CYS I 228 " pdb=" SG CYS I 239 " pdb=" CB CYS I 239 " ideal model delta sinusoidal sigma weight residual 93.00 161.54 -68.54 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 161.54 -68.54 1 1.00e+01 1.00e-02 6.09e+01 ... (remaining 13035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2392 0.102 - 0.203: 747 0.203 - 0.305: 119 0.305 - 0.406: 15 0.406 - 0.508: 6 Chirality restraints: 3279 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.56e+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 -2.65 0.25 2.00e-02 2.50e+03 1.56e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.53e+02 ... (remaining 3276 not shown) Planarity restraints: 3405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 702 " 0.309 2.00e-02 2.50e+03 2.61e-01 8.51e+02 pdb=" C7 NAG J 702 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG J 702 " 0.188 2.00e-02 2.50e+03 pdb=" N2 NAG J 702 " -0.449 2.00e-02 2.50e+03 pdb=" O7 NAG J 702 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 702 " -0.309 2.00e-02 2.50e+03 2.61e-01 8.50e+02 pdb=" C7 NAG B 702 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG B 702 " -0.188 2.00e-02 2.50e+03 pdb=" N2 NAG B 702 " 0.449 2.00e-02 2.50e+03 pdb=" O7 NAG B 702 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 702 " -0.309 2.00e-02 2.50e+03 2.61e-01 8.48e+02 pdb=" C7 NAG T 702 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG T 702 " -0.188 2.00e-02 2.50e+03 pdb=" N2 NAG T 702 " 0.448 2.00e-02 2.50e+03 pdb=" O7 NAG T 702 " -0.032 2.00e-02 2.50e+03 ... (remaining 3402 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 2526 2.72 - 3.26: 17362 3.26 - 3.81: 31341 3.81 - 4.35: 39033 4.35 - 4.90: 65334 Nonbonded interactions: 155596 Sorted by model distance: nonbonded pdb=" O3 NAG B 702 " pdb=" O7 NAG B 702 " model vdw 2.174 3.040 nonbonded pdb=" O3 NAG J 702 " pdb=" O7 NAG J 702 " model vdw 2.175 3.040 nonbonded pdb=" O3 NAG T 702 " pdb=" O7 NAG T 702 " model vdw 2.175 3.040 nonbonded pdb=" OG1 THR S 37 " pdb=" OG1 THR S 499 " model vdw 2.237 3.040 nonbonded pdb=" OG1 THR I 37 " pdb=" OG1 THR I 499 " model vdw 2.237 3.040 ... (remaining 155591 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'C' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'W' selection = chain 'X' selection = chain 'Z' } ncs_group { reference = chain 'A' selection = chain 'I' selection = chain 'S' } ncs_group { reference = chain 'B' selection = chain 'J' selection = chain 'T' } ncs_group { reference = chain 'E' selection = chain 'P' selection = chain 'Y' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'U' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 18.790 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.025 0.162 20097 Z= 1.279 Angle : 1.713 12.797 27426 Z= 1.105 Chirality : 0.099 0.508 3279 Planarity : 0.013 0.261 3339 Dihedral : 11.511 109.137 8598 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.26 % Favored : 96.48 % Rotamer: Outliers : 0.15 % Allowed : 0.29 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.17), residues: 2304 helix: -0.32 (0.24), residues: 387 sheet: 0.76 (0.20), residues: 645 loop : 0.37 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 66 TYR 0.049 0.007 TYR V 36 PHE 0.036 0.006 PHE S 383 TRP 0.071 0.010 TRP S 427 HIS 0.007 0.002 HIS I 216 Details of bonding type rmsd covalent geometry : bond 0.02449 (19974) covalent geometry : angle 1.68783 (27093) SS BOND : bond 0.04067 ( 36) SS BOND : angle 2.64047 ( 72) hydrogen bonds : bond 0.15905 ( 732) hydrogen bonds : angle 7.00409 ( 1926) link_ALPHA1-3 : bond 0.03310 ( 3) link_ALPHA1-3 : angle 2.27500 ( 9) link_BETA1-4 : bond 0.02599 ( 18) link_BETA1-4 : angle 3.68499 ( 54) link_NAG-ASN : bond 0.03221 ( 66) link_NAG-ASN : angle 3.20199 ( 198) *********************** 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 481 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 478 time to evaluate : 0.691 Fit side-chains REVERT: A 104 MET cc_start: 0.9051 (ttt) cc_final: 0.8760 (ttt) REVERT: A 502 LYS cc_start: 0.6674 (mmtp) cc_final: 0.6241 (mmtt) REVERT: I 502 LYS cc_start: 0.6590 (mmtp) cc_final: 0.5679 (mmtt) REVERT: M 47 MET cc_start: 0.8342 (mmm) cc_final: 0.7927 (mmp) REVERT: S 326 ILE cc_start: 0.8587 (mm) cc_final: 0.8349 (mt) REVERT: S 502 LYS cc_start: 0.6881 (mmtp) cc_final: 0.6107 (mmtt) outliers start: 3 outliers final: 0 residues processed: 481 average time/residue: 0.1614 time to fit residues: 113.1555 Evaluate side-chains 237 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN B 607 ASN H 73 ASN L 39 HIS J 607 ASN J 630 GLN T 577 GLN V 39 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.123746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.098099 restraints weight = 28877.531| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.27 r_work: 0.2948 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20097 Z= 0.168 Angle : 0.724 11.192 27426 Z= 0.370 Chirality : 0.047 0.282 3279 Planarity : 0.004 0.032 3339 Dihedral : 8.516 68.383 4335 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.17 % Favored : 96.57 % Rotamer: Outliers : 2.10 % Allowed : 6.79 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.17), residues: 2304 helix: 1.54 (0.27), residues: 384 sheet: 0.64 (0.20), residues: 648 loop : 0.16 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG S 444 TYR 0.014 0.002 TYR A 173 PHE 0.021 0.002 PHE A 383 TRP 0.016 0.002 TRP A 479 HIS 0.005 0.001 HIS U 82A Details of bonding type rmsd covalent geometry : bond 0.00362 (19974) covalent geometry : angle 0.67855 (27093) SS BOND : bond 0.00280 ( 36) SS BOND : angle 0.92558 ( 72) hydrogen bonds : bond 0.05640 ( 732) hydrogen bonds : angle 5.57958 ( 1926) link_ALPHA1-3 : bond 0.00838 ( 3) link_ALPHA1-3 : angle 2.33863 ( 9) link_BETA1-4 : bond 0.00517 ( 18) link_BETA1-4 : angle 2.16307 ( 54) link_NAG-ASN : bond 0.00359 ( 66) link_NAG-ASN : angle 2.79501 ( 198) *********************** 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 324 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 281 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: A 104 MET cc_start: 0.9344 (ttt) cc_final: 0.9057 (ttt) REVERT: A 150 MET cc_start: 0.8574 (mmp) cc_final: 0.8210 (mmp) REVERT: A 502 LYS cc_start: 0.6479 (mmtp) cc_final: 0.5570 (mmtm) REVERT: L 33 VAL cc_start: 0.9039 (t) cc_final: 0.8807 (m) REVERT: I 213 ILE cc_start: 0.8801 (mt) cc_final: 0.8557 (tt) REVERT: I 358 ILE cc_start: 0.8282 (mt) cc_final: 0.7988 (mp) REVERT: I 502 LYS cc_start: 0.6619 (mmtp) cc_final: 0.5441 (mmtm) REVERT: J 626 MET cc_start: 0.8961 (mtt) cc_final: 0.8751 (mtp) REVERT: K 101 ASP cc_start: 0.8459 (m-30) cc_final: 0.8209 (m-30) REVERT: M 47 MET cc_start: 0.8853 (mmm) cc_final: 0.8547 (mmt) REVERT: M 58 VAL cc_start: 0.8184 (t) cc_final: 0.7950 (p) REVERT: S 502 LYS cc_start: 0.7115 (mmtp) cc_final: 0.6339 (mmtm) REVERT: U 13 GLN cc_start: 0.7825 (pm20) cc_final: 0.7578 (tt0) REVERT: U 52 ASP cc_start: 0.8688 (p0) cc_final: 0.8408 (p0) REVERT: U 64 LYS cc_start: 0.8487 (ttmm) cc_final: 0.8229 (tttt) outliers start: 43 outliers final: 28 residues processed: 315 average time/residue: 0.1406 time to fit residues: 69.1423 Evaluate side-chains 259 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 231 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 607 ASN Chi-restraints excluded: chain J residue 620 SER Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 82 HIS Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain T residue 620 SER Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 85 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 221 optimal weight: 8.9990 chunk 155 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 116 optimal weight: 8.9990 chunk 192 optimal weight: 2.9990 chunk 186 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 175 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 302 ASN B 577 GLN B 607 ASN I 377 ASN J 607 ASN S 302 ASN U 82AHIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.120392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.094491 restraints weight = 29011.402| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.27 r_work: 0.2887 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20097 Z= 0.178 Angle : 0.657 8.788 27426 Z= 0.331 Chirality : 0.045 0.193 3279 Planarity : 0.004 0.035 3339 Dihedral : 7.001 52.924 4335 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.56 % Favored : 96.18 % Rotamer: Outliers : 1.76 % Allowed : 8.94 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.17), residues: 2304 helix: 1.83 (0.28), residues: 381 sheet: 0.57 (0.20), residues: 669 loop : -0.10 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 71 TYR 0.012 0.001 TYR K 90 PHE 0.019 0.002 PHE I 383 TRP 0.011 0.001 TRP S 45 HIS 0.004 0.001 HIS S 105 Details of bonding type rmsd covalent geometry : bond 0.00418 (19974) covalent geometry : angle 0.61886 (27093) SS BOND : bond 0.00334 ( 36) SS BOND : angle 1.06816 ( 72) hydrogen bonds : bond 0.04947 ( 732) hydrogen bonds : angle 5.15328 ( 1926) link_ALPHA1-3 : bond 0.01259 ( 3) link_ALPHA1-3 : angle 1.54548 ( 9) link_BETA1-4 : bond 0.00404 ( 18) link_BETA1-4 : angle 1.55762 ( 54) link_NAG-ASN : bond 0.00341 ( 66) link_NAG-ASN : angle 2.48033 ( 198) *********************** 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 279 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 243 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: A 42 VAL cc_start: 0.9157 (t) cc_final: 0.8893 (m) REVERT: A 104 MET cc_start: 0.9347 (ttt) cc_final: 0.9088 (ttt) REVERT: A 502 LYS cc_start: 0.6777 (mmtp) cc_final: 0.5728 (mmtm) REVERT: L 33 VAL cc_start: 0.9022 (t) cc_final: 0.8776 (m) REVERT: I 136 ASN cc_start: 0.7964 (m-40) cc_final: 0.7676 (t0) REVERT: I 213 ILE cc_start: 0.8926 (mt) cc_final: 0.8677 (tt) REVERT: I 217 TYR cc_start: 0.9036 (m-80) cc_final: 0.7840 (m-80) REVERT: I 502 LYS cc_start: 0.7046 (mmtp) cc_final: 0.5957 (mmtm) REVERT: M 47 MET cc_start: 0.8915 (mmm) cc_final: 0.8685 (mmt) REVERT: M 58 VAL cc_start: 0.8249 (t) cc_final: 0.8029 (p) REVERT: S 117 LYS cc_start: 0.7434 (tttt) cc_final: 0.7168 (tttt) REVERT: S 326 ILE cc_start: 0.8782 (mm) cc_final: 0.8513 (mt) REVERT: S 395 TRP cc_start: 0.6885 (m-10) cc_final: 0.6677 (m-10) REVERT: S 502 LYS cc_start: 0.7326 (mmtp) cc_final: 0.6500 (mmtt) outliers start: 36 outliers final: 28 residues processed: 269 average time/residue: 0.1543 time to fit residues: 62.6022 Evaluate side-chains 250 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 222 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain J residue 620 SER Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain T residue 574 LYS Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain T residue 620 SER Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 52 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 159 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 81 optimal weight: 0.4980 chunk 192 optimal weight: 2.9990 chunk 182 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN T 607 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.119710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.093937 restraints weight = 28766.560| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.25 r_work: 0.2875 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20097 Z= 0.155 Angle : 0.606 8.389 27426 Z= 0.306 Chirality : 0.045 0.217 3279 Planarity : 0.004 0.039 3339 Dihedral : 6.145 51.549 4335 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.56 % Favored : 96.27 % Rotamer: Outliers : 1.81 % Allowed : 9.48 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.18), residues: 2304 helix: 1.96 (0.28), residues: 381 sheet: 0.42 (0.19), residues: 753 loop : -0.16 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 151 TYR 0.016 0.001 TYR K 90 PHE 0.017 0.002 PHE I 383 TRP 0.010 0.001 TRP H 103 HIS 0.004 0.001 HIS S 105 Details of bonding type rmsd covalent geometry : bond 0.00362 (19974) covalent geometry : angle 0.57271 (27093) SS BOND : bond 0.00450 ( 36) SS BOND : angle 0.88752 ( 72) hydrogen bonds : bond 0.04533 ( 732) hydrogen bonds : angle 4.91616 ( 1926) link_ALPHA1-3 : bond 0.01024 ( 3) link_ALPHA1-3 : angle 1.58809 ( 9) link_BETA1-4 : bond 0.00371 ( 18) link_BETA1-4 : angle 1.38001 ( 54) link_NAG-ASN : bond 0.00312 ( 66) link_NAG-ASN : angle 2.24966 ( 198) *********************** 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 275 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 238 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: A 42 VAL cc_start: 0.9181 (OUTLIER) cc_final: 0.8892 (m) REVERT: A 104 MET cc_start: 0.9323 (ttt) cc_final: 0.9082 (ttt) REVERT: A 113 ASP cc_start: 0.8840 (m-30) cc_final: 0.8624 (m-30) REVERT: A 502 LYS cc_start: 0.6848 (mmtp) cc_final: 0.5759 (mmtm) REVERT: L 33 VAL cc_start: 0.9029 (t) cc_final: 0.8779 (m) REVERT: L 36 TYR cc_start: 0.9190 (m-80) cc_final: 0.8586 (m-80) REVERT: I 136 ASN cc_start: 0.8027 (m-40) cc_final: 0.7721 (t0) REVERT: I 213 ILE cc_start: 0.8932 (mt) cc_final: 0.8688 (tt) REVERT: I 217 TYR cc_start: 0.8934 (m-80) cc_final: 0.7847 (m-80) REVERT: I 502 LYS cc_start: 0.6969 (mmtp) cc_final: 0.5846 (mmtm) REVERT: K 101 ASP cc_start: 0.8673 (m-30) cc_final: 0.8420 (m-30) REVERT: S 326 ILE cc_start: 0.8822 (mm) cc_final: 0.8586 (mt) REVERT: S 502 LYS cc_start: 0.7483 (mmtp) cc_final: 0.6560 (mmtm) REVERT: T 657 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8687 (mm-30) REVERT: V 33 VAL cc_start: 0.9057 (t) cc_final: 0.8795 (m) outliers start: 37 outliers final: 28 residues processed: 267 average time/residue: 0.1453 time to fit residues: 59.8398 Evaluate side-chains 251 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 222 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain J residue 620 SER Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain T residue 607 ASN Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain T residue 654 GLU Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 52 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 135 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 184 optimal weight: 8.9990 chunk 180 optimal weight: 5.9990 chunk 228 optimal weight: 5.9990 chunk 121 optimal weight: 0.0370 chunk 132 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 overall best weight: 2.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN B 607 ASN I 374 HIS J 651 ASN S 374 HIS V 69 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.116128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.089995 restraints weight = 28839.222| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.28 r_work: 0.2819 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 20097 Z= 0.238 Angle : 0.677 11.956 27426 Z= 0.340 Chirality : 0.047 0.192 3279 Planarity : 0.004 0.042 3339 Dihedral : 6.203 42.457 4335 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.38 % Favored : 95.49 % Rotamer: Outliers : 2.20 % Allowed : 10.31 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.18), residues: 2304 helix: 1.57 (0.28), residues: 390 sheet: 0.33 (0.19), residues: 717 loop : -0.42 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG S 480 TYR 0.019 0.002 TYR K 90 PHE 0.021 0.002 PHE I 383 TRP 0.013 0.002 TRP H 103 HIS 0.004 0.001 HIS S 105 Details of bonding type rmsd covalent geometry : bond 0.00571 (19974) covalent geometry : angle 0.64588 (27093) SS BOND : bond 0.00461 ( 36) SS BOND : angle 1.23095 ( 72) hydrogen bonds : bond 0.05238 ( 732) hydrogen bonds : angle 4.95362 ( 1926) link_ALPHA1-3 : bond 0.00871 ( 3) link_ALPHA1-3 : angle 1.44523 ( 9) link_BETA1-4 : bond 0.00375 ( 18) link_BETA1-4 : angle 1.46249 ( 54) link_NAG-ASN : bond 0.00490 ( 66) link_NAG-ASN : angle 2.28222 ( 198) *********************** 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 283 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 238 time to evaluate : 0.720 Fit side-chains revert: symmetry clash REVERT: A 502 LYS cc_start: 0.7092 (mmtp) cc_final: 0.6669 (mmtt) REVERT: I 136 ASN cc_start: 0.7998 (m-40) cc_final: 0.7715 (t0) REVERT: I 213 ILE cc_start: 0.9001 (mt) cc_final: 0.8777 (tt) REVERT: I 502 LYS cc_start: 0.7208 (mmtp) cc_final: 0.6149 (mmtm) REVERT: K 100 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.8977 (mp) REVERT: K 101 ASP cc_start: 0.8729 (m-30) cc_final: 0.8494 (m-30) REVERT: S 211 GLU cc_start: 0.8252 (mp0) cc_final: 0.7956 (mp0) REVERT: S 502 LYS cc_start: 0.7429 (mmtp) cc_final: 0.6528 (mmtm) REVERT: T 657 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8768 (mm-30) REVERT: U 67 PHE cc_start: 0.8789 (m-80) cc_final: 0.8485 (m-80) outliers start: 45 outliers final: 39 residues processed: 272 average time/residue: 0.1514 time to fit residues: 63.0049 Evaluate side-chains 265 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 225 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain J residue 620 SER Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 213 ILE Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain T residue 654 GLU Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 20 THR Chi-restraints excluded: chain V residue 52 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 38 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 201 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 197 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN B 607 ASN J 577 GLN T 577 GLN T 607 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.118066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.092268 restraints weight = 28641.476| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.25 r_work: 0.2861 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20097 Z= 0.132 Angle : 0.583 10.302 27426 Z= 0.293 Chirality : 0.044 0.201 3279 Planarity : 0.004 0.041 3339 Dihedral : 5.850 45.882 4335 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.12 % Favored : 95.75 % Rotamer: Outliers : 2.20 % Allowed : 11.00 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.18), residues: 2304 helix: 2.01 (0.28), residues: 381 sheet: 0.29 (0.19), residues: 747 loop : -0.36 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 151 TYR 0.018 0.001 TYR K 90 PHE 0.025 0.001 PHE H 67 TRP 0.009 0.001 TRP A 427 HIS 0.003 0.001 HIS S 105 Details of bonding type rmsd covalent geometry : bond 0.00304 (19974) covalent geometry : angle 0.55194 (27093) SS BOND : bond 0.00318 ( 36) SS BOND : angle 0.72432 ( 72) hydrogen bonds : bond 0.04351 ( 732) hydrogen bonds : angle 4.75033 ( 1926) link_ALPHA1-3 : bond 0.01000 ( 3) link_ALPHA1-3 : angle 1.30760 ( 9) link_BETA1-4 : bond 0.00341 ( 18) link_BETA1-4 : angle 1.28048 ( 54) link_NAG-ASN : bond 0.00294 ( 66) link_NAG-ASN : angle 2.14504 ( 198) *********************** 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 267 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 222 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: A 502 LYS cc_start: 0.6875 (mmtp) cc_final: 0.6485 (mmtt) REVERT: L 33 VAL cc_start: 0.9055 (t) cc_final: 0.8837 (m) REVERT: I 136 ASN cc_start: 0.8013 (m-40) cc_final: 0.7709 (t0) REVERT: I 217 TYR cc_start: 0.8927 (m-80) cc_final: 0.7916 (m-80) REVERT: I 502 LYS cc_start: 0.7004 (mmtp) cc_final: 0.6640 (mmtt) REVERT: K 100 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8986 (mp) REVERT: S 211 GLU cc_start: 0.8230 (mp0) cc_final: 0.7911 (mp0) REVERT: S 502 LYS cc_start: 0.7209 (mmtp) cc_final: 0.5939 (mmtm) REVERT: T 657 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8735 (mm-30) REVERT: U 67 PHE cc_start: 0.8675 (m-80) cc_final: 0.8342 (m-80) REVERT: U 100 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9008 (mp) REVERT: V 33 VAL cc_start: 0.9025 (t) cc_final: 0.8786 (m) outliers start: 45 outliers final: 35 residues processed: 256 average time/residue: 0.1476 time to fit residues: 57.3864 Evaluate side-chains 248 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 211 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain J residue 620 SER Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 213 ILE Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain T residue 620 SER Chi-restraints excluded: chain T residue 654 GLU Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 13 GLN Chi-restraints excluded: chain U residue 23 ARG Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 52 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 65 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 225 optimal weight: 0.3980 chunk 128 optimal weight: 0.2980 chunk 86 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 109 optimal weight: 0.0020 chunk 4 optimal weight: 0.5980 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN T 577 GLN T 607 ASN T 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.119260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.093539 restraints weight = 28735.536| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.25 r_work: 0.2879 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20097 Z= 0.109 Angle : 0.559 9.236 27426 Z= 0.281 Chirality : 0.043 0.257 3279 Planarity : 0.004 0.042 3339 Dihedral : 5.657 53.054 4335 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.12 % Favored : 95.75 % Rotamer: Outliers : 1.76 % Allowed : 11.29 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.18), residues: 2304 helix: 2.15 (0.27), residues: 378 sheet: 0.36 (0.19), residues: 741 loop : -0.36 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 151 TYR 0.014 0.001 TYR K 90 PHE 0.015 0.001 PHE H 67 TRP 0.008 0.001 TRP I 479 HIS 0.003 0.001 HIS S 105 Details of bonding type rmsd covalent geometry : bond 0.00242 (19974) covalent geometry : angle 0.52457 (27093) SS BOND : bond 0.00289 ( 36) SS BOND : angle 0.72991 ( 72) hydrogen bonds : bond 0.03967 ( 732) hydrogen bonds : angle 4.60961 ( 1926) link_ALPHA1-3 : bond 0.00960 ( 3) link_ALPHA1-3 : angle 1.23030 ( 9) link_BETA1-4 : bond 0.00368 ( 18) link_BETA1-4 : angle 1.23882 ( 54) link_NAG-ASN : bond 0.00281 ( 66) link_NAG-ASN : angle 2.22598 ( 198) *********************** 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 259 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 223 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: A 42 VAL cc_start: 0.9200 (OUTLIER) cc_final: 0.8894 (m) REVERT: A 502 LYS cc_start: 0.6824 (mmtp) cc_final: 0.6554 (mmtt) REVERT: H 70 SER cc_start: 0.8814 (t) cc_final: 0.8593 (t) REVERT: H 82 MET cc_start: 0.8580 (mtm) cc_final: 0.8231 (mtt) REVERT: L 33 VAL cc_start: 0.9041 (t) cc_final: 0.8821 (m) REVERT: L 36 TYR cc_start: 0.9170 (m-80) cc_final: 0.8680 (m-80) REVERT: I 136 ASN cc_start: 0.8003 (m-40) cc_final: 0.7671 (t0) REVERT: I 217 TYR cc_start: 0.8933 (m-80) cc_final: 0.7943 (m-80) REVERT: I 502 LYS cc_start: 0.6944 (mmtp) cc_final: 0.6457 (mmtt) REVERT: K 100 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9018 (mp) REVERT: S 211 GLU cc_start: 0.8290 (mp0) cc_final: 0.7992 (mp0) REVERT: S 502 LYS cc_start: 0.7159 (mmtp) cc_final: 0.6208 (mmtt) REVERT: T 657 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8719 (mm-30) REVERT: V 33 VAL cc_start: 0.9056 (t) cc_final: 0.8837 (m) outliers start: 36 outliers final: 29 residues processed: 249 average time/residue: 0.1478 time to fit residues: 55.9921 Evaluate side-chains 244 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 213 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 97 LYS Chi-restraints excluded: chain S residue 213 ILE Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain T residue 654 GLU Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 13 GLN Chi-restraints excluded: chain U residue 23 ARG Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 52 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 188 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 173 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 185 optimal weight: 9.9990 chunk 125 optimal weight: 0.0870 chunk 4 optimal weight: 0.0980 chunk 31 optimal weight: 6.9990 chunk 205 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 overall best weight: 2.6364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 607 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.116306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.090154 restraints weight = 28833.262| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.28 r_work: 0.2818 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 20097 Z= 0.212 Angle : 0.633 9.202 27426 Z= 0.319 Chirality : 0.046 0.302 3279 Planarity : 0.004 0.043 3339 Dihedral : 6.019 57.061 4335 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.38 % Favored : 95.49 % Rotamer: Outliers : 2.30 % Allowed : 11.34 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.18), residues: 2304 helix: 1.85 (0.27), residues: 378 sheet: 0.29 (0.19), residues: 753 loop : -0.46 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 151 TYR 0.020 0.002 TYR K 90 PHE 0.025 0.002 PHE H 67 TRP 0.013 0.001 TRP H 103 HIS 0.003 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00510 (19974) covalent geometry : angle 0.60154 (27093) SS BOND : bond 0.00436 ( 36) SS BOND : angle 1.01039 ( 72) hydrogen bonds : bond 0.04972 ( 732) hydrogen bonds : angle 4.81305 ( 1926) link_ALPHA1-3 : bond 0.00886 ( 3) link_ALPHA1-3 : angle 1.28458 ( 9) link_BETA1-4 : bond 0.00324 ( 18) link_BETA1-4 : angle 1.37360 ( 54) link_NAG-ASN : bond 0.00401 ( 66) link_NAG-ASN : angle 2.22900 ( 198) *********************** 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 268 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 221 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: A 151 ARG cc_start: 0.7837 (ttm110) cc_final: 0.7444 (ttm110) REVERT: A 502 LYS cc_start: 0.7179 (mmtp) cc_final: 0.6803 (mmtt) REVERT: H 100 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9066 (mp) REVERT: I 136 ASN cc_start: 0.8141 (m-40) cc_final: 0.7825 (t0) REVERT: I 428 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8431 (mm110) REVERT: I 502 LYS cc_start: 0.7152 (mmtp) cc_final: 0.6648 (mmtt) REVERT: K 100 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9058 (mp) REVERT: S 211 GLU cc_start: 0.8274 (mp0) cc_final: 0.8029 (mp0) REVERT: S 502 LYS cc_start: 0.7355 (mmtp) cc_final: 0.6358 (mmtm) REVERT: T 657 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8783 (mm-30) REVERT: U 100 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.8942 (mp) outliers start: 47 outliers final: 36 residues processed: 253 average time/residue: 0.1468 time to fit residues: 56.8691 Evaluate side-chains 253 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 214 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 52 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 97 LYS Chi-restraints excluded: chain S residue 110 SER Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain T residue 613 SER Chi-restraints excluded: chain T residue 654 GLU Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 23 ARG Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 81 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 187 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 174 optimal weight: 0.6980 chunk 147 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 203 optimal weight: 0.7980 chunk 163 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 156 optimal weight: 0.0870 chunk 148 optimal weight: 1.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN B 607 ASN K 39 GLN M 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.119021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.093260 restraints weight = 28503.502| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.25 r_work: 0.2845 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20097 Z= 0.110 Angle : 0.554 9.998 27426 Z= 0.280 Chirality : 0.043 0.218 3279 Planarity : 0.004 0.043 3339 Dihedral : 5.720 59.972 4335 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.91 % Favored : 95.96 % Rotamer: Outliers : 1.52 % Allowed : 11.88 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.18), residues: 2304 helix: 2.16 (0.27), residues: 378 sheet: 0.38 (0.19), residues: 726 loop : -0.43 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 151 TYR 0.018 0.001 TYR K 90 PHE 0.014 0.001 PHE H 67 TRP 0.008 0.001 TRP T 571 HIS 0.003 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00248 (19974) covalent geometry : angle 0.52529 (27093) SS BOND : bond 0.00335 ( 36) SS BOND : angle 0.68022 ( 72) hydrogen bonds : bond 0.03999 ( 732) hydrogen bonds : angle 4.61513 ( 1926) link_ALPHA1-3 : bond 0.00856 ( 3) link_ALPHA1-3 : angle 1.17673 ( 9) link_BETA1-4 : bond 0.00350 ( 18) link_BETA1-4 : angle 1.23348 ( 54) link_NAG-ASN : bond 0.00247 ( 66) link_NAG-ASN : angle 2.03569 ( 198) *********************** 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 259 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 228 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 502 LYS cc_start: 0.6790 (mmtp) cc_final: 0.6502 (mmtt) REVERT: H 70 SER cc_start: 0.8815 (t) cc_final: 0.8581 (t) REVERT: L 33 VAL cc_start: 0.9014 (t) cc_final: 0.8766 (m) REVERT: I 136 ASN cc_start: 0.8095 (m-40) cc_final: 0.7806 (t0) REVERT: I 217 TYR cc_start: 0.8937 (m-80) cc_final: 0.7943 (m-80) REVERT: I 428 GLN cc_start: 0.8608 (mm-40) cc_final: 0.8391 (mm110) REVERT: I 502 LYS cc_start: 0.6862 (mmtp) cc_final: 0.6337 (mmtt) REVERT: K 100 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9090 (mp) REVERT: S 211 GLU cc_start: 0.8272 (mp0) cc_final: 0.7957 (mp0) REVERT: S 308 ARG cc_start: 0.9061 (mtp85) cc_final: 0.8856 (mtp180) REVERT: S 502 LYS cc_start: 0.7201 (mmtp) cc_final: 0.6333 (mmtt) REVERT: T 657 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8685 (mm-30) REVERT: V 33 VAL cc_start: 0.9050 (t) cc_final: 0.8790 (m) outliers start: 31 outliers final: 25 residues processed: 249 average time/residue: 0.1469 time to fit residues: 55.4897 Evaluate side-chains 248 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 222 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 97 LYS Chi-restraints excluded: chain S residue 110 SER Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain T residue 654 GLU Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain V residue 9 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 226 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 208 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 159 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 218 optimal weight: 7.9990 chunk 196 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 607 ASN U 52 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.116727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.088540 restraints weight = 29002.987| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.60 r_work: 0.2746 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20097 Z= 0.219 Angle : 0.627 8.870 27426 Z= 0.317 Chirality : 0.046 0.230 3279 Planarity : 0.004 0.043 3339 Dihedral : 5.992 59.997 4335 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.69 % Favored : 95.18 % Rotamer: Outliers : 1.71 % Allowed : 11.93 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.18), residues: 2304 helix: 1.86 (0.27), residues: 378 sheet: 0.24 (0.19), residues: 753 loop : -0.49 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 151 TYR 0.023 0.002 TYR V 49 PHE 0.019 0.002 PHE I 383 TRP 0.016 0.002 TRP T 623 HIS 0.003 0.001 HIS S 105 Details of bonding type rmsd covalent geometry : bond 0.00528 (19974) covalent geometry : angle 0.59723 (27093) SS BOND : bond 0.00432 ( 36) SS BOND : angle 0.97824 ( 72) hydrogen bonds : bond 0.04883 ( 732) hydrogen bonds : angle 4.79654 ( 1926) link_ALPHA1-3 : bond 0.00902 ( 3) link_ALPHA1-3 : angle 1.26383 ( 9) link_BETA1-4 : bond 0.00320 ( 18) link_BETA1-4 : angle 1.35015 ( 54) link_NAG-ASN : bond 0.00408 ( 66) link_NAG-ASN : angle 2.16881 ( 198) ********************** 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 256 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 221 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: A 151 ARG cc_start: 0.7775 (ttm110) cc_final: 0.7341 (ttm110) REVERT: A 502 LYS cc_start: 0.7138 (mmtp) cc_final: 0.6706 (mmtt) REVERT: H 100 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9130 (mp) REVERT: I 136 ASN cc_start: 0.8113 (m-40) cc_final: 0.7826 (t0) REVERT: I 428 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8468 (mm110) REVERT: I 502 LYS cc_start: 0.7150 (mmtp) cc_final: 0.6747 (mmtt) REVERT: K 52 ASN cc_start: 0.8718 (t0) cc_final: 0.8288 (t0) REVERT: K 100 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9120 (mp) REVERT: S 211 GLU cc_start: 0.8362 (mp0) cc_final: 0.8017 (mp0) REVERT: S 308 ARG cc_start: 0.9136 (mtp85) cc_final: 0.8908 (mtp180) REVERT: S 502 LYS cc_start: 0.7417 (mmtp) cc_final: 0.6823 (mmtt) REVERT: T 657 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8772 (mm-30) outliers start: 35 outliers final: 31 residues processed: 246 average time/residue: 0.1489 time to fit residues: 55.7856 Evaluate side-chains 250 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 217 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 378 CYS Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain S residue 35 TRP Chi-restraints excluded: chain S residue 97 LYS Chi-restraints excluded: chain S residue 110 SER Chi-restraints excluded: chain S residue 355 ASN Chi-restraints excluded: chain S residue 378 CYS Chi-restraints excluded: chain T residue 654 GLU Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 23 ARG Chi-restraints excluded: chain V residue 9 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 27 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 68 optimal weight: 9.9990 chunk 206 optimal weight: 0.8980 chunk 175 optimal weight: 0.9980 chunk 191 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 163 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN U 52 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.118175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.090226 restraints weight = 28793.227| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.58 r_work: 0.2782 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20097 Z= 0.145 Angle : 0.573 8.482 27426 Z= 0.291 Chirality : 0.044 0.202 3279 Planarity : 0.004 0.043 3339 Dihedral : 5.807 59.754 4335 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.34 % Favored : 95.53 % Rotamer: Outliers : 1.86 % Allowed : 11.58 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.18), residues: 2304 helix: 2.04 (0.27), residues: 378 sheet: 0.28 (0.19), residues: 726 loop : -0.51 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 151 TYR 0.024 0.001 TYR V 49 PHE 0.018 0.001 PHE U 67 TRP 0.011 0.001 TRP S 395 HIS 0.003 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00341 (19974) covalent geometry : angle 0.54452 (27093) SS BOND : bond 0.00353 ( 36) SS BOND : angle 0.75624 ( 72) hydrogen bonds : bond 0.04313 ( 732) hydrogen bonds : angle 4.68399 ( 1926) link_ALPHA1-3 : bond 0.00813 ( 3) link_ALPHA1-3 : angle 1.17851 ( 9) link_BETA1-4 : bond 0.00324 ( 18) link_BETA1-4 : angle 1.26578 ( 54) link_NAG-ASN : bond 0.00283 ( 66) link_NAG-ASN : angle 2.05184 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5074.90 seconds wall clock time: 87 minutes 41.35 seconds (5261.35 seconds total)